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- PDB-4v5b: Structure of PDF binding helix in complex with the ribosome. -

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Basic information

Entry
Database: PDB / ID: 4v5b
TitleStructure of PDF binding helix in complex with the ribosome.
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 29
  • 16S RIBOSOMAL RNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • C-TERM HELIX PDF
KeywordsRIBOSOME / TRANSLATION / PEPTIDE DEFORMYLASE / RNA-PROTEIN COMPLEX / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / 50S RIBOSOMAL SUBUNIT / ANTIBIOTIC RESISTANCE / NASCENT CHAIN PROCESSING / RNA-BINDING / TRANSLATION REGULATION / TRNA BINDING / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / : / negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding ...peptide deformylase / peptide deformylase activity / : / negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / response to reactive oxygen species / ribosome assembly / transcription elongation factor complex / DNA endonuclease activity / transcription antitermination / regulation of cell growth / translational initiation / ferrous iron binding / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / large ribosomal subunit / ribosome biogenesis / ribosome binding / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / endonuclease activity / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / hydrolase activity / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Ribosomal protein L11, bacterial-type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily ...Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Ribosomal protein L11, bacterial-type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / : / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS6 / Peptide deformylase / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.74 Å
AuthorsBingel-Erlenmeyer, R. / Kohler, R. / Kramer, G. / Sandikci, A. / Antolic, S. / Maier, T. / Schaffitzel, C. / Wiedmann, B. / Bukau, B. / Ban, N.
CitationJournal: Nature / Year: 2008
Title: A Peptide Deformylase-Ribosome Complex Reveals Mechanism of Nascent Chain Processing.
Authors: Bingel-Erlenmeyer, R. / Kohler, R. / Kramer, G. / Sandikci, A. / Antolic, S. / Maier, T. / Schaffitzel, C. / Wiedmann, B. / Bukau, B. / Ban, N.
History
DepositionNov 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2VHM, 2VHN, 2VHO, 2VHP
