[English] 日本語
Yorodumi
- PDB-6x2e: Crystal Structure of Chlamydia trachomatis mixed (apo/holo) Glyce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x2e
TitleCrystal Structure of Chlamydia trachomatis mixed (apo/holo) Glyceraldehyde 3-phosphate dehydrogenase
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GAPDH / NAD / Glycolysis / Chlamydia
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchormann, N. / Chattopadhyay, D.
CitationJournal: Protein Sci. / Year: 2020
Title: Chlamydia trachomatis glyceraldehyde 3-phosphate dehydrogenase: Enzyme kinetics, high-resolution crystal structure, and plasminogen binding.
Authors: Schormann, N. / Campos, J. / Motamed, R. / Hayden, K.L. / Gould, J.R. / Green, T.J. / Senkovich, O. / Banerjee, S. / Ulett, G.C. / Chattopadhyay, D.
History
DepositionMay 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 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_ncs_dom_lim
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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6657
Polymers145,6744
Non-polymers1,9903
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18200 Å2
ΔGint-127 kcal/mol
Surface area44880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.222, 104.240, 85.990
Angle α, β, γ (deg.)90.000, 97.480, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 51 or resid 53...
21(chain B and (resid 1 through 51 or resid 53...
31(chain C and (resid 1 through 51 or resid 53...
41(chain D and (resid 1 through 51 or resid 53...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLY(chain A and (resid 1 through 51 or resid 53...AA1 - 511 - 51
12PHEPHEGLYGLY(chain A and (resid 1 through 51 or resid 53...AA53 - 6753 - 67
13ARGARGGLNGLN(chain A and (resid 1 through 51 or resid 53...AA69 - 8069 - 80
14LYSLYSLYSLYS(chain A and (resid 1 through 51 or resid 53...AA8181
15METMETSERSER(chain A and (resid 1 through 51 or resid 53...AA1 - 3331 - 333
16METMETSERSER(chain A and (resid 1 through 51 or resid 53...AA1 - 3331 - 333
17METMETSERSER(chain A and (resid 1 through 51 or resid 53...AA1 - 3331 - 333
18METMETSERSER(chain A and (resid 1 through 51 or resid 53...AA1 - 3331 - 333
21METMETGLYGLY(chain B and (resid 1 through 51 or resid 53...BB1 - 511 - 51
22PHEPHEGLYGLY(chain B and (resid 1 through 51 or resid 53...BB53 - 6753 - 67
23METMETSERSER(chain B and (resid 1 through 51 or resid 53...BB1 - 3331 - 333
24ASPASPALAALA(chain B and (resid 1 through 51 or resid 53...BB78 - 20778 - 207
25THRTHRLEULEU(chain B and (resid 1 through 51 or resid 53...BB209 - 217209 - 217
26LEULEUSERSER(chain B and (resid 1 through 51 or resid 53...BB219 - 248219 - 248
27ALAALAGLUGLU(chain B and (resid 1 through 51 or resid 53...BB250 - 276250 - 276
28ALAALAASNASN(chain B and (resid 1 through 51 or resid 53...BB278 - 332278 - 332
31METMETGLYGLY(chain C and (resid 1 through 51 or resid 53...CC1 - 511 - 51
32PHEPHEGLYGLY(chain C and (resid 1 through 51 or resid 53...CC53 - 6753 - 67
33METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
34METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
35LYSLYSLYSLYS(chain C and (resid 1 through 51 or resid 53...CC8181
36METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
37METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
38METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
39METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
310METMETSERSER(chain C and (resid 1 through 51 or resid 53...CC1 - 3331 - 333
41METMETGLYGLY(chain D and (resid 1 through 51 or resid 53...DD1 - 511 - 51
42PHEPHEGLUGLU(chain D and (resid 1 through 51 or resid 53...DD53 - 7653 - 76
43ASPASPGLNGLN(chain D and (resid 1 through 51 or resid 53...DD78 - 8078 - 80
44METMETNADNAD(chain D and (resid 1 through 51 or resid 53...DD - G1 - 4001
45METMETNADNAD(chain D and (resid 1 through 51 or resid 53...DD - G1 - 4001
46METMETNADNAD(chain D and (resid 1 through 51 or resid 53...DD - G1 - 4001
47METMETNADNAD(chain D and (resid 1 through 51 or resid 53...DD - G1 - 4001
48METMETNADNAD(chain D and (resid 1 through 51 or resid 53...DD - G1 - 4001

-
Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / GAPDH / NAD-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 36418.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (strain D/UW-3/Cx) (bacteria)
Strain: D/UW-3/Cx / Gene: gap, gapA, CT_505 / Plasmid: pJ411 / Production host: Escherichia coli (E. coli)
References: UniProt: P0CE13, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 2000 MME, 0.1 M Hepes, pH 7.5; prior to crystallization the protein (at 30 mg/ml) was incubated with 1 mM NAD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→85.26 Å / Num. obs: 104308 / % possible obs: 97.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 17.1 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.059 / Rrim(I) all: 0.104 / Χ2: 1.03 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.80.6691.652730.640.470.822199.1
9.86-85.263.10.0316450.9980.020.03793.6

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18rc2_3794refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WYC

6wyc


Resolution: 1.8→85.26 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 5133 4.92 %
Rwork0.1749 99130 -
obs0.1771 104263 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.84 Å2 / Biso mean: 24.091 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 1.8→85.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10142 0 132 766 11040
Biso mean--22.8 30.34 -
Num. residues----1328
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3804X-RAY DIFFRACTION6.325TORSIONAL
12B3804X-RAY DIFFRACTION6.325TORSIONAL
13C3804X-RAY DIFFRACTION6.325TORSIONAL
14D3804X-RAY DIFFRACTION6.325TORSIONAL
LS refinement shellResolution: 1.8→1.82 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3312 144 -
Rwork0.287 3373 -
obs--99 %

+
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