[English] 日本語
Yorodumi
- PDB-8hrq: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hrq
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 (L36S/T37K) in complex with NAD
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsSTRUCTURAL PROTEIN / Dehydrogenase
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, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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 / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSon, H.F. / Kim, K.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Structure-Guided Protein Engineering of Glyceraldehyde-3-phosphate Dehydrogenase from Corynebacterium glutamicum for Dual NAD/NADP Cofactor Specificity.
Authors: Son, H.F. / Yu, H. / Hong, J. / Lee, D. / Kim, I.K. / Kim, K.J.
History
DepositionDec 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,41012
Polymers74,3192
Non-polymers2,09110
Water4,342241
1
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,82024
Polymers148,6384
Non-polymers4,18220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area22130 Å2
ΔGint-280 kcal/mol
Surface area43890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.710, 117.891, 77.128
Angle α, β, γ (deg.)90.00, 116.92, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 37159.566 Da / Num. of mol.: 2 / Mutation: L36S,T37K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: gap, Cgl1588, cg1791 / Production host: Escherichia coli (E. coli)
References: UniProt: Q01651, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

-
Non-polymers , 6 types, 251 molecules

#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Cesium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 39134 / % possible obs: 92.1 % / Redundancy: 1.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.991 / Rsym value: 0.055 / Χ2: 0.049 / Net I/σ(I): 18.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.09-2.141.60.2436061.688187.1
2.14-2.181.60.22736271.697187
2.18-2.221.60.20436101.878188.6
2.22-2.261.60.18236462.043187.9
2.26-2.311.60.16436962.044188.9
2.31-2.371.70.15437462.1190.1
2.37-2.421.60.13936882.342189.8
2.42-2.491.70.12437212.454189.5
2.49-2.561.70.11737342.682190.2
2.56-2.651.70.10837192.762189.8
2.65-2.741.70.0937922.984191.8
2.74-2.851.70.0838253.391192.4
2.85-2.981.70.07638734.038193.8
2.98-3.141.80.06739384.314194.8
3.14-3.331.80.05839564.264196.1
3.33-3.591.80.05240224.72197.2
3.59-3.951.90.04840875.103198.3
3.95-4.521.90.04240595.443198.2
4.52-5.71.90.03841185.37198.8
5.7-501.80.03737954.927191.9

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0403refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HRO

8hro


Resolution: 2.09→26.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.516 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 2077 5 %RANDOM
Rwork0.17692 ---
obs0.18023 39134 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.838 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å2-0.9 Å2
2--0.85 Å20 Å2
3---1.52 Å2
Refinement stepCycle: 1 / Resolution: 2.09→26.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5093 0 120 241 5454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125300
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164954
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.6467211
X-RAY DIFFRACTIONr_angle_other_deg0.5281.57511395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8845668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.659532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94410849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021160
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0493.9862678
X-RAY DIFFRACTIONr_mcbond_other4.0373.9852678
X-RAY DIFFRACTIONr_mcangle_it5.237.1433344
X-RAY DIFFRACTIONr_mcangle_other5.2487.1453345
X-RAY DIFFRACTIONr_scbond_it5.2384.5592622
X-RAY DIFFRACTIONr_scbond_other5.1684.5472615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4968.1073856
X-RAY DIFFRACTIONr_long_range_B_refined8.84544.045711
X-RAY DIFFRACTIONr_long_range_B_other8.84444.055712
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.091→2.145 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 157 -
Rwork0.244 2616 -
obs--88.74 %

+
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