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 14, 2018Group: Database references / Structure summary / Category: citation / entity
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _entity.src_method
Revision 1.3Apr 20, 2022Group: Database references / Derived calculations / Category: database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Mar 8, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.5Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A0: 50S RIBOSOMAL PROTEIN L32
A1: 50S RIBOSOMAL PROTEIN L33
A2: 50S RIBOSOMAL PROTEIN L34
A3: 50S RIBOSOMAL PROTEIN L35
A4: 50S RIBOSOMAL PROTEIN L36
A5: C-TERM HELIX PDF
AA: 5S RIBOSOMAL RNA
AB: 23S RIBOSOMAL RNA
AC: 50S RIBOSOMAL PROTEIN L2
AD: 50S RIBOSOMAL PROTEIN L3
AE: 50S RIBOSOMAL PROTEIN L4
AF: 50S RIBOSOMAL PROTEIN L5
AG: 50S RIBOSOMAL PROTEIN L6
AH: 50S RIBOSOMAL PROTEIN L9
AI: 50S RIBOSOMAL PROTEIN L11
AJ: 50S RIBOSOMAL PROTEIN L13
AK: 50S RIBOSOMAL PROTEIN L14
AL: 50S RIBOSOMAL PROTEIN L15
AM: 50S RIBOSOMAL PROTEIN L16
AN: 50S RIBOSOMAL PROTEIN L17
AO: 50S RIBOSOMAL PROTEIN L18
AP: 50S RIBOSOMAL PROTEIN L19
AQ: 50S RIBOSOMAL PROTEIN L20
AR: 50S RIBOSOMAL PROTEIN L21
AS: 50S RIBOSOMAL PROTEIN L22
AT: 50S RIBOSOMAL PROTEIN L23
AU: 50S RIBOSOMAL PROTEIN L24
AV: 50S RIBOSOMAL PROTEIN L25
AW: 50S RIBOSOMAL PROTEIN L27
AX: 50S RIBOSOMAL PROTEIN L29
AY: 50S RIBOSOMAL PROTEIN L30
AZ: 50S RIBOSOMAL PROTEIN L31
BA: 16S RIBOSOMAL RNA
BB: 30S RIBOSOMAL PROTEIN S2
BC: 30S RIBOSOMAL PROTEIN S3
BD: 30S RIBOSOMAL PROTEIN S4
BE: 30S RIBOSOMAL PROTEIN S5
BF: 30S RIBOSOMAL PROTEIN S6
BG: 30S RIBOSOMAL PROTEIN S7
BH: 30S RIBOSOMAL PROTEIN S8
BI: 30S RIBOSOMAL PROTEIN S9
BJ: 30S RIBOSOMAL PROTEIN S10
BK: 30S RIBOSOMAL PROTEIN S11
BL: 30S RIBOSOMAL PROTEIN S12
BM: 30S RIBOSOMAL PROTEIN S13
BN: 30S RIBOSOMAL PROTEIN S14
BO: 30S RIBOSOMAL PROTEIN S15
BP: 30S RIBOSOMAL PROTEIN S16
BQ: 30S RIBOSOMAL PROTEIN S17
BR: 30S RIBOSOMAL PROTEIN S18
BS: 30S RIBOSOMAL PROTEIN S19
BT: 30S RIBOSOMAL PROTEIN S20
BU: 30S RIBOSOMAL PROTEIN S21
C0: 50S RIBOSOMAL PROTEIN L32
C1: 50S RIBOSOMAL PROTEIN L33
C2: 50S RIBOSOMAL PROTEIN L34
C3: 50S RIBOSOMAL PROTEIN L35
C4: 50S RIBOSOMAL PROTEIN L36
CA: 5S RIBOSOMAL RNA
CB: 23S RIBOSOMAL RNA
CC: 50S RIBOSOMAL PROTEIN L2
CD: 50S RIBOSOMAL PROTEIN L3
CE: 50S RIBOSOMAL PROTEIN L4
CF: 50S RIBOSOMAL PROTEIN L5
CG: 50S RIBOSOMAL PROTEIN L6
CH: 50S RIBOSOMAL PROTEIN L9
CI: 50S RIBOSOMAL PROTEIN L11
CJ: 50S RIBOSOMAL PROTEIN L13
