[English] 日本語
Yorodumi
- PDB-5ucv: Crystal Structure of a Ribosome Biogenesis GTP-binding protein (Y... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ucv
TitleCrystal Structure of a Ribosome Biogenesis GTP-binding protein (YsxC) from Neisseria gonorrhoeae with bound GDP
ComponentsProbable GTP-binding protein EngB
KeywordsCELL CYCLE / SSGCID / GDP / YsxC / engB / ribosome biogensis / GTP-binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


division septum assembly / GTP binding / metal ion binding
Similarity search - Function
GTP-binding protein, ribosome biogenesis, YsxC / EngB-type guanine nucleotide-binding (G) domain profile. / EngB-type guanine nucleotide-binding (G) domain / 50S ribosome-binding GTPase / GTP binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Probable GTP-binding protein EngB
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Ribosome Biogenesis GTP-binding protein (YsxC) from Neisseria gonorrhoeae with bound GDP
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable GTP-binding protein EngB
B: Probable GTP-binding protein EngB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1148
Polymers49,3302
Non-polymers7846
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-29 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.110, 68.440, 126.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Probable GTP-binding protein EngB


Mass: 24665.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria)
Strain: NCCP11945 / Gene: engB, NGK_0143 / Plasmid: NegoA.00252.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4RQ29

-
Non-polymers , 6 types, 321 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NegoA.00252.a.B1.PW37899 at 17.5 mg/ml, incubated with 4 mM MgCl2, 3 mM GTP, protein mixed 1:1 and incubated with an equal volume MCSG1(c4): 25.5% (w/v) PEG-4000, 15% (v/v) glycerol, 0.085 M ...Details: NegoA.00252.a.B1.PW37899 at 17.5 mg/ml, incubated with 4 mM MgCl2, 3 mM GTP, protein mixed 1:1 and incubated with an equal volume MCSG1(c4): 25.5% (w/v) PEG-4000, 15% (v/v) glycerol, 0.085 M sodium acetate:HCl, 0.17 M ammonium acetate, cryoprotected with 20% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→48.204 Å / Num. obs: 42802 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.058 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.081 / Χ2: 0.966 / Net I/σ(I): 17.88 / Num. measured all: 259276 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.855.3510.562.95164923090308230820.8080.62199.7
1.85-1.96.0750.4544.1318576306030580.8790.49699.9
1.9-1.956.1580.3525.4818252296729640.9320.38599.9
1.95-2.016.180.2916.5417830288728850.9510.31799.9
2.01-2.086.1760.2378.0417242279527920.9650.25999.9
2.08-2.156.160.18310.0716620270026980.9790.299.9
2.15-2.236.1730.14812.2716032259925970.9850.16199.9
2.23-2.326.1440.1313.8615550253325310.9880.14299.9
2.32-2.436.1670.11415.3914814240424020.9920.12599.9
2.43-2.556.1540.09917.4614376233623360.9930.108100
2.55-2.686.1590.08519.9513605221022090.9950.093100
2.68-2.856.1450.07222.3912922210321030.9960.079100
2.85-3.046.1430.0626.6112120197319730.9970.065100
3.04-3.296.1190.0531.4911388186218610.9980.05499.9
3.29-3.66.0820.04137.2810334170116990.9980.04599.9
3.6-4.026.0740.03542.089487156315620.9990.03899.9
4.02-4.656.0330.03246.168289137413740.9990.035100
4.65-5.695.9350.03144.717098119611960.9990.034100
5.69-8.055.7830.03342.3753789349300.9990.03699.6
8.05-48.2045.220.02748.0628715625500.9990.0397.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DHE

