[English] 日本語
Yorodumi
- PDB-4v4q: Crystal structure of the bacterial ribosome from Escherichia coli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v4q
TitleCrystal structure of the bacterial ribosome from Escherichia coli at 3.5 A resolution.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / RNA-protein complex / 30S RIBOSOMAL SUBUNIT
Function / homology
Function and homology information


mRNA binding involved in posttranscriptional gene silencing / stringent response / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity ...mRNA binding involved in posttranscriptional gene silencing / stringent response / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / mature ribosome assembly / translational initiation / translational termination / translation repressor activity, mRNA regulatory element binding / endodeoxyribonuclease activity / polysomal ribosome / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / DNA-templated transcription, termination / response to reactive oxygen species / positive regulation of translational fidelity / maintenance of translational fidelity / regulation of cell growth / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosome binding / ribosomal large subunit assembly / 5S rRNA binding / response to radiation / cytosolic small ribosomal subunit / regulation of translation / regulation of mRNA stability / small ribosomal subunit / negative regulation of translation / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / RNA binding / zinc ion binding / membrane / cytosol
Ribosomal protein L31 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S10 domain ...Ribosomal protein L31 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S10 domain / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L18e/L15P / 30s ribosomal protein S13, C-terminal / Ribosomal protein L31 type A / Ribosomal protein S19 conserved site / Ribosomal protein S8 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L21-like / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L34, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S18, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S11, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L16, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / 30S ribosomal protein S17 / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S20 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L29, conserved site / Ribosomal protein L3 / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, N-terminal domain / Ribosomal protein L6 / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L4/L1 family / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L36 / Ribosomal protein L35 / Ribosomal protein L34 / Ribosomal protein L33 / Ribosomal L32p protein family / Ribosomal protein S21 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L13 / Ribosomal protein S19 / Ribosomal protein L23 / Ribosomal protein L30p/L7e / Ribosomal L29 protein / Ribosomal L27 protein