CK: 50S RIBOSOMAL PROTEIN L14
CL: 50S RIBOSOMAL PROTEIN L15
CM: 50S RIBOSOMAL PROTEIN L16
CN: 50S RIBOSOMAL PROTEIN L17
CO: 50S RIBOSOMAL PROTEIN L18
CP: 50S RIBOSOMAL PROTEIN L19
CQ: 50S RIBOSOMAL PROTEIN L20
CR: 50S RIBOSOMAL PROTEIN L21
CS: 50S RIBOSOMAL PROTEIN L22
CT: 50S RIBOSOMAL PROTEIN L23
CU: 50S RIBOSOMAL PROTEIN L24
CV: 50S RIBOSOMAL PROTEIN L25
CW: 50S RIBOSOMAL PROTEIN L27
CX: 50S RIBOSOMAL PROTEIN L29
CY: 50S RIBOSOMAL PROTEIN L30
CZ: 50S RIBOSOMAL PROTEIN L31
DA: 16S RIBOSOMAL RNA
DB: 30S RIBOSOMAL PROTEIN S2
DC: 30S RIBOSOMAL PROTEIN S3
DD: 30S RIBOSOMAL PROTEIN S4
DE: 30S RIBOSOMAL PROTEIN S5
DF: 30S RIBOSOMAL PROTEIN S6
DG: 30S RIBOSOMAL PROTEIN S7
DH: 30S RIBOSOMAL PROTEIN S8
DI: 30S RIBOSOMAL PROTEIN S9
DJ: 30S RIBOSOMAL PROTEIN S10
DK: 30S RIBOSOMAL PROTEIN S11
DL: 30S RIBOSOMAL PROTEIN S12
DM: 30S RIBOSOMAL PROTEIN S13
DN: 30S RIBOSOMAL PROTEIN S14
DO: 30S RIBOSOMAL PROTEIN S15
DP: 30S RIBOSOMAL PROTEIN S16
DQ: 30S RIBOSOMAL PROTEIN S17
DR: 30S RIBOSOMAL PROTEIN S18
DS: 30S RIBOSOMAL PROTEIN S19
DT: 30S RIBOSOMAL PROTEIN S20
DU: 30S RIBOSOMAL PROTEIN S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,295,349448
Polymers4,287,012105
Non-polymers8,337343
Water29,1301617
1
A0: 50S RIBOSOMAL PROTEIN L32
A1: 50S RIBOSOMAL PROTEIN L33
A2: 50S RIBOSOMAL PROTEIN L34
A3: 50S RIBOSOMAL PROTEIN L35
A4: 50S RIBOSOMAL PROTEIN L36
A5: C-TERM HELIX PDF
AA: 5S RIBOSOMAL RNA
AB: 23S RIBOSOMAL RNA
AC: 50S RIBOSOMAL PROTEIN L2
AD: 50S RIBOSOMAL PROTEIN L3
AE: 50S RIBOSOMAL PROTEIN L4
AF: 50S RIBOSOMAL PROTEIN L5
AG: 50S RIBOSOMAL PROTEIN L6
AH: 50S RIBOSOMAL PROTEIN L9
AI: 50S RIBOSOMAL PROTEIN L11
AJ: 50S RIBOSOMAL PROTEIN L13
AK: 50S RIBOSOMAL PROTEIN L14
AL: 50S RIBOSOMAL PROTEIN L15
AM: 50S RIBOSOMAL PROTEIN L16
AN: 50S RIBOSOMAL PROTEIN L17
AO: 50S RIBOSOMAL PROTEIN L18
AP: 50S RIBOSOMAL PROTEIN L19
AQ: 50S RIBOSOMAL PROTEIN L20
AR: 50S RIBOSOMAL PROTEIN L21
AS: 50S RIBOSOMAL PROTEIN L22
AT: 50S RIBOSOMAL PROTEIN L23
AU: 50S RIBOSOMAL PROTEIN L24
AV: 50S RIBOSOMAL PROTEIN L25
AW: 50S RIBOSOMAL PROTEIN L27
AX: 50S RIBOSOMAL PROTEIN L29
AY: 50S RIBOSOMAL PROTEIN L30
AZ: 50S RIBOSOMAL PROTEIN L31
BA: 16S RIBOSOMAL RNA
BB: 30S RIBOSOMAL PROTEIN S2
BC: 30S RIBOSOMAL PROTEIN S3
BD: 30S RIBOSOMAL PROTEIN S4
BE: 30S RIBOSOMAL PROTEIN S5
BF: 30S RIBOSOMAL PROTEIN S6
BG: 30S RIBOSOMAL PROTEIN S7
BH: 30S RIBOSOMAL PROTEIN S8
BI: 30S RIBOSOMAL PROTEIN S9
BJ: 30S RIBOSOMAL PROTEIN S10