4dhe


Resolution: 1.8→48.204 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.11
RfactorNum. reflection% reflection
Rfree0.2071 2046 4.78 %
Rwork0.1672 --
obs0.1691 42797 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.42 Å2 / Biso mean: 23.7496 Å2 / Biso min: 7.13 Å2
Refinement stepCycle: final / Resolution: 1.8→48.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 54 319 3278
Biso mean--40.55 33.66 -
Num. residues----373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063074
X-RAY DIFFRACTIONf_angle_d0.8184181
X-RAY DIFFRACTIONf_chiral_restr0.052477
X-RAY DIFFRACTIONf_plane_restr0.005532
X-RAY DIFFRACTIONf_dihedral_angle_d12.4751846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.8420.27511520.244626152767
1.842-1.8880.25151210.214726922813
1.888-1.93910.23631450.18726602805
1.9391-1.99620.23381330.177326932826
1.9962-2.06060.23571170.177327002817
2.0606-2.13420.21111310.168326852816
2.1342-2.21970.18341430.163427102853
2.2197-2.32070.20661200.153826972817
2.3207-2.44310.24021260.159827262852
2.4431-2.59610.20061460.16227022848
2.5961-2.79650.20821420.171526922834
2.7965-3.07790.21531520.170127312883
3.0779-3.52320.20731410.163927452886
3.5232-4.43840.181380.144927912929
4.4384-48.22080.1871390.170129123051
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.507-0.1964-0.28852.3745-1.87784.0353-0.09960.053-0.0075-0.2471-0.1491-0.3461-0.08240.47640.17640.1772-0.01540.02310.17470.03290.1628-2.59673.009110.6273
25.17741.7093.83482.99741.95813.4164-0.0195-0.18740.51650.0208-0.094-0.261-0.4077-0.03340.09970.1502-0.01120.01410.1514-0.02040.1733-8.172312.09321.7633
31.07610.5505-0.50652.0511-0.9411.4826-0.0276-0.0196-0.1088-0.1414-0.0978-0.15770.15150.03790.06930.08230.01040.00330.11080.00220.1016-12.4925-5.856119.8993
42.3058-0.4977-0.0523.6374-1.69071.7983-0.01540.1282-0.0855-0.01790.00880.38410.0773-0.1893-0.02960.0997-0.0210.02060.116-0.03540.1821-37.78036.127438.9302
52.4043-1.0692-0.4983.5415-3.08763.69320.07290.0008-0.19410.20940.16610.8153-0.0006-0.2914-0.00860.1317-0.0220.07050.1612-0.00670.2312-41.11160.845444.4171
61.8483-0.456-0.11973.15320.44392.02190.05620.1947-0.25250.0852-0.09780.29030.3329-0.17760.03420.1015-0.0233-0.00130.1605-0.02420.1394-33.9957-1.738234.7331
71.0515-1.02560.45977.6623-3.55443.20090.0425-0.05380.00450.1313-0.1132-0.15340.01710.04860.06710.0674-0.01550.03020.1022-0.03070.0789-28.9483-1.115542.7512
81.06940.2758-0.87061.6162-0.95373.61470.0586-0.0148-0.04220.1848-0.09010.040.11940.01570.02140.0775-0.01960.00230.1063-0.00810.0915-25.2172-5.342943.7652
95.21033.2891-5.16534.4368-4.81647.44020.1222-0.3065-0.1220.2705-0.2796-0.2822-0.05840.58640.17150.1544-0.0396-0.0680.15790.00290.1676-19.0617-8.071552.9001
101.8625-0.2136-0.04982.9864-0.6872.6414-0.0448-0.11470.06640.64520.03090.1659-0.2521-0.067-0.03240.2376-0.02480.02220.1454-0.03520.1229-28.39694.049952.1652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 75 )A2 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 102 )A76 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 201 )A103 - 201
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 32 )B2 - 32
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 66 )B33 - 66
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 102 )B67 - 102
7X-RAY DIFFRACTION7chain 'B' and (resid 103 through 117 )B103 - 117
8X-RAY DIFFRACTION8chain 'B' and (resid 118 through 148 )B118 - 148
9X-RAY DIFFRACTION9chain 'B' and (resid 149 through 168 )B149 - 168
10X-RAY DIFFRACTION10chain 'B' and (resid 169 through 200 )B169 - 200

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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. 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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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

Read more