50S ribosomal protein L20 / 50S ribosomal protein L27 / 50S ribosomal protein L29 / 50S ribosomal protein L19 / 50S ribosomal protein L31 / 30S ribosomal protein S4 / 50S ribosomal protein L11 / 50S ribosomal protein L30 / 50S ribosomal protein L33 / 50S ribosomal protein L23 ...50S ribosomal protein L20 / 50S ribosomal protein L27 / 50S ribosomal protein L29 / 50S ribosomal protein L19 / 50S ribosomal protein L31 / 30S ribosomal protein S4 / 50S ribosomal protein L11 / 50S ribosomal protein L30 / 50S ribosomal protein L33 / 50S ribosomal protein L23 / 50S ribosomal protein L21 / 50S ribosomal protein L16 / 50S ribosomal protein L15 / 50S ribosomal protein L14 / 50S ribosomal protein L13 / 50S ribosomal protein L6 / 30S ribosomal protein S17 / 30S ribosomal protein S15 / 30S ribosomal protein S14 / 30S ribosomal protein S7 / 30S ribosomal protein S6 / 50S ribosomal protein L32 / 50S ribosomal protein L36 / 50S ribosomal protein L34 / 50S ribosomal protein L21 / 50S ribosomal protein L3 / 50S ribosomal protein L2 / 50S ribosomal protein L18 / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 50S ribosomal protein L6 / 50S ribosomal protein L30 / 50S ribosomal protein L17 / 50S ribosomal protein L4 / 30S ribosomal protein S15 / 50S ribosomal protein L23 / 50S ribosomal protein L16 / 50S ribosomal protein L14 / 50S ribosomal protein L13 / 30S ribosomal protein S9 / 30S ribosomal protein S8 / 50S ribosomal protein L24 / 50S ribosomal protein L22 / 50S ribosomal protein L35 / 30S ribosomal protein S18 / 30S ribosomal protein S5 / 50S ribosomal protein L9 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 30S ribosomal protein S16 / 30S ribosomal protein S19 / 50S ribosomal protein L5 / 30S ribosomal protein S20 / 30S ribosomal protein S2 / 30S ribosomal protein S3 / gb:33357927: / gb:33357928: / gb:33357879: / 50S ribosomal protein L25 / 30S ribosomal protein S21 / 50S ribosomal protein L17
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 Å
AuthorsSchuwirth, B.S. / Borovinskaya, M.A. / Hau, C.W. / Zhang, W. / Vila-Sanjurjo, A. / Holton, J.M. / Cate, J.H.D.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2AVY, 2AW4, 2AW7, 2AWB
Revision 1.1Dec 10, 2014Group: Other
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS PART OF THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE BIOLOGICAL ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS PART OF THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE BIOLOGICAL UNIT CONSISTS OF TWO SUBUNITS. THERE ARE 2 BIOLOGICAL UNITS IN THE ASYMMETRIC UNIT.
Remark 400COMPOUND THIS FILE, 2AVY, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL ...COMPOUND THIS FILE, 2AVY, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AND ARE DEPOSITED UNDER: 70S RIBOSOME ONE: 2AVY (30S SUBUNIT), 2AW4 (50S SUBUNIT) 70S RIBOSOME TWO: 2AW7 (30S SUBUNIT), 2AWB (50S SUBUNIT)
Remark 600HETEROGEN RESIDUE MO4 at 38 HAS SQUARE-PLANAR HYDRATION OF MG2+. RESIDUES MO4 at ...HETEROGEN RESIDUE MO4 at 38 HAS SQUARE-PLANAR HYDRATION OF MG2+. RESIDUES MO4 at 10,16,30,31,34,40,43,44,51 HAVE 2 VICINAL WATERS MISSING FROM HYDRATION OF MG2+. RESIDUES MO3 at 11,48 HAVE ALL WATER BONDS MUTUALLY ORTHOGONAL TO OTHER MG2+-WATER BONDS. RESIDUES MO3 at 4,9,53 HAVE ALL WATERS AND MG2+ IN-PLANE. RESIDUE MO2 at 35 HAS ALL WATERS AND MG2+ ORTHOGONAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: 16S ribosomal RNA
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AB: 30S ribosomal protein S2
AU: 30S ribosomal protein S21
BA: 5S ribosomal RNA
BB: 23S ribosomal RNA
BV: 50S ribosomal protein L25
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L29
BY: 50S ribosomal protein L30
BZ: 50S ribosomal protein L31
B0: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36
BI: 50S ribosomal protein L11
CA: 16S ribosomal RNA
CC: 30S ribosomal protein S3
CD: 30S ribosomal protein S4
CE: 30S ribosomal protein S5
