[English] 日本語
Yorodumi
- PDB-3k73: Crystal Structure of Phosphate bound Holo Glyceraldehyde-3-phosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k73
TitleCrystal Structure of Phosphate bound Holo Glyceraldehyde-3-phosphate dehydrogenase 1 from MRSA252 at 2.5 Angstrom resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1
KeywordsOXIDOREDUCTASE / Rossmann fold / Glycolysis / NAD
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytoplasm
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMukherjee, S. / Dutta, D. / Saha, B. / Das, A.K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism.
Authors: Mukherjee, S. / Dutta, D. / Saha, B. / Das, A.K.
History
DepositionOct 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 4, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Q: Glyceraldehyde-3-phosphate dehydrogenase 1
O: Glyceraldehyde-3-phosphate dehydrogenase 1
P: Glyceraldehyde-3-phosphate dehydrogenase 1
R: Glyceraldehyde-3-phosphate dehydrogenase 1
Q: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
O: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
P: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
R: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,69716
Polymers145,2834
Non-polymers3,41312
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22690 Å2
ΔGint-167 kcal/mol
Surface area43550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.200, 104.851, 90.604
Angle α, β, γ (deg.)90.000, 107.570, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Q
21P
31R
41O

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 1 - 336 / Label seq-ID: 1 - 336

Dom-IDAuth asym-IDLabel asym-ID
1QA
2PC
3RD
4OB

-
Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase 1 / GAPDH 1


Mass: 36320.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: gap, gap1, gapA, gapA1, SAR0828 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4)
References: UniProt: Q6GIL8, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.13 Å3/Da / Density % sol: 42.14 % / Mosaicity: 0.796 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 25% PEG 4000, 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: May 10, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→86.38 Å / Num. obs: 41937 / % possible obs: 99.8 % / Redundancy: 3.02 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.085 / Χ2: 0.99 / Net I/σ(I): 8.1 / Scaling rejects: 959
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.86 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.5 / Num. measured all: 12030 / Num. unique all: 4163 / Χ2: 1.25 / % possible all: 99.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.69 Å19.14 Å
Translation2.69 Å19.14 Å

-
Processing

Software
NameVersionClassificationNB
d*TREK9.8Ldata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H48

3h48
PDB Unreleased entry


Resolution: 2.5→19.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.164 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.853 / SU B: 22.984 / SU ML: 0.224 / SU R Cruickshank DPI: 0.244 / SU Rfree: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2115 5 %RANDOM
Rwork0.177 ---
obs0.179 41927 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 100.97 Å2 / Biso mean: 60.342 Å2 / Biso min: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å21.43 Å2
2---1.51 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10184 0 216 174 10574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210550
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.98314326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54651342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67625.401461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.463151793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5461556
X-RAY DIFFRACTIONr_chiral_restr0.0950.21673
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027812
X-RAY DIFFRACTIONr_mcbond_it0.6361.56639
X-RAY DIFFRACTIONr_mcangle_it1.3942.510674
X-RAY DIFFRACTIONr_scbond_it4.06353911
X-RAY DIFFRACTIONr_scangle_it6.93103651
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
Q1343TIGHT POSITIONAL0.050.05
O1343TIGHT POSITIONAL0.050.05
P1343TIGHT POSITIONAL0.060.05
R1343TIGHT POSITIONAL0.060.05
Q1198MEDIUM POSITIONAL0.060.5
O1198MEDIUM POSITIONAL0.060.5
P1198MEDIUM POSITIONAL0.060.5
R1198MEDIUM POSITIONAL0.060.5
Q1343TIGHT THERMAL0.130.5
O1343TIGHT THERMAL0.130.5
P1343TIGHT THERMAL0.130.5
R1343TIGHT THERMAL0.130.5
Q1198MEDIUM THERMAL0.152
O1198MEDIUM THERMAL0.162
P1198MEDIUM THERMAL0.152
R1198MEDIUM THERMAL0.152
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 160 -
Rwork0.287 2920 -
all-3080 -
obs--99.58 %
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)
10.7498-0.014-0.1191.68190.17930.95480.02340.12190.1446-0.2443-0.058-0.2006-0.06440.05070.03460.04170.0180.04390.09530.06640.101123.6654-0.66497.8518
21.1812-0.1763-0.17811.00860.01311.2794-0.0393-0.1525-0.02330.0565-0.0505-0.20640.10880.1460.08990.0399-0.0109-0.040.08210.04760.103628.4858-21.600239.6276
30.9676-0.2309-0.07961.0133-0.34281.26080.0003-0.08110.03150.05220.0220.182-0.0006-0.1873-0.02220.0111-0.02250.01470.0987-0.03350.0598-6.172-5.962134.3962
40.77370.11250.48871.61250.02041.83550.09530.0707-0.1487-0.2234-0.06660.10270.4668-0.1823-0.02860.1782-0.039-0.03870.0864-0.04770.06334.1047-33.64039.7408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Q1 - 336
2X-RAY DIFFRACTION2O1 - 336
3X-RAY DIFFRACTION3P1 - 336
4X-RAY DIFFRACTION4R1 - 336

+
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