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- PDB-3vaz: Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group -

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Basic information

Entry
Database: PDB / ID: 3vaz
TitleCrystal structure of Staphylococcal GAPDH1 in a hexagonal space group
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1Glyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold
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 / 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
(2R)-2,3-DIHYDROXYPROPANOIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.19 Å
AuthorsRoychowdhury, A. / Mukherjee, S. / Dutta, D. / Das, A.K.
CitationJournal: To be Published
Title: Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group
Authors: Roychowdhury, A. / Mukherjee, S. / Dutta, D. / Das, A.K.
History
DepositionDec 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Nov 8, 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 / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

Deposited unit
P: Glyceraldehyde-3-phosphate dehydrogenase 1
R: Glyceraldehyde-3-phosphate dehydrogenase 1
O: Glyceraldehyde-3-phosphate dehydrogenase 1
Q: Glyceraldehyde-3-phosphate dehydrogenase 1
B: Glyceraldehyde-3-phosphate dehydrogenase 1
A: Glyceraldehyde-3-phosphate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,52520
Polymers223,7636
Non-polymers4,76314
Water7,458414
1
P: Glyceraldehyde-3-phosphate dehydrogenase 1
O: Glyceraldehyde-3-phosphate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4009
Polymers74,5882
Non-polymers1,8137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-40 kcal/mol
Surface area26020 Å2
MethodPISA
2
R: Glyceraldehyde-3-phosphate dehydrogenase 1
Q: Glyceraldehyde-3-phosphate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9144
Polymers74,5882
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-34 kcal/mol
Surface area25920 Å2
MethodPISA
3
B: Glyceraldehyde-3-phosphate dehydrogenase 1
A: Glyceraldehyde-3-phosphate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2107
Polymers74,5882
Non-polymers1,6235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-36 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.389, 155.389, 317.849
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-403-

DGY

21A-403-

DGY

31O-554-

HOH

41Q-550-

HOH

51B-511-

HOH

61B-571-

HOH

71A-506-

HOH

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase 1 / Glyceraldehyde 3-phosphate dehydrogenase / GAPDH 1


Mass: 37293.777 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: gap, gapA, gapA1, SAR0828 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q6GIL8, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-DGY / (2R)-2,3-DIHYDROXYPROPANOIC ACID


Mass: 106.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 50.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 400, 0.2M CaCl2, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 25, 2011
RadiationMonochromator: Varimax optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.19→29.742 Å / Num. obs: 38297 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.228 Å2 / Rmerge(I) obs: 0.315 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.19-3.390.3040.7335.35127071601359520.75199
3.39-3.620.2230.5547.18124485570257010.567100
3.62-3.90.1620.4029.65115187528852880.411100
3.9-4.270.120.28613.14106735490449040.293100
4.27-4.760.0790.19918.1696473446844650.20499.9
4.76-5.470.090.21316.886223401640150.218100
5.47-6.640.1050.23515.1273215344334400.24199.9
6.64-9.170.0660.13324.5457157276627610.13799.8
9.170.0350.0740.5733699185017710.07295.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.19 Å29.74 Å
Translation3.19 Å29.74 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K73

3k73


Resolution: 3.19→29.74 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.811 / WRfactor Rfree: 0.2326 / WRfactor Rwork: 0.1724 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8497 / SU B: 48.435 / SU ML: 0.39 / SU R Cruickshank DPI: 0.3487 / SU Rfree: 0.5924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.592 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ANISOU CARDS HAVE BEEN REMOVED AS PER AUTHOR REQUEST.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1915 5 %RANDOM
Rwork0.2022 ---
obs0.2059 38297 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.82 Å2 / Biso mean: 19.828 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å2-0.88 Å20 Å2
2---1.77 Å20 Å2
3---2.65 Å2
Refinement stepCycle: LAST / Resolution: 3.19→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14999 0 308 414 15721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215537
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.9821137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.01852001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93425.378662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.637152534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3421578
X-RAY DIFFRACTIONr_chiral_restr0.0640.22510
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111572
X-RAY DIFFRACTIONr_mcbond_it0.1631.59905
X-RAY DIFFRACTIONr_mcangle_it0.291215889
X-RAY DIFFRACTIONr_scbond_it0.05735632
X-RAY DIFFRACTIONr_scangle_it0.1224.55248
LS refinement shellResolution: 3.194→3.276 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 135 -
Rwork0.244 2563 -
all-2698 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4991-0.2057-0.11511.33760.19580.7109-0.0148-0.0107-0.0523-0.1238-0.0406-0.1476-0.08440.09440.05540.0701-0.01380.0340.09220.00550.0447-21.410514.952225.235
21.4315-0.5818-0.15381.33890.08680.9721-0.1096-0.1859-0.09210.2390.0767-0.0842-0.02640.10270.03290.11440.00020.00430.08290.03050.0332-40.39189.795558.6532
30.24540.0836-0.00621.11240.06470.5468-0.06920.0542-0.1406-0.0376-0.01060.1310.1127-0.02380.07980.1066-0.020.03830.0789-0.0660.1322-43.7504-16.463227.3614
41.1358-0.1182-0.2110.79810.00491.0828-0.01060.146-0.0175-0.1415-0.02310.2537-0.0346-0.13920.03370.04840.0095-0.04440.0964-0.0340.0931-62.406217.232728.0938
50.7508-0.1767-0.07540.94750.34190.661-0.0472-0.11440.12250.07590.0633-0.1293-0.02540.0398-0.01610.0428-0.0056-0.02540.0679-0.01210.0357-20.897174.510131.0632
60.5868-0.3241-0.10570.62470.01930.55990.01150.0535-0.1309-0.1255-0.02770.01440.0166-0.0360.01630.06340.01760.01660.0596-0.01310.0378-29.129650.59492.2045
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1P1 - 336
2X-RAY DIFFRACTION2R2 - 335
3X-RAY DIFFRACTION3O2 - 335
4X-RAY DIFFRACTION4Q2 - 334
5X-RAY DIFFRACTION5B2 - 335
6X-RAY DIFFRACTION6A2 - 335

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