[English] 日本語
Yorodumi
- PDB-7xzg: High resolution crystal Structure of Glyceraldehyde-3-Phosphate D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xzg
TitleHigh resolution crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Candida albicans complexed with NAD+
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Glycolysis / Homotetramer
Function / homology
Function and homology information


symbiont-mediated perturbation of host immune response / yeast-form cell wall / fungal biofilm matrix / hyphal cell wall / symbiont cell surface / adhesion of symbiont to host / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / fungal-type cell wall / biological process involved in interaction with host / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity ...symbiont-mediated perturbation of host immune response / yeast-form cell wall / fungal biofilm matrix / hyphal cell wall / symbiont cell surface / adhesion of symbiont to host / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / fungal-type cell wall / biological process involved in interaction with host / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / extracellular matrix binding / fibronectin binding / laminin binding / cell-matrix adhesion / glycolytic process / glucose metabolic process / NAD binding / NADP binding / extracellular vesicle / cell surface / plasma membrane / cytoplasm / cytosol
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 speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.879 Å
AuthorsCao, H. / Meng, J. / Ren, Y. / Wan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177036 China
CitationJournal: To Be Published
Title: High resolution crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Candida albicans complexed with NAD+
Authors: Cao, H. / Meng, J. / Ren, Y. / Wan, J.
History
DepositionJun 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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)146,84817
Polymers143,6354
Non-polymers3,21213
Water19,5641086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19220 Å2
ΔGint-124 kcal/mol
Surface area43910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.643, 127.421, 87.855
Angle α, β, γ (deg.)90.000, 102.120, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase


Mass: 35908.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Gene: TDH3, orf19.6814, CAALFM_C306870WA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5ADM7, 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 32.5% v/v mPEG 550, 0.1M Trisodium citrate, pH 5.4, 1.0M sodium chloride, 20mM Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.879→35.612 Å / Num. obs: 124242 / % possible obs: 99.3 % / Redundancy: 4.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.1652 / Net I/σ(I): 10.24
Reflection shellResolution: 1.879→1.947 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 12367 / CC1/2: 0.829 / % possible all: 99.28

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PYM

3pym


Resolution: 1.879→35.612 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1964 2000 1.61 %
Rwork0.1687 122199 -
obs0.1691 124199 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.08 Å2 / Biso mean: 24.4586 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: final / Resolution: 1.879→35.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10072 0 212 1086 11370
Biso mean--22.14 32.96 -
Num. residues----1336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8794-1.92640.28421420.2358866499
1.9264-1.97850.24311430.20338741100
1.9785-2.03670.22951430.1929869499
2.0367-2.10240.22531420.1894868899
2.1024-2.17750.23031430.17498757100
2.1775-2.26470.20731430.17488746100
2.2647-2.36780.2191430.16918759100
2.3678-2.49260.251430.1799872199
2.4926-2.64870.21781430.17118755100
2.6487-2.85310.20551430.17078744100
2.8531-3.14010.18841440.17168781100
3.1401-3.59410.18331420.1598871799
3.5941-4.52670.17071430.1427868499
4.5267-35.6120.14591430.16874898

+
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