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- PDB-3hq4: Crystal Structure of C151S mutant of Glyceraldehyde-3-phosphate d... -

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Basic information

Entry
Database: PDB / ID: 3hq4
TitleCrystal Structure of C151S mutant of Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) complexed with NAD from Staphylococcus aureus MRSA252 at 2.2 angstrom resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1
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, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / 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, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / 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 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMukherjee, S. / Dutta, D. / Saha, B. / Das, A.K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism.
Authors: Mukherjee, S. / Dutta, D. / Saha, B. / Das, A.K.
History
DepositionJun 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Glyceraldehyde-3-phosphate dehydrogenase 1
O: Glyceraldehyde-3-phosphate dehydrogenase 1
P: Glyceraldehyde-3-phosphate dehydrogenase 1
Q: Glyceraldehyde-3-phosphate dehydrogenase 1
R: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
O: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
P: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Q: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,8728
Polymers145,2194
Non-polymers2,6544
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20260 Å2
ΔGint-86 kcal/mol
Surface area44890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.671, 105.920, 91.374
Angle α, β, γ (deg.)90.000, 108.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36304.699 Da / Num. of mol.: 4 / Mutation: C151S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MRSA252 / Gene: gap, gap1, 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


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


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.18 Å3/Da / Density % sol: 43.48 % / Mosaicity: 1.246 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28% PEG 4000, 0.1M Tris, pH8.5, 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: Apr 10, 2009 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→29.87 Å / Num. obs: 60629 / % possible obs: 96.1 % / Redundancy: 3.53 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.05 / Χ2: 0.98 / Net I/σ(I): 14 / Scaling rejects: 1619
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 4.4 / Num. measured all: 19042 / Num. unique all: 5774 / Χ2: 1.18 / % possible all: 91.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.62 Å29.87 Å
Translation2.62 Å29.87 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.8Ldata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H48

3h48
PDB Unreleased entry


Resolution: 2.2→29.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.84 / SU B: 13.339 / SU ML: 0.154 / SU R Cruickshank DPI: 0.356 / SU Rfree: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.356 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3076 5.1 %RANDOM
Rwork0.184 ---
obs0.187 60613 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.68 Å2 / Biso mean: 31.848 Å2 / Biso min: 4.42 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10124 0 176 392 10692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.019
X-RAY DIFFRACTIONr_angle_refined_deg1.857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 225 -
Rwork0.263 4030 -
all-4255 -
obs--91.72 %
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)
10.42510.1183-0.0530.71720.01240.73990.00920.02510.0877-0.0548-0.0167-0.0338-0.04910.04210.00750.0125-0.0058-0.00160.01180.01520.046123.7652-0.75558.1131
20.6844-0.0778-0.08520.5157-0.12280.74170.0361-0.03220.09430.02940.00030.1271-0.0975-0.0736-0.03640.0389-0.0110.00690.0316-0.01590.0777-6.4995-5.954934.9047
30.5869-0.0039-0.19220.80930.25221.3262-0.0009-0.1531-0.04770.0915-0.0386-0.14610.17560.17730.03950.0554-0.0065-0.02780.07290.03830.07728.0897-21.428440.1916
40.55970.23270.05650.71370.12571.6522-0.04980.0796-0.1517-0.10670.01520.00750.3476-0.13990.03460.1315-0.05080.00360.035-0.03660.09023.6173-33.50049.8612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1R1 - 334
2X-RAY DIFFRACTION2O1 - 334
3X-RAY DIFFRACTION3P1 - 334
4X-RAY DIFFRACTION4Q1 - 334

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