[English] 日本語
Yorodumi
- PDB-3b20: Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b20
TitleCrystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with NADfrom Synechococcus elongatus"
ComponentsGlyceraldehyde 3-phosphate dehydrogenase (NADP+)
KeywordsOXIDOREDUCTASE / alpha/beta fold
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / metal ion binding
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 / Dihydrodipicolinate Reductase; domain 2 ...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 / 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 / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsMatsumura, H. / Kai, A. / Maeda, T. / Inoue, T.
CitationJournal: Structure / Year: 2011
Title: Structure Basis for the Regulation of Glyceraldehyde-3-Phosphate Dehydrogenase Activity via the Intrinsically Disordered Protein CP12.
Authors: Matsumura, H. / Kai, A. / Maeda, T. / Tamoi, M. / Satoh, A. / Tamura, H. / Hirose, M. / Ogawa, T. / Kizu, N. / Wadano, A. / Inoue, T. / Shigeoka, S.
History
DepositionJul 17, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Structure summary
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
B: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
O: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
P: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
Q: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
R: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,32624
Polymers222,1926
Non-polymers5,13318
Water6,918384
1
A: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
B: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
hetero molecules

A: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
B: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,55016
Polymers148,1284
Non-polymers3,42212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area21640 Å2
ΔGint-275 kcal/mol
Surface area44740 Å2
MethodPISA
2
O: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
P: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
Q: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
R: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,55016
Polymers148,1284
Non-polymers3,42212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21700 Å2
ΔGint-274 kcal/mol
Surface area44720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.589, 79.847, 206.794
Angle α, β, γ (deg.)90.00, 101.65, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Glyceraldehyde 3-phosphate dehydrogenase (NADP+)


Mass: 37032.070 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: gap2, Synpcc7942_1742 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9R6W2, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% saturated ammonium sulfate, 0.1M citrate buffer pH 5.2, 0.2M potassium sodium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.398→50 Å / Num. all: 94315 / Num. obs: 94315 / % possible obs: 99.8 % / Observed criterion σ(I): 31.7
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.367 / % possible all: 100

-
Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.398→45.433 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 30.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 4728 5.02 %RANDOM
Rwork0.2133 ---
obs0.216 94248 99.72 %-
all-94248 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.333 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.1701 Å20 Å2-13.8657 Å2
2--4.1076 Å2-0 Å2
3---4.0625 Å2
Refinement stepCycle: LAST / Resolution: 2.398→45.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15568 0 324 384 16276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916169
X-RAY DIFFRACTIONf_angle_d1.21622047
X-RAY DIFFRACTIONf_dihedral_angle_d20.1455849
X-RAY DIFFRACTIONf_chiral_restr0.0822622
X-RAY DIFFRACTIONf_plane_restr0.0042771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3983-2.42560.3581380.29296998
2.4256-2.45410.34261580.28392919100
2.4541-2.4840.35371530.28622978100
2.484-2.51550.39591690.28722981100
2.5155-2.54860.37011570.28822938100
2.5486-2.58350.33911490.28333049100
2.5835-2.62040.33991660.25712893100
2.6204-2.65950.31781600.25443014100
2.6595-2.7010.30371470.25252938100
2.701-2.74530.30631760.24962990100
2.7453-2.79260.30831590.24172944100
2.7926-2.84340.30381580.25113023100
2.8434-2.89810.37961570.2622912100
2.8981-2.95720.37011470.26173036100
2.9572-3.02150.30951540.24942948100
3.0215-3.09180.33411630.24572981100
3.0918-3.16910.32121710.24632982100
3.1691-3.25480.28981660.23332982100
3.2548-3.35050.27641810.22272936100
3.3505-3.45860.26661580.20383001100
3.4586-3.58220.25321540.20312973100
3.5822-3.72550.25681620.19343002100
3.7255-3.8950.25221320.19722995100
3.895-4.10020.27741640.1898297299
4.1002-4.35690.2131440.1764297199
4.3569-4.6930.20541640.1699303499
4.693-5.16470.22061480.1767296599
5.1647-5.91070.26171540.21663037100
5.9107-7.44150.23951540.20283055100
7.4415-45.44130.20121650.1804310299

+
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