[English] 日本語
Yorodumi
- PDB-5vog: Crystal Structure of a Hypothetical Protein from Neisseria gonorr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vog
TitleCrystal Structure of a Hypothetical Protein from Neisseria gonorrhoeae with bound ppGpp
ComponentsPutative phosphoribosyltransferase
KeywordsTRANSFERASE / SSGCID / ppGpp / possible Phosphoribosyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyRossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / GUANOSINE-5',3'-TETRAPHOSPHATE / Phosphoribosyltransferase
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Hypothetical Protein from Neisseria gonorrhoeae with bound ppGpp
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Data collection
Revision 1.2Jul 5, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7536
Polymers20,9771
Non-polymers7765
Water3,621201
1
A: Putative phosphoribosyltransferase
hetero molecules

A: Putative phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,50612
Polymers41,9542
Non-polymers1,55210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+1/2,y,-z+1/21
Buried area6090 Å2
ΔGint-48 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.270, 103.930, 105.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-428-

HOH

-
Components

#1: Protein Putative phosphoribosyltransferase


Mass: 20977.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria)
Gene: ESCNG_40048, WHOF_00431, WHOF_02526C, WHOG_01129, WHOG_02374C, WHOK_01250, WHOK_02372C, WHOM_00300, WHOM_02380C, WHON_00453, WHON_02375C, WHOU_01208, WHOU_02454C, WHOV_00719, WHOV_02442C, WHOW_ ...Gene: ESCNG_40048, WHOF_00431, WHOF_02526C, WHOG_01129, WHOG_02374C, WHOK_01250, WHOK_02372C, WHOM_00300, WHOM_02380C, WHON_00453, WHON_02375C, WHOU_01208, WHOU_02454C, WHOV_00719, WHOV_02442C, WHOW_01101, WHOW_02437C, WHOX_00398, WHOX_02372C, WHOZ_01227, WHOZ_02445C
Plasmid: NegoA.19192.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1D3HIA2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: NegoA.19192.a.B1.PS38045 at 17 mg/ml mixed 1:1 with Morpheus(a2): 10% (w/v) PEG-8000, 20% (v/v) ethylene glycol, 0.1 M MES/imidazole, pH = 5.5, 0.03 M each magnesium chloride and calcium chloride, direct cryo

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40.635 Å / Num. obs: 35700 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.493 % / Biso Wilson estimate: 24.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.034 / Χ2: 0.993 / Net I/σ(I): 26.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.545.5650.4033.6926190.940.44599.9
1.54-1.585.4460.2944.9225570.9680.32599.5
1.58-1.635.2540.2286.2924660.9760.25399.2
1.63-1.685.4970.1748.3324030.9840.192100
1.68-1.735.6570.12711.4323530.9910.14100
1.73-1.795.6060.09814.3322700.9950.108100
1.79-1.865.4790.07418.7521880.9970.08199.9
1.86-1.945.2080.0622.7420960.9970.06699.4
1.94-2.025.5480.04728.6220160.9990.05299.9
2.02-2.125.7060.03934.1919560.9990.043100
2.12-2.245.6620.03339.4518360.9990.03699.9
2.24-2.375.4290.03241.3117570.9990.03699.8
2.37-2.545.2240.0343.6616440.9990.03399.9
2.54-2.745.7940.02848.9215430.9990.03199.9
2.74-35.6870.02851.1614120.9990.03199.8
3-3.355.4020.02852.0712920.9990.03199.6
3.35-3.875.2160.02853.0411360.9980.03199.1
3.87-4.745.6840.02755.79710.9990.02998.9
4.74-6.715.2260.02953.567520.9990.03298.3
6.71-40.6355.3140.02954.414330.9990.03295.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX(dev_2744: ???)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JKZ

2jkz


Resolution: 1.5→40.635 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.19
RfactorNum. reflection% reflection
Rfree0.1765 1921 5.38 %
Rwork0.1492 --
obs0.1507 35688 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.28 Å2 / Biso mean: 35.5166 Å2 / Biso min: 18.86 Å2
Refinement stepCycle: final / Resolution: 1.5→40.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 46 204 1630
Biso mean--28.89 45.1 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051531
X-RAY DIFFRACTIONf_angle_d0.8692108
X-RAY DIFFRACTIONf_chiral_restr0.055237
X-RAY DIFFRACTIONf_plane_restr0.004277
X-RAY DIFFRACTIONf_dihedral_angle_d9.454919
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53750.20281380.161823892527100
1.5375-1.57910.20551250.1472401252699
1.5791-1.62560.1731600.14182356251699
1.6256-1.6780.18971470.13423632510100
1.678-1.7380.17141390.13224042543100
1.738-1.80760.15911270.126924082535100
1.8076-1.88990.18861290.135724102539100
1.8899-1.98950.19051420.147623912533100
1.9895-2.11410.18341210.151224362557100
2.1141-2.27740.16911270.143924122539100
2.2774-2.50650.17881380.152824162554100
2.5065-2.86910.18551390.151824472586100
2.8691-3.61450.1761430.15324242567100
3.6145-40.64990.16971460.15152510265698

+
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