[English] 日本語
Yorodumi
- PDB-9jkp: Crystal structure of the Staphylococcus aureus GTPase Era in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jkp
TitleCrystal structure of the Staphylococcus aureus GTPase Era in complex with GDP
ComponentsGTPase Era
KeywordsRNA BINDING PROTEIN / ribosome / maturation / GTPase
Function / homology
Function and homology information


ribosomal small subunit binding / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA binding / GTPase activity / GTP binding / plasma membrane / cytosol
Similarity search - Function
GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / K homology domain superfamily, prokaryotic type / Small GTP-binding protein domain ...GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / K homology domain superfamily, prokaryotic type / Small GTP-binding protein domain / K homology domain-like, alpha/beta / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase Era
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsKlochkova, E. / Biktimirov, A. / Islamov, D. / Belousov, A. / Yusupov, M. / Usachev, K.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation21-74-20034 Russian Federation
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structure of the GDP-bound GTPase Era from Staphylococcus aureus.
Authors: Klochkova, E. / Biktimirov, A. / Islamov, D. / Belousov, A. / Validov, S. / Yusupov, M. / Usachev, K.
History
DepositionSep 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: GTPase Era
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8473
Polymers34,3801
Non-polymers4682
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-12 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.146, 78.146, 244.905
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein GTPase Era


Mass: 34379.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Gene: era, SAOUHSC_01668 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FY06
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.44 Å3/Da / Density % sol: 77.38 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.228M tri-Potassium citrate pH 8.3, 25% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.76→48.2 Å / Num. obs: 20362 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.025 / Rrim(I) all: 0.036 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.12-4.710.01926.420470.9990.0190.027100
3.74-4.120.02916.520410.9980.0290.041100
3.47-3.740.0549.620390.9960.0540.077100
3.27-3.470.1115.219960.9740.1110.157100
3.11-3.270.2022.920200.9160.2020.285100
2.97-3.110.331.820010.8520.330.467100
2.86-2.970.5421.119950.6220.5420.766100
2.76-2.861.0370.618790.41794.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
XDSJanuary 10, 2022data scaling
Coot0.9.8.95model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→48.195 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 31.059 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / ESU R Free: 0.224
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2236 1018 5.003 %
Rwork0.1698 19330 -
all0.173 --
obs-20348 99.569 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 98.104 Å2
Baniso -1Baniso -2Baniso -3
1--3.498 Å20 Å20 Å2
2---3.498 Å20 Å2
3---6.996 Å2
Refinement stepCycle: LAST / Resolution: 2.76→48.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 29 17 2450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122478
X-RAY DIFFRACTIONr_bond_other_d0.0070.0162417
X-RAY DIFFRACTIONr_angle_refined_deg2.571.8343345
X-RAY DIFFRACTIONr_angle_other_deg1.291.795584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1795298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.724515
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.53851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81910474
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.59510114
X-RAY DIFFRACTIONr_chiral_restr0.1360.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022828
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02526
X-RAY DIFFRACTIONr_nbd_refined0.140.2330
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1030.22092
X-RAY DIFFRACTIONr_nbtor_refined0.1310.21077
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.060.21301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0720.236
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0530.213
X-RAY DIFFRACTIONr_nbd_other0.0820.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.090.23
X-RAY DIFFRACTIONr_mcbond_it19.7157.0961195
X-RAY DIFFRACTIONr_mcbond_other19.7077.0981196
X-RAY DIFFRACTIONr_mcangle_it28.86112.8591492
X-RAY DIFFRACTIONr_mcangle_other28.86412.861493
X-RAY DIFFRACTIONr_scbond_it20.0837.5031283
X-RAY DIFFRACTIONr_scbond_other20.0657.5041283
X-RAY DIFFRACTIONr_scangle_it29.52413.7611853
X-RAY DIFFRACTIONr_scangle_other29.51613.7611854
X-RAY DIFFRACTIONr_lrange_it35.594692444
X-RAY DIFFRACTIONr_lrange_other35.58268.9982444
X-RAY DIFFRACTIONr_rigid_bond_restr4.91834895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.76-2.8310.372700.37813170.37714620.940.89894.870.373
2.831-2.9090.339720.34913690.34914410.9250.9381000.338
2.909-2.9930.341690.30813230.3113920.9310.9531000.281
2.993-3.0840.319680.27912780.28213460.9410.9591000.25
3.084-3.1850.337650.24512440.24913090.9380.9731000.203
3.185-3.2960.272650.20912270.21212930.9570.98199.92270.168
3.296-3.420.25610.18411690.18712300.940.9831000.148
3.42-3.5590.214600.16611380.16911980.9740.9871000.137
3.559-3.7170.232580.15310950.15711530.9750.9911000.129
3.717-3.8970.167550.12810420.1310970.9880.9931000.108
3.897-4.1060.176520.129970.12310490.9830.9921000.101
4.106-4.3530.146500.1129540.11410040.990.9921000.097
4.353-4.6510.214470.0978860.1029330.9760.9951000.087
4.651-5.020.158440.1188450.128890.990.9941000.108
5.02-5.4930.198420.1267830.138250.9780.9921000.115
5.493-6.1310.21370.1637190.1667560.9750.9841000.147
6.131-7.0610.18340.156430.1526770.9790.9851000.135
7.061-8.6020.222290.1655520.1685810.9730.9821000.168
8.602-11.9760.216240.1824470.1844710.9840.9841000.2
11.976-48.1950.419160.3082990.3133150.9210.9461000.342
Refinement TLS params.Method: refined / Origin x: 31.921 Å / Origin y: 18.1211 Å / Origin z: -43.3582 Å
111213212223313233
T0.0637 Å20.0094 Å2-0.0129 Å2-0.3966 Å20.067 Å2--0.0327 Å2
L1.649 °20.819 °2-2.4749 °2-1.855 °2-1.5349 °2--4.8259 °2
S-0.0193 Å °0.1064 Å °-0.0723 Å °-0.2756 Å °0.0579 Å °-0.0088 Å °0.1271 Å °-0.2894 Å °-0.0386 Å °
Refinement TLS groupSelection: ALL

+
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