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- PDB-4b3m: Crystal structure of the 30S ribosome in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 4b3m
TitleCrystal structure of the 30S ribosome in complex with compound 1
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S RIBOSOMAL RNA
  • 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP)-3'
  • 5'-R(*UP*UP*CP*AP*AP*AP)-3'
KeywordsRIBOSOME / ANTIBIOTIC
Function / homology
Function and homology information


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain ...S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Ribosomal protein S3 C-terminal domain / Ribosomal protein S6/Translation elongation factor EF1B / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / S15/NS1, RNA-binding / Helix hairpin bin / Ribosomal Protein S7 / Ribosomal protein S7/S5 / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Ribosomal protein S14, type Z / Double Stranded RNA Binding Domain / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Few Secondary Structures / Irregular / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / : / Ribosomal protein S5, N-terminal, conserved site
Similarity search - Domain/homology
: / Chem-ON0 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...: / Chem-ON0 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsNg, C.L. / Lang, K. / Shcherbakov, D. / Matt, T. / Perez-Fernandez, D. / Patak, R. / Meyer, M. / Duscha, S. / Akbergenov, R. / Boukari, H. ...Ng, C.L. / Lang, K. / Shcherbakov, D. / Matt, T. / Perez-Fernandez, D. / Patak, R. / Meyer, M. / Duscha, S. / Akbergenov, R. / Boukari, H. / Freihofer, P. / Kudyba, I. / Reddy, M.S.K. / Nandurikar, R.S. / Ramakrishnan, V. / Vasella, A. / Bottger, E.C.
CitationJournal: Nat.Commun. / Year: 2014
Title: 4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics
Authors: Perez-Fernandez, D. / Shcherbakov, D. / Matt, T. / Leong, N.C. / Kudyba, I. / Duscha, S. / Boukari, H. / Patak, R. / Dubakka, S.R. / Lang, K. / Meyer, M. / Akbergenov, R. / Freihofer, P. / ...Authors: Perez-Fernandez, D. / Shcherbakov, D. / Matt, T. / Leong, N.C. / Kudyba, I. / Duscha, S. / Boukari, H. / Patak, R. / Dubakka, S.R. / Lang, K. / Meyer, M. / Akbergenov, R. / Freihofer, P. / Vaddi, S. / Thommes, P. / Ramakrishnan, V. / Vasella, A. / Bottger, E.C.
History
DepositionJul 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Other / Structure summary
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Feb 12, 2014Group: Database references
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.5Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
B: 30S RIBOSOMAL PROTEIN S2
C: 30S RIBOSOMAL PROTEIN S3
D: 30S RIBOSOMAL PROTEIN S4
E: 30S RIBOSOMAL PROTEIN S5
F: 30S RIBOSOMAL PROTEIN S6
G: 30S RIBOSOMAL PROTEIN S7
H: 30S RIBOSOMAL PROTEIN S8
I: 30S RIBOSOMAL PROTEIN S9
J: 30S RIBOSOMAL PROTEIN S10
K: 30S RIBOSOMAL PROTEIN S11
L: 30S RIBOSOMAL PROTEIN S12
M: 30S RIBOSOMAL PROTEIN S13
N: 30S RIBOSOMAL PROTEIN S14 TYPE Z
O: 30S RIBOSOMAL PROTEIN S15
P: 30S RIBOSOMAL PROTEIN S16
Q: 30S RIBOSOMAL PROTEIN S17
R: 30S RIBOSOMAL PROTEIN S18
S: 30S RIBOSOMAL PROTEIN S19
T: 30S RIBOSOMAL PROTEIN S20
V: 30S RIBOSOMAL PROTEIN THX
W: 5'-R(*UP*UP*CP*AP*AP*AP)-3'
Z: 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)796,251283
Polymers788,91923
Non-polymers7,332260
Water1267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)401.650, 401.650, 175.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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RNA chain , 3 types, 3 molecules AWZ

#1: RNA chain 16S RIBOSOMAL RNA


Mass: 493652.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: GenBank: 55771382
#22: RNA chain 5'-R(*UP*UP*CP*AP*AP*AP)-3' / MRNA


Mass: 1860.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria)
#23: RNA chain 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP)-3' / ANTICODON STEM LOOP ASL


Mass: 5161.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria)

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30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV

#2: Protein 30S RIBOSOMAL PROTEIN S2


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80371
#3: Protein 30S RIBOSOMAL PROTEIN S3


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80372
#4: Protein 30S RIBOSOMAL PROTEIN S4


Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80373
#5: Protein 30S RIBOSOMAL PROTEIN S5


Mass: 17452.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHQ5
#6: Protein 30S RIBOSOMAL PROTEIN S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SLP8
#7: Protein 30S RIBOSOMAL PROTEIN S7


Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P17291
#8: Protein 30S RIBOSOMAL PROTEIN S8


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S9


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80374
#10: Protein 30S RIBOSOMAL PROTEIN S10


Mass: 11823.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHN7
#11: Protein 30S RIBOSOMAL PROTEIN S11


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80376
#12: Protein 30S RIBOSOMAL PROTEIN S12


Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHN3
#13: Protein 30S RIBOSOMAL PROTEIN S13


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80377
#14: Protein 30S RIBOSOMAL PROTEIN S14 TYPE Z


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S15


Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SJ76
#16: Protein 30S RIBOSOMAL PROTEIN S16


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SJH3
#17: Protein 30S RIBOSOMAL PROTEIN S17


Mass: 12193.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18


Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SLQ0
#19: Protein 30S RIBOSOMAL PROTEIN S19


Mass: 10474.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SHP2
#20: Protein 30S RIBOSOMAL PROTEIN S20


Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: P80380
#21: Protein/peptide 30S RIBOSOMAL PROTEIN THX


Mass: 3218.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS HB8 (bacteria) / References: UniProt: Q5SIH3

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Non-polymers , 5 types, 267 molecules

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


Mass: 24.305 Da / Num. of mol.: 240 / Source method: obtained synthetically / Formula: Mg
#25: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: K
#26: Chemical ChemComp-ON0 / (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranoside


Mass: 703.735 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H49N5O14
#27: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#28: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.15 %
Description: DATA WAS USED TO REFINE AGAINST THE MODEL FROM PDB ID 1J5E STRUCTURE USING CNS. THE OBTAINED DIFFERENCE MAP WAS USED TO ANALYSE THE BINDING OF LIGAND ON0, FURTHER MANUAL MODEL FITTING USING COOT.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: MPD, NH4CL, KCL, CACL2, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 6.5,VAPOUR DIFFUSION, HANGING DROP AT 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 311372 / % possible obs: 99.5 % / Observed criterion σ(I): 1.9 / Redundancy: 7.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 1.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1J5E

1j5e


Resolution: 2.9→40 Å / Data cutoff high absF: 10000 / Cross valid method: NA / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2513 15586 5 %
Rwork0.218 --
obs0.218 311372 99.6 %
Solvent computationBsol: 47.0833 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.443 Å20 Å20 Å2
2---6.443 Å20 Å2
3---12.886 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19239 32951 308 7 52505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ETO_AXIAL.PARETO_AXIAL.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION4PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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  • 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

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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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

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