[English] 日本語
Yorodumi
- PDB-4dg5: Crystal structure of staphylococcal Phosphoglycerate kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dg5
TitleCrystal structure of staphylococcal Phosphoglycerate kinase
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / Bi-lobal protein / ATP Synthesis / phosphorylation / cytosol
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglycerate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsRoychowdhury, A. / Mukherjee, S. / Dutta, D. / Das, A.K.
CitationJournal: To be Published
Title: Structure based functional analysis of Staphylococcal Phosphoglycerate kinase
Authors: Roychowdhury, A. / Mukherjee, S. / Dutta, D. / Das, A.K.
History
DepositionJan 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoglycerate kinase


Theoretical massNumber of molelcules
Total (without water)43,4991
Polymers43,4991
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.137, 74.748, 58.665
Angle α, β, γ (deg.)90.000, 95.720, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Phosphoglycerate kinase /


Mass: 43499.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: pgk, SAR0829 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q6GIL7, phosphoglycerate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.26 Å3/Da / Density % sol: 45.66 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.15M Calcium chloride dihydrate, 0.1M HEPES-Na, 20% (w/v)Polyethylene glycol 2000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2010 / Details: Varimax mirror
RadiationMonochromator: Varimax optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→58.373 Å / Num. all: 16871 / Num. obs: 16871 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.094 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.423.60.2750.2353.2855524010.1430.2750.2355.295.9
2.42-2.573.70.2530.2163.4844323030.130.2530.2165.996.6
2.57-2.753.70.1950.1684.4806721590.10.1950.1687.497.3
2.75-2.973.80.1490.1285.7771420420.0760.1490.1289.597.8
2.97-3.253.80.1070.0927.9717918870.0540.1070.09212.697.8
3.25-3.643.80.0860.0749.6653117130.0440.0860.07416.298.9
3.64-4.23.80.0730.06311.4578215220.0370.0730.0632098.7
4.2-5.143.80.0670.05812.1489812920.0340.0670.05821.699.1
5.14-7.273.80.0780.06710.2381810110.040.0780.06717.499.7
7.27-19.4583.70.0540.04613.519765410.0280.0540.04624.994.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å19.46 Å
Translation4 Å19.46 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PHP

1php


Resolution: 2.3→58.37 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.842 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.015 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 850 5 %RANDOM
Rwork0.1724 ---
obs0.1769 16852 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 15.703 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å2-0.42 Å2
2--0.6 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→58.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 0 260 3245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223047
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9774117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58826.504123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14115562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.866156
X-RAY DIFFRACTIONr_chiral_restr0.1130.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212230
X-RAY DIFFRACTIONr_mcbond_it0.7591.51957
X-RAY DIFFRACTIONr_mcangle_it1.41623150
X-RAY DIFFRACTIONr_scbond_it2.51531090
X-RAY DIFFRACTIONr_scangle_it4.1794.5964
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 52 -
Rwork0.169 1149 -
all-1201 -
obs--94.72 %
Refinement TLS params.Method: refined / Origin x: -3.9813 Å / Origin y: 8.927 Å / Origin z: -23.8766 Å
111213212223313233
T0.0141 Å20.0049 Å20.0159 Å2-0.0039 Å20.0086 Å2--0.0273 Å2
L0.6187 °20.184 °20.4823 °2-0.3317 °20.2049 °2--0.8203 °2
S0.0009 Å °-0.0326 Å °-0.0435 Å °0.0359 Å °0.0096 Å °0.0247 Å °-0.0096 Å °-0.0258 Å °-0.0106 Å °

+
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