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- PDB-3lc1: Crystal Structure of H178N mutant of Glyceraldehyde-3-phosphate-d... -

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Basic information

Entry
Database: PDB / ID: 3lc1
TitleCrystal Structure of H178N mutant of Glyceraldehyde-3-phosphate-dehydrogenase 1 (GAPDH 1) from Staphylococcus aureus MRSA252 complexed with NAD at 2.0 angstrom resolution.
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1
KeywordsOXIDOREDUCTASE / glycolysis
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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 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
DepositionJan 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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

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
P: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
R: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
O: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Q: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,9339
Polymers145,1874
Non-polymers2,7465
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15750 Å2
ΔGint-54 kcal/mol
Surface area46370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.849, 105.945, 91.473
Angle α, β, γ (deg.)90.000, 108.343, 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: 36296.719 Da / Num. of mol.: 4 / Mutation: H178N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 43.6 % / Mosaicity: 0.974 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1M Tris-HCl, pH 8.2, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: May 5, 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→86.82 Å / Num. obs: 80071 / % possible obs: 95.3 % / Redundancy: 3.73 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1 / Net I/σ(I): 9.9 / Scaling rejects: 2260
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.5 / Num. measured all: 28098 / Num. unique all: 7739 / Χ2: 1.25 / % possible all: 92.4

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Processing

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

3h48
PDB Unreleased entry


Resolution: 2→29.06 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.822 / SU B: 10.98 / SU ML: 0.141 / SU R Cruickshank DPI: 0.233 / SU Rfree: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 4003 5 %RANDOM
Rwork0.197 ---
obs0.199 80066 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.53 Å2 / Biso mean: 32.455 Å2 / Biso min: 10.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å2-0.92 Å2
2---1.89 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10142 0 182 413 10737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210493
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9814249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97551342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56925.455462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.235151783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5471557
X-RAY DIFFRACTIONr_chiral_restr0.0820.21671
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027805
X-RAY DIFFRACTIONr_mcbond_it0.4971.56628
X-RAY DIFFRACTIONr_mcangle_it0.915210659
X-RAY DIFFRACTIONr_scbond_it1.53833865
X-RAY DIFFRACTIONr_scangle_it2.4524.53588
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 251 -
Rwork0.322 5418 -
all-5669 -
obs--92.22 %
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)
10.5032-0.0253-0.12210.666-0.01651.0249-0.01320.1181-0.0245-0.0737-0.04620.16020.0978-0.21940.05930.05190.0054-0.01780.0811-0.03250.0633-7.98840.30753.1276
20.3166-0.027-0.11951.0078-0.10120.8970.013-0.02030.08930.1637-0.01580.0919-0.0497-0.11270.00280.0523-0.00660.02820.0258-0.02230.0476-3.947220.856335.4554
30.46010.1594-0.00680.67330.14170.93030.04090.0490.0537-0.04630.0052-0.1667-0.12490.1301-0.04610.04310.00570.02940.03910.01350.076626.55815.54428.5581
40.5728-0.30560.19791.04040.03871.15330.0627-0.0156-0.120.2035-0.0338-0.07820.27680.1004-0.02880.17390.0221-0.03560.01770.01810.058816.2139-11.885233.818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1P1 - 336
2X-RAY DIFFRACTION2R1 - 336
3X-RAY DIFFRACTION3O2 - 335
4X-RAY DIFFRACTION4Q2 - 335

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