CF: 30S ribosomal protein S6
CG: 30S ribosomal protein S7
CH: 30S ribosomal protein S8
CI: 30S ribosomal protein S9
CJ: 30S ribosomal protein S10
CK: 30S ribosomal protein S11
CL: 30S ribosomal protein S12
CM: 30S ribosomal protein S13
CN: 30S ribosomal protein S14
CO: 30S ribosomal protein S15
CP: 30S ribosomal protein S16
CQ: 30S ribosomal protein S17
CR: 30S ribosomal protein S18
CS: 30S ribosomal protein S19
CT: 30S ribosomal protein S20
CB: 30S ribosomal protein S2
CU: 30S ribosomal protein S21
DA: 5S ribosomal RNA
DB: 23S ribosomal RNA
DV: 50S ribosomal protein L25
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DJ: 50S ribosomal protein L13
DK: 50S ribosomal protein L14
DL: 50S ribosomal protein L15
DM: 50S ribosomal protein L16
DN: 50S ribosomal protein L17
DO: 50S ribosomal protein L18
DP: 50S ribosomal protein L19
DQ: 50S ribosomal protein L20
DR: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DW: 50S ribosomal protein L27
DX: 50S ribosomal protein L29
DY: 50S ribosomal protein L30
DZ: 50S ribosomal protein L31
D0: 50S ribosomal protein L32
D1: 50S ribosomal protein L33
D2: 50S ribosomal protein L34
D3: 50S ribosomal protein L35
D4: 50S ribosomal protein L36
DI: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,293,422447
Polymers4,285,085104
Non-polymers8,337343
Water29,3101627
1
AA: 16S ribosomal RNA
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AB: 30S ribosomal protein S2
AU: 30S ribosomal protein S21
BA: 5S ribosomal RNA
BB: 23S ribosomal RNA
BV: 50S ribosomal protein L25
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L29
BY: 50S ribosomal protein L30
BZ: 50S ribosomal protein L31
B0: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36
BI: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,146,674222
Polymers2,142,54352
Non-polymers4,132170
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S ribosomal RNA
CC: 30S ribosomal protein S3
CD: 30S ribosomal protein S4
CE: 30S ribosomal protein S5
CF: 30S ribosomal protein S6
CG: 30S ribosomal protein S7
CH: 30S ribosomal protein S8
CI: 30S ribosomal protein S9
CJ: 30S ribosomal protein S10
CK: 30S ribosomal protein S11
CL: 30S ribosomal protein S12
CM: 30S ribosomal protein S13
CN: 30S ribosomal protein S14
CO: 30S ribosomal protein S15
CP: 30S ribosomal protein S16
CQ: 30S ribosomal protein S17
CR: 30S ribosomal protein S18
CS: 30S ribosomal protein S19
CT: 30S ribosomal protein S20
CB: 30S ribosomal protein S2
CU: 30S ribosomal protein S21
DA: 5S ribosomal RNA
DB: 23S ribosomal RNA
DV: 50S ribosomal protein L25
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DJ: 50S ribosomal protein L13
DK: 50S ribosomal protein L14
DL: 50S ribosomal protein L15
DM: 50S ribosomal protein L16
DN: 50S ribosomal protein L17
DO: 50S ribosomal protein L18
DP: 50S ribosomal protein L19
DQ: 50S ribosomal protein L20
DR: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DW: 50S ribosomal protein L27
DX: 50S ribosomal protein L29
DY: 50S ribosomal protein L30
DZ: 50S ribosomal protein L31
D0: 50S ribosomal protein L32
D1: 50S ribosomal protein L33
D2: 50S ribosomal protein L34
D3: 50S ribosomal protein L35
D4: 50S ribosomal protein L36
DI: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,146,747225
Polymers2,142,54352
Non-polymers4,205173
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)208.850, 379.200, 739.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
RNA chain , 3 types, 6 molecules AACABADABBDB