BK: 30S RIBOSOMAL PROTEIN S11
BL: 30S RIBOSOMAL PROTEIN S12
BM: 30S RIBOSOMAL PROTEIN S13
BN: 30S RIBOSOMAL PROTEIN S14
BO: 30S RIBOSOMAL PROTEIN S15
BP: 30S RIBOSOMAL PROTEIN S16
BQ: 30S RIBOSOMAL PROTEIN S17
BR: 30S RIBOSOMAL PROTEIN S18
BS: 30S RIBOSOMAL PROTEIN S19
BT: 30S RIBOSOMAL PROTEIN S20
BU: 30S RIBOSOMAL PROTEIN S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,148,602223
Polymers2,144,47053
Non-polymers4,132170
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C0: 50S RIBOSOMAL PROTEIN L32
C1: 50S RIBOSOMAL PROTEIN L33
C2: 50S RIBOSOMAL PROTEIN L34
C3: 50S RIBOSOMAL PROTEIN L35
C4: 50S RIBOSOMAL PROTEIN L36
CA: 5S RIBOSOMAL RNA
CB: 23S RIBOSOMAL RNA
CC: 50S RIBOSOMAL PROTEIN L2
CD: 50S RIBOSOMAL PROTEIN L3
CE: 50S RIBOSOMAL PROTEIN L4
CF: 50S RIBOSOMAL PROTEIN L5
CG: 50S RIBOSOMAL PROTEIN L6
CH: 50S RIBOSOMAL PROTEIN L9
CI: 50S RIBOSOMAL PROTEIN L11
CJ: 50S RIBOSOMAL PROTEIN L13
CK: 50S RIBOSOMAL PROTEIN L14
CL: 50S RIBOSOMAL PROTEIN L15
CM: 50S RIBOSOMAL PROTEIN L16
CN: 50S RIBOSOMAL PROTEIN L17
CO: 50S RIBOSOMAL PROTEIN L18
CP: 50S RIBOSOMAL PROTEIN L19
CQ: 50S RIBOSOMAL PROTEIN L20
CR: 50S RIBOSOMAL PROTEIN L21
CS: 50S RIBOSOMAL PROTEIN L22
CT: 50S RIBOSOMAL PROTEIN L23
CU: 50S RIBOSOMAL PROTEIN L24
CV: 50S RIBOSOMAL PROTEIN L25
CW: 50S RIBOSOMAL PROTEIN L27
CX: 50S RIBOSOMAL PROTEIN L29
CY: 50S RIBOSOMAL PROTEIN L30
CZ: 50S RIBOSOMAL PROTEIN L31
DA: 16S RIBOSOMAL RNA
DB: 30S RIBOSOMAL PROTEIN S2
DC: 30S RIBOSOMAL PROTEIN S3
DD: 30S RIBOSOMAL PROTEIN S4
DE: 30S RIBOSOMAL PROTEIN S5
DF: 30S RIBOSOMAL PROTEIN S6
DG: 30S RIBOSOMAL PROTEIN S7
DH: 30S RIBOSOMAL PROTEIN S8
DI: 30S RIBOSOMAL PROTEIN S9
DJ: 30S RIBOSOMAL PROTEIN S10
DK: 30S RIBOSOMAL PROTEIN S11
DL: 30S RIBOSOMAL PROTEIN S12
DM: 30S RIBOSOMAL PROTEIN S13
DN: 30S RIBOSOMAL PROTEIN S14
DO: 30S RIBOSOMAL PROTEIN S15
DP: 30S RIBOSOMAL PROTEIN S16
DQ: 30S RIBOSOMAL PROTEIN S17
DR: 30S RIBOSOMAL PROTEIN S18
DS: 30S RIBOSOMAL PROTEIN S19
DT: 30S RIBOSOMAL PROTEIN S20
DU: 30S RIBOSOMAL PROTEIN S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,146,747225
Polymers2,142,54352
Non-polymers4,205173
Water39622
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)208.181, 380.083, 736.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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50S RIBOSOMAL PROTEIN ... , 29 types, 58 molecules A0C0A1C1A2C2A3C3A4C4ACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCL...

