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- PDB-3ksd: Crystal Structure of C151S+H178N mutant of Glyceraldehyde-3-phosp... -

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Basic information

Entry
Database: PDB / ID: 3ksd
TitleCrystal Structure of C151S+H178N mutant of Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from Staphylococcus aureus MRSA252 complexed with NAD at 2.2 angstrom resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1
KeywordsOXIDOREDUCTASE / glycolysis / NAD
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
DepositionNov 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 11, 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
Q: Glyceraldehyde-3-phosphate dehydrogenase 1
R: Glyceraldehyde-3-phosphate dehydrogenase 1
O: Glyceraldehyde-3-phosphate dehydrogenase 1
P: Glyceraldehyde-3-phosphate dehydrogenase 1
R: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
O: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
P: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7768
Polymers145,1234
Non-polymers2,6544
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint-45 kcal/mol
Surface area44360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.654, 94.315, 87.981
Angle α, β, γ (deg.)90.000, 106.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Q
21R
31O
41P

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112Q2 - 334
2112R2 - 334
3112O2 - 334
4112P2 - 334

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Components

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


Mass: 36280.656 Da / Num. of mol.: 4 / Mutation: C151S, H178N
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.: 316 / 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: 1.83 Å3/Da / Density % sol: 32.84 % / Mosaicity: 0.746 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH8.5, 30% PEG 4000, 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: Nov 6, 2009 / Details: Varimax mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→84.56 Å / Num. obs: 47907 / % possible obs: 90.1 % / Redundancy: 2.41 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.061 / Χ2: 0.96 / Net I/σ(I): 9.6 / Scaling rejects: 874
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.9 / Num. measured all: 10947 / Num. unique all: 4906 / Χ2: 1.19 / % possible all: 93.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.58 Å25.84 Å
Translation2.58 Å25.84 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→25.84 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.197 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.831 / SU B: 15.875 / SU ML: 0.195 / SU R Cruickshank DPI: 0.889 / SU Rfree: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.889 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2438 5.1 %RANDOM
Rwork0.205 ---
obs0.208 47902 90.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.63 Å2 / Biso mean: 38.235 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å2-1.14 Å2
2---0.68 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10079 0 175 316 10570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210430
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.97914165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06751335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92225.522460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.136151768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7151555
X-RAY DIFFRACTIONr_chiral_restr0.1080.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027763
X-RAY DIFFRACTIONr_mcbond_it0.7371.56594
X-RAY DIFFRACTIONr_mcangle_it1.436210603
X-RAY DIFFRACTIONr_scbond_it2.74933836
X-RAY DIFFRACTIONr_scangle_it4.6924.53559
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
Q1318TIGHT POSITIONAL0.110.05
R1318TIGHT POSITIONAL0.080.05
O1318TIGHT POSITIONAL0.090.05
P1318TIGHT POSITIONAL0.070.05
Q1166MEDIUM POSITIONAL0.10.5
R1166MEDIUM POSITIONAL0.080.5
O1166MEDIUM POSITIONAL0.090.5
P1166MEDIUM POSITIONAL0.070.5
Q1318TIGHT THERMAL0.210.5
R1318TIGHT THERMAL0.190.5
O1318TIGHT THERMAL0.190.5
P1318TIGHT THERMAL0.170.5
Q1166MEDIUM THERMAL0.222
R1166MEDIUM THERMAL0.212
O1166MEDIUM THERMAL0.22
P1166MEDIUM THERMAL0.22
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 176 -
Rwork0.266 3498 -
all-3674 -
obs--93.27 %
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)
10.39330.12820.0811.1231-0.28330.91220.0450.0514-0.1085-0.0228-0.00320.00110.133-0.0558-0.04190.0388-0.0123-0.00720.0206-0.02830.0774.27560.90119.1214
20.9376-0.0111-0.00661.05550.3240.89570.00970.13340.13810.00520.0409-0.095-0.06530.0708-0.05060.0167-0.00280.01830.02770.02370.079622.469634.48717.573
32.045-0.3285-0.96070.6133-0.35461.45180.127-0.13620.19770.08720.01520.0363-0.1568-0.0849-0.14220.1062-0.01130.03720.0548-0.02540.0589-7.077627.383733.9094
42.1256-0.09451.1420.8960.16512.7916-0.0989-0.341-0.17120.14940.0305-0.1862-0.20130.32740.06840.1049-0.0432-0.05390.18120.07530.128.695714.094439.0913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Q2 - 334
2X-RAY DIFFRACTION2R1 - 333
3X-RAY DIFFRACTION3O2 - 333
4X-RAY DIFFRACTION4P2 - 335

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