#1: 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 / References: GenBank: 33357879
#22: 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 / References: GenBank: 33357928
#23: 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 / References: GenBank: 33357927

+
30S ribosomal protein ... , 20 types, 40 molecules ACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCPAQCQ...

#2: Protein 30S ribosomal protein S3 /


Mass: 25900.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V3
#3: Protein 30S ribosomal protein S4 /


Mass: 23383.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V8
#4: Protein 30S ribosomal protein S5 /


Mass: 17498.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W1
#5: 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: P02358
#6: Protein 30S ribosomal protein S7 /


Mass: 19923.959 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02359
#7: Protein 30S ribosomal protein S8 /


Mass: 14015.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W7
#8: Protein 30S ribosomal protein S9 /


Mass: 14755.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7X3
#9: 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
#10: Protein 30S ribosomal protein S11 /


Mass: 13739.778 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R9
#11: Protein 30S ribosomal protein S12 /


Mass: 13636.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7S3
#12: Protein 30S ribosomal protein S13 /


Mass: 12997.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7S9
#13: Protein 30S ribosomal protein S14 /


Mass: 11475.364 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02370, UniProt: P0AG59*PLUS
#14: 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: P02371, UniProt: P0ADZ4*PLUS
#15: 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
#16: Protein 30S ribosomal protein S17 /


Mass: 9593.296 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02373, UniProt: P0AG63*PLUS
#17: Protein 30S ribosomal protein S18 /


Mass: 8874.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7T7
#18: Protein 30S ribosomal protein S19 /


Mass: 10324.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7U3
#19: Protein 30S ribosomal protein S20 /


Mass: 9577.268 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7U7
#20: Protein 30S ribosomal protein S2 /


Mass: 26650.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V0
#21: 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: P68679

+
50S ribosomal protein ... , 29 types, 58 molecules BVDVBCDCBDDDBEDEBFDFBGDGBHDHBJDJBKDKBLDLBMDMBNDNBODOBPDPBQDQ...

#24: 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
#25: 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: P60422
#26: 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: P60438
#27: 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: P60723
#28: Protein 50S ribosomal protein L5 /


Mass: 20202.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P62399
#29: Protein 50S ribosomal protein L6 /


Mass: 18801.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02390, UniProt: P0AG55*PLUS
#30: 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
#31: 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: P02410, UniProt: P0AA10*PLUS
#32: 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: P02411, UniProt: P0ADY3*PLUS
#33: 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
#34: 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: P02414, UniProt: P0ADY7*PLUS
#35: 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: P02416, UniProt: P0AG44*PLUS
#36: Protein 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0C018
#37: Protein 50S ribosomal protein L19 /


Mass: 13028.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7K6
#38: Protein 50S ribosomal protein L20 /


Mass: 13396.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7L3
#39: 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: P02422, UniProt: P0AG48*PLUS
#40: 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: P61175
#41: 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: P02424, UniProt: P0ADZ0*PLUS
#42: Protein 50S ribosomal protein L24 /


Mass: 11208.054 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60624
#43: Protein 50S ribosomal protein L27 /


Mass: 9015.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7L8
#44: 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: P0A7M6
#45: Protein 50S ribosomal protein L30 /


Mass: 6423.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02430, UniProt: P0AG51*PLUS
#46: 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: P0A7M9
#47: 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: P0A7N4
#48: Protein 50S ribosomal protein L33 /


Mass: 6257.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7N9
#49: 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: P0A7P5
#50: Protein 50S ribosomal protein L35 / / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q1
#51: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B


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: P0A7Q6
#52: Protein 50S ribosomal protein L11 /


Mass: 14763.165 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7J7

-
Non-polymers , 2 types, 1970 molecules

#53: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


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


Mass: 18.015 Da / Num. of mol.: 1627 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 277 K / Method: batch / pH: 7.5
Details: MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2PEG 800011
3MgCl211
4NH4Cl11
5spermine11
6spermidine11
7TRIS11
8EDTAEthylenediaminetetraacetic acid11
9H2O11
10MPD12
11PEG 800012
12MgCl212
13NH4Cl12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.46→70 Å / Num. obs: 693093 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 7.4
Reflection shellResolution: 3.46→3.55 Å / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2 / Num. unique obs: 49172 / % possible all: 87.9

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1PNS, 1PNU

1pns
PDB Unreleased entry

1pnu
PDB Unreleased entry


Resolution: 3.46→70 Å / Isotropic thermal model: Grouped by residue / σ(F): 0 / Stereochemistry target values: torsional dynamics
RfactorNum. reflection% reflectionSelection details
Rfree0.331 --random 5%
Rwork0.279 ---
All-756754 --
Obs-692904 91.6 %-
Displacement parametersBiso mean: 58.688 Å2
Refinement stepCycle: LAST / Resolution: 3.46→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18538 32831 60 300 51729
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_angle_deg1.155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefinement-ID% reflection obs (%)
3.46-3.480.3983590.342X-RAY DIFFRACTION87.9
3.48-700.331342460.279X-RAY DIFFRACTION92.3

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more