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- PDB-3gnq: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, ty... -

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Basic information

Entry
Database: PDB / ID: 3gnq
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei
ComponentsGlyceraldehyde-3-phosphate dehydrogenase, type IGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / deCODE biostructures / SSGCID / UWPPG / SBRI / NIAID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1obf / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei
Authors: Edwards, T.E.
History
DepositionMar 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase, type I
B: Glyceraldehyde-3-phosphate dehydrogenase, type I
C: Glyceraldehyde-3-phosphate dehydrogenase, type I
D: Glyceraldehyde-3-phosphate dehydrogenase, type I
E: Glyceraldehyde-3-phosphate dehydrogenase, type I
F: Glyceraldehyde-3-phosphate dehydrogenase, type I
G: Glyceraldehyde-3-phosphate dehydrogenase, type I
H: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,19715
Polymers297,5538
Non-polymers4,6447
Water9,692538
1
A: Glyceraldehyde-3-phosphate dehydrogenase, type I
B: Glyceraldehyde-3-phosphate dehydrogenase, type I
C: Glyceraldehyde-3-phosphate dehydrogenase, type I
D: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,7677
Polymers148,7764
Non-polymers1,9903
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18400 Å2
ΔGint-121 kcal/mol
Surface area42940 Å2
MethodPISA
2
A: Glyceraldehyde-3-phosphate dehydrogenase, type I
B: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0523
Polymers74,3882
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-30 kcal/mol
Surface area26130 Å2
MethodPISA
3
A: Glyceraldehyde-3-phosphate dehydrogenase, type I
C: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0523
Polymers74,3882
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-26 kcal/mol
Surface area25360 Å2
MethodPISA
4
B: Glyceraldehyde-3-phosphate dehydrogenase, type I
D: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7154
Polymers74,3882
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-33 kcal/mol
Surface area24940 Å2
MethodPISA
5
C: Glyceraldehyde-3-phosphate dehydrogenase, type I
D: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7154
Polymers74,3882
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-41 kcal/mol
Surface area26020 Å2
MethodPISA
6
E: Glyceraldehyde-3-phosphate dehydrogenase, type I
F: Glyceraldehyde-3-phosphate dehydrogenase, type I
G: Glyceraldehyde-3-phosphate dehydrogenase, type I
H: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,4308
Polymers148,7764
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19720 Å2
ΔGint-134 kcal/mol
Surface area42670 Å2
MethodPISA
7
E: Glyceraldehyde-3-phosphate dehydrogenase, type I
F: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7154
Polymers74,3882
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-39 kcal/mol
Surface area25930 Å2
MethodPISA
8
E: Glyceraldehyde-3-phosphate dehydrogenase, type I
G: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7154
Polymers74,3882
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-32 kcal/mol
Surface area25180 Å2
MethodPISA
9
F: Glyceraldehyde-3-phosphate dehydrogenase, type I
H: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7154
Polymers74,3882
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-32 kcal/mol
Surface area25010 Å2
MethodPISA
10
G: Glyceraldehyde-3-phosphate dehydrogenase, type I
H: Glyceraldehyde-3-phosphate dehydrogenase, type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7154
Polymers74,3882
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-43 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.932, 173.797, 93.501
Angle α, β, γ (deg.)90.000, 93.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 37194.086 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: expressed with a non-cleavable N-terminal hexahis tag
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: gap, BURPS1710b_3466 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JNL6, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Molecular Dimensions PACT Premier screen condition E1, 25% PEG 3350, 0.2 M NaF with 25% glycerol as cryo-protectant, 33.4 mg/mL protein, crystal ID 201195e1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97934 Å
DetectorDate: Dec 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 112883 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.096 / Χ2: 0.958 / Net I/σ(I): 13.554
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.74 / Num. unique all: 11064 / Χ2: 0.829 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: 1obf / Resolution: 2.4→48.84 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.813 / SU B: 9.108 / SU ML: 0.212 / SU R Cruickshank DPI: 0.475 / SU Rfree: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.475 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.263 5649 5 %RANDOM
Rwork0.204 ---
obs0.207 112829 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.5 Å2 / Biso mean: 36.647 Å2 / Biso min: 7.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20.34 Å2
2---0.55 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20161 0 308 538 21007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02220849
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213409
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.96928415
X-RAY DIFFRACTIONr_angle_other_deg0.887332909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29252671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36824.562857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.013153335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.28715109
X-RAY DIFFRACTIONr_chiral_restr0.070.23351
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0223285
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023939
X-RAY DIFFRACTIONr_mcbond_it0.5871.513251
X-RAY DIFFRACTIONr_mcbond_other0.0861.55486
X-RAY DIFFRACTIONr_mcangle_it1.099221290
X-RAY DIFFRACTIONr_scbond_it1.42137598
X-RAY DIFFRACTIONr_scangle_it2.384.57125
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 358 -
Rwork0.316 7731 -
all-8089 -
obs--96.98 %

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