#1: Protein 50S RIBOSOMAL PROTEIN L32


Mass: 6332.249 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q0TIY5, UniProt: P0A7N4*PLUS
#2: Protein 50S RIBOSOMAL PROTEIN L33


Mass: 6257.436 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-55 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7N9
#3: Protein/peptide 50S RIBOSOMAL PROTEIN L34


Mass: 5397.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7P6, UniProt: P0A7P5*PLUS
#4: Protein 50S RIBOSOMAL PROTEIN L35


Mass: 7181.835 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-65 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q1
#5: Protein/peptide 50S RIBOSOMAL PROTEIN L36


Mass: 4377.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q7, UniProt: P0A7Q6*PLUS
#9: Protein 50S RIBOSOMAL PROTEIN L2


Mass: 29923.619 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P60424, UniProt: P60422*PLUS
#10: Protein 50S RIBOSOMAL PROTEIN L3


Mass: 22277.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P60439, UniProt: P60438*PLUS
#11: Protein 50S RIBOSOMAL PROTEIN L4


Mass: 22121.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P60725, UniProt: P60723*PLUS
#12: Protein 50S RIBOSOMAL PROTEIN L5


Mass: 20202.416 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-179 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P62401, UniProt: P62399*PLUS
#13: Protein 50S RIBOSOMAL PROTEIN L6


Mass: 18801.598 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-177 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0AG57, UniProt: P0AG55*PLUS
#14: Protein 50S RIBOSOMAL PROTEIN L9


Mass: 15789.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7R1
#15: Protein 50S RIBOSOMAL PROTEIN L11


Mass: 14763.165 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-142 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7J8, UniProt: P0A7J7*PLUS
#16: Protein 50S RIBOSOMAL PROTEIN L13


Mass: 16050.606 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q1R6A9, UniProt: P0AA10*PLUS
#17: Protein 50S RIBOSOMAL PROTEIN L14


Mass: 13565.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q1R617, UniProt: P0ADY3*PLUS
#18: Protein 50S RIBOSOMAL PROTEIN L15


Mass: 15008.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P02413
#19: Protein 50S RIBOSOMAL PROTEIN L16


Mass: 15312.269 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0ADY7
#20: Protein 50S RIBOSOMAL PROTEIN L17


Mass: 14393.657 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q0TCG7, UniProt: P0AG44*PLUS
#21: Protein 50S RIBOSOMAL PROTEIN L18


Mass: 12794.668 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-57 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0C018
#22: Protein 50S RIBOSOMAL PROTEIN L19


Mass: 13028.082 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-115 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7K6
#23: Protein 50S RIBOSOMAL PROTEIN L20


Mass: 13396.828 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-118 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7L3
#24: Protein 50S RIBOSOMAL PROTEIN L21


Mass: 11586.374 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q0TCS4, UniProt: P0AG48*PLUS
#25: Protein 50S RIBOSOMAL PROTEIN L22


Mass: 12253.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P61176, UniProt: P61175*PLUS
#26: Protein 50S RIBOSOMAL PROTEIN L23


Mass: 11222.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q1R606, UniProt: P0ADZ0*PLUS
#27: Protein 50S RIBOSOMAL PROTEIN L24


Mass: 11208.054 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-104 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P60625, UniProt: P60624*PLUS
#28: Protein 50S RIBOSOMAL PROTEIN L25


Mass: 10713.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P68919
#29: Protein 50S RIBOSOMAL PROTEIN L27


Mass: 9015.344 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-85 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7L9, UniProt: P0A7L8*PLUS
#30: Protein 50S RIBOSOMAL PROTEIN L29


Mass: 7286.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7M7, UniProt: P0A7M6*PLUS
#31: Protein 50S RIBOSOMAL PROTEIN L30


Mass: 6423.625 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-59 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q0TCF9, UniProt: P0AG51*PLUS
#32: Protein 50S RIBOSOMAL PROTEIN L31


Mass: 7887.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7N0, UniProt: P0A7M9*PLUS

-
Protein/peptide , 1 types, 1 molecules A5

#6: Protein/peptide C-TERM HELIX PDF


Mass: 1927.317 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6K3

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RNA chain , 3 types, 6 molecules AACAABCBBADA

#7: RNA chain 5S RIBOSOMAL RNA


Mass: 38790.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
#8: RNA chain 23S RIBOSOMAL RNA


Mass: 941612.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
#33: RNA chain 16S RIBOSOMAL RNA


Mass: 499690.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600

-
30S RIBOSOMAL PROTEIN ... , 20 types, 40 molecules BBDBBCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBLDLBMDMBNDNBODOBPDP...

