[English] 日本語
Yorodumi
- PDB-2pkq: Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-pho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pkq
TitleCrystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP
Components
  • Glyceraldehyde-3-phosphate dehydrogenase A
  • Glyceraldehyde-3-phosphate dehydrogenase B
KeywordsOXIDOREDUCTASE / Rossmann fold / protein-NADP complex
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / apoplast / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / chloroplast / glucose metabolic process / NAD binding / NADP 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
Chem-NDP / Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic / Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFermani, S. / Falini, G. / Ripamonti, A.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular mechanism of thioredoxin regulation in photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase.
Authors: Fermani, S. / Sparla, F. / Falini, G. / Martelli, P.L. / Casadio, R. / Pupillo, P. / Ripamonti, A. / Trost, P.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Coenzyme Site-directed Mutants of Photosynthetic A4-GAPDH Show Selectively Reduced NADPH-dependent Catalysis, Similar to Regulatory AB-GAPDH Inhibited by Oxidized Thioredoxin
Authors: Sparla, F. / Fermani, S. / Falini, G. / Zaffagnini, M. / Ripamonti, A. / Sabatino, P. / Pupillo, P. / Trost, P.
#2: Journal: Biochemistry / Year: 2003
Title: Dual Coenzyme Specificity of Photosynthetic Glyceraldehyde-3-phosphate Dehydrogenase Interpreted by the Crystal Structure of A4 Isoform Complexed with NAD
Authors: Falini, G. / Fermani, S. / Ripamonti, A. / Sabatino, P. / Sparla, F. / Pupillo, P. / Trost, P.
#3: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the non-regulatory A4 isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP.
Authors: Fermani, S. / Ripamonti, A. / Sabatino, P. / Zanotti, G. / Scagliarini, S. / Sparla, F. / Trost, P. / Pupillo, P.
History
DepositionApr 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 30, 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_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
Remark 999SEQUENCE Database reference was not available at the time of processing.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase B
P: Glyceraldehyde-3-phosphate dehydrogenase A
Q: Glyceraldehyde-3-phosphate dehydrogenase B
R: Glyceraldehyde-3-phosphate dehydrogenase A
S: Glyceraldehyde-3-phosphate dehydrogenase A
T: Glyceraldehyde-3-phosphate dehydrogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,89527
Polymers226,9816
Non-polymers5,91321
Water00
1
O: Glyceraldehyde-3-phosphate dehydrogenase B
P: Glyceraldehyde-3-phosphate dehydrogenase A
Q: Glyceraldehyde-3-phosphate dehydrogenase B
R: Glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,16717
Polymers151,3214
Non-polymers3,84613
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20860 Å2
ΔGint-259 kcal/mol
Surface area46110 Å2
MethodPISA, PQS
2
S: Glyceraldehyde-3-phosphate dehydrogenase A
T: Glyceraldehyde-3-phosphate dehydrogenase B
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)155,45520
Polymers151,3214
Non-polymers4,13416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)186.147, 215.687, 81.469
Angle α, β, γ (deg.)90.00, 102.52, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase B / NADP-dependent glyceraldehydephosphate dehydrogenase subunit B


Mass: 39403.957 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: chloroplasts (leaves) / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P12860, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Protein Glyceraldehyde-3-phosphate dehydrogenase A / NADP-dependent glyceraldehydephosphate dehydrogenase subunit A


Mass: 36256.391 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: chloroplasts (leaves) / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P19866, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0-2.5 M ammonium sulfate, 0.1 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-210.933
SYNCHROTRONESRF ID14-220.933
SYNCHROTRONELETTRA 5.2R31
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDMay 3, 2003mirrors
ADSC QUANTUM 42CCDMay 3, 2003mirrors
MAR CCD 165 mm3CCDOct 18, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond (111), Ge(220)SINGLE WAVELENGTHMx-ray1
2Diamond (111), Ge(220)SINGLE WAVELENGTHMx-ray1
3Silicon (111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
211
ReflectionResolution: 3.6→91 Å / Num. all: 36736 / Num. obs: 36699 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.359 / Rsym value: 0.359 / Net I/σ(I): 4.5
Reflection shellResolution: 3.6→3.73 Å / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3647 / Rsym value: 0.694 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
CNS1refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RM4

1rm4


Resolution: 3.6→90.86 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 5783074.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1802 5 %RANDOM
Rwork0.261 ---
obs0.261 36271 99.9 %-
all-36736 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.336 Å2 / ksol: 0.344771 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.13 Å20 Å2-10.38 Å2
2--7 Å20 Å2
3----13.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.48 Å
Luzzati d res low-8 Å
Luzzati sigma a0.65 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3.6→90.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15477 0 363 0 15840
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d5.21
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.252
X-RAY DIFFRACTIONc_scangle_it2.132.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.6→3.83 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 286 4.8 %
Rwork0.324 5675 -
obs-5961 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ndp.paramndp.top
X-RAY DIFFRACTION3ion.paramion.top

+
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://pdbjlvh1.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