[English] 日本語
Yorodumi
- PDB-7oiw: Structure of S. aureus Rel catalytic domains in complex with pppGpp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oiw
TitleStructure of S. aureus Rel catalytic domains in complex with pppGpp
ComponentsGTP pyrophosphokinase
KeywordsTRANSFERASE / bifunctional GTP pyrophosphokinase / hydrolase / alarmone synthetase / hydrolase / ppGpp
Function / homology
Function and homology information


GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / GTP binding / ATP binding
Similarity search - Function
RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / ACT domain profile. ...RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / ACT domain profile. / ACT domain / ACT-like domain / HD domain profile. / TGS domain profile. / TGS / TGS-like / HD domain / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Chem-0O2 / IODIDE ION / : / Chem-VF5 / GTP pyrophosphokinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsGarcia-Pino, A.
CitationJournal: To Be Published
Title: Structure of S. aureus Rel catalytic domains in complex with pppGpp
Authors: Garcia-Pino, A.
History
DepositionMay 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP pyrophosphokinase
B: GTP pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,23125
Polymers102,1152
Non-polymers5,11523
Water99155
1
A: GTP pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,73713
Polymers51,0581
Non-polymers2,67912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,49412
Polymers51,0581
Non-polymers2,43611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.410, 132.540, 73.470
Angle α, β, γ (deg.)90.00, 103.59, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein GTP pyrophosphokinase / (p)ppGpp synthase / ATP:GTP 3'-pyrophosphotransferase / ppGpp synthase I


Mass: 51057.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the missing residues are not visible in the electron density
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: relA, SAV1634 / Production host: Escherichia coli (E. coli) / References: UniProt: Q931Q4, GTP diphosphokinase

-
Non-polymers , 7 types, 78 molecules

#2: Chemical
ChemComp-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H18N5O20P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-VF5 / [[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-2-oxidanyl-2-oxidanylidene-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 585.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O16P4
#4: 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
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 293.16 K / Method: vapor diffusion, sitting drop
Details: 6% w/vPEG 3350 0.15 M Sodium chloride 0.4 M Potassium iodide pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.63→42.25 Å / Num. obs: 31024 / % possible obs: 99.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 59.19 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.07 / Net I/σ(I): 8.2
Reflection shellResolution: 2.63→2.72 Å / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2954 / CC1/2: 0.667 / Rpim(I) all: 0.47

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S2U

6s2u


Resolution: 2.63→42.25 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 1550 5 %
Rwork0.2149 --
obs0.2171 31024 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5204 0 218 55 5477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035554
X-RAY DIFFRACTIONf_angle_d0.7417583
X-RAY DIFFRACTIONf_dihedral_angle_d23.0492113
X-RAY DIFFRACTIONf_chiral_restr0.047849
X-RAY DIFFRACTIONf_plane_restr0.0041005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.710.32241300.28572479X-RAY DIFFRACTION92
2.71-2.810.31031410.27232672X-RAY DIFFRACTION100
2.81-2.920.33671410.27982690X-RAY DIFFRACTION100
2.92-3.050.34111420.27222698X-RAY DIFFRACTION100
3.05-3.220.27431420.25532684X-RAY DIFFRACTION100
3.22-3.420.27071410.23532692X-RAY DIFFRACTION100
3.42-3.680.27741430.2142702X-RAY DIFFRACTION100
3.68-4.050.23121420.18732697X-RAY DIFFRACTION100
4.05-4.640.23811420.16962703X-RAY DIFFRACTION100
4.64-5.840.24711430.19712708X-RAY DIFFRACTION100
5.84-42.250.23571430.21612749X-RAY DIFFRACTION100
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)
14.67510.04890.34084.2676-0.59254.199-0.0766-0.25240.25980.5186-0.1033-0.33-0.5622-0.18960.21860.5638-0.0213-0.0960.3958-0.01830.552-17.172712.6856.0713
20.27170.33720.73091.31840.10954.019-0.13150.03830.01410.09630.07660.11470.21270.19070.07860.25480.0217-0.02110.4176-0.00430.5061-23.2153-9.1481-3.1758
31.2828-0.4101-0.27391.90111.66487.5326-0.07890.0532-0.05960.0996-0.0233-0.07190.04070.10810.09330.34960.0327-0.050.4578-0.00870.4268-23.4843-10.6087-19.5824
48.6134-1.50021.7642.45950.06314.79640.04770.3050.2524-0.0824-0.0015-0.32360.05620.1183-0.04380.4803-0.01690.05110.29610.00650.4954-10.502-39.23264.0694
54.55733.2708-0.26416.99460.09475.67040.4197-0.3045-0.20640.9535-0.07110.3430.7505-0.3636-0.30490.5905-0.0427-0.06620.46440.02580.5161-15.5566-47.810316.0761
64.4994-0.55221.584.10480.13033.61930.028-0.37310.08470.40570.05960.32020.0945-0.2618-0.08960.4843-0.01720.09050.36280.00270.3803-17.3709-27.868319.9955
79.24690.82473.20820.7663-0.03261.7509-0.21181.11730.6333-0.2049-0.0005-0.0617-0.22370.59020.24640.4639-0.03860.02380.51230.03170.36091.7437-9.162721.2179
88.92311.18392.17990.9444-0.58721.5185-0.4148-0.33060.54580.29540.2945-0.0372-0.1060.15190.09070.5286-0.00730.03690.4073-0.01170.4362-4.8999-13.814127.5726
91.96211.08170.7644.779-0.27212.12260.09950.1516-0.0588-0.1697-0.0632-0.0118-0.02170.254-0.04450.43110.04010.02190.5185-0.0690.3468.0368-18.7532.6516
106.2674-0.08910.38130.5025-0.85144.89660.05430.6138-0.8365-0.87960.2699-0.19930.68440.5971-0.09870.44910.0373-0.06430.5495-0.04220.3943.5383-27.957625.556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 141 )
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 239 )
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 352 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 70 )
5X-RAY DIFFRACTION5chain 'B' and (resid 71 through 141 )
6X-RAY DIFFRACTION6chain 'B' and (resid 142 through 203 )
7X-RAY DIFFRACTION7chain 'B' and (resid 204 through 239 )
8X-RAY DIFFRACTION8chain 'B' and (resid 240 through 272 )
9X-RAY DIFFRACTION9chain 'B' and (resid 273 through 328 )
10X-RAY DIFFRACTION10chain 'B' and (resid 329 through 351 )

+
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