#34: Protein 30S RIBOSOMAL PROTEIN S2


Mass: 26650.475 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-241 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7V1, UniProt: P0A7V0
#35: Protein 30S RIBOSOMAL PROTEIN S3


Mass: 25900.117 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-233 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7V4, UniProt: P0A7V3
#36: Protein 30S RIBOSOMAL PROTEIN S4


Mass: 23383.002 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-206 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
References: UniProt: Q0TCG5, UniProt: A1AGI7, UniProt: P0A7V8*PLUS
#37: Protein 30S RIBOSOMAL PROTEIN S5


Mass: 17498.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-167 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7W1, UniProt: P0A7W3
#38: Protein 30S RIBOSOMAL PROTEIN S6


Mass: 15727.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
References: UniProt: P0A4D0, UniProt: P0A4D1, UniProt: P02358*PLUS
#39: Protein 30S RIBOSOMAL PROTEIN S7


Mass: 19923.959 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-156 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P66606, UniProt: P02359*PLUS
#40: Protein 30S RIBOSOMAL PROTEIN S8


Mass: 14015.361 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-130 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: A1AGJ5, UniProt: P0A7W7
#41: Protein 30S RIBOSOMAL PROTEIN S9


Mass: 14755.074 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-130 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7X3, UniProt: P0A7X4
#42: Protein 30S RIBOSOMAL PROTEIN S10


Mass: 11755.597 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7R5, UniProt: P0A7R6
#43: Protein 30S RIBOSOMAL PROTEIN S11


Mass: 13739.778 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-129 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: A1AGI8, UniProt: P0A7R9*PLUS
#44: Protein 30S RIBOSOMAL PROTEIN S12


Mass: 13636.961 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-124 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7S3, UniProt: P0A7S4
#45: Protein 30S RIBOSOMAL PROTEIN S13


Mass: 12997.271 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-118 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7T1, UniProt: P0A7S9
#46: Protein 30S RIBOSOMAL PROTEIN S14


Mass: 11475.364 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-101 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0AG59, UniProt: P0AG61
#47: Protein 30S RIBOSOMAL PROTEIN S15


Mass: 10319.882 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q8X9M2, UniProt: P0ADZ4*PLUS
#48: Protein 30S RIBOSOMAL PROTEIN S16


Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7T3, UniProt: P0A7T4
#49: Protein 30S RIBOSOMAL PROTEIN S17


Mass: 9593.296 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-84 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
References: UniProt: Q1R616, UniProt: P0AG65, UniProt: P0AG63*PLUS
#50: Protein 30S RIBOSOMAL PROTEIN S18


Mass: 8874.276 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-75 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7T7, UniProt: P0A7T9
#51: Protein 30S RIBOSOMAL PROTEIN S19


Mass: 10324.160 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-92 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q0TCE5, UniProt: P0A7U3*PLUS
#52: Protein 30S RIBOSOMAL PROTEIN S20


Mass: 9577.268 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-87 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
References: UniProt: Q0TLW7, UniProt: P0A7U9, UniProt: P0A7U7*PLUS
#53: Protein 30S RIBOSOMAL PROTEIN S21


Mass: 8524.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P68680, UniProt: P68679

-
Non-polymers , 2 types, 1960 molecules

#54: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 343 / Source method: obtained synthetically / Formula: Mg
#55: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1617 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A5, LEU 147 TO ALA
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.82 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.74→50 Å / Num. obs: 546832 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.1

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AW4

2aw4
PDB Unreleased entry


Resolution: 3.74→50 Å / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.323 5544 1 %
Rwork0.259 --
obs-546832 91.5 %
Refinement stepCycle: LAST / Resolution: 3.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26327 63502 110 503 90442

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