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- PDB-3lvf: Crystal Structure of holo Glyceraldehyde-3-phosphate dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 3lvf
TitleCrystal Structure of holo Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from methicillin resistant Staphylococcus aureus MRSA252 at 1.7 Angstrom resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1
KeywordsOXIDOREDUCTASE / Glycolysis / 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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionFeb 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,5138
Polymers145,8604
Non-polymers2,6544
Water12,088671
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15730 Å2
ΔGint-54 kcal/mol
Surface area46160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.180, 104.874, 91.191
Angle α, β, γ (deg.)90.00, 107.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36464.898 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.13 Å3/Da / Density % sol: 42.23 % / Mosaicity: 1.319 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH8.5, 20% (w/v)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 14, 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: 1.7→30.78 Å / Num. obs: 126584 / % possible obs: 94.5 % / Redundancy: 3.52 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.059 / Χ2: 0.99 / Net I/σ(I): 8.7 / Num. measured all: 448834 / Scaling rejects: 3367
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.7-1.763.360.432.442059125061.1593.6
1.76-1.833.450.3742.742913124331.1193.2
1.83-1.913.460.3113.142774123411.192.4
1.91-2.023.480.2353.842733122881.0691.9
2.02-2.143.510.1714.942706121531.0390.9
2.14-2.313.520.1276.342968121530.9991.2
2.31-2.543.50.1018.244347126130.9793.9
2.54-2.913.550.07410.547407132450.8898.9
2.91-3.663.680.04816.149978134070.8399.8
3.66-30.783.640.03525.250949134450.8799

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Processing

Software
NameVersionClassificationNB
d*TREK9.8Ldata scaling
REFMAC5.5.0095refinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
d*TREKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HDG

1hdg


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.845 / SU B: 5.673 / SU ML: 0.083 / SU R Cruickshank DPI: 0.127 / SU Rfree: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 6358 5 %RANDOM
Rwork0.189 120156 --
obs0.19 126514 94.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80.6 Å2 / Biso mean: 39.013 Å2 / Biso min: 21.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0.02 Å2
2--0.48 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10152 0 176 671 10999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02210544
X-RAY DIFFRACTIONr_angle_refined_deg1.041.97914333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40651359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57625.398465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.685151792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2741557
X-RAY DIFFRACTIONr_chiral_restr0.0650.21680
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027861
X-RAY DIFFRACTIONr_mcbond_it0.3171.56656
X-RAY DIFFRACTIONr_mcangle_it0.6582.510713
X-RAY DIFFRACTIONr_scbond_it1.84453888
X-RAY DIFFRACTIONr_scangle_it3.23103610
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 469 -
Rwork0.291 8698 -
all-9167 -
obs--93.67 %
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)
10.54490.0547-0.06510.4468-0.09720.8161-0.00860.0824-0.0224-0.0508-0.01010.08640.0985-0.08170.01870.0248-0.0049-0.0140.0213-0.01320.0349-8.03990.08073.1221
20.2936-0.0033-0.05650.5314-0.18840.64110.0056-0.05430.06390.06990.01070.0677-0.0535-0.0331-0.01630.014-0.00160.01220.0193-0.01930.0346-3.630820.72735.4682
30.41790.10530.0060.37060.13980.54440.00510.0250.0507-0.02090.019-0.0698-0.03980.0977-0.0240.009-0.00060.00950.0270.00810.032426.475215.48268.6545
40.5255-0.19680.2150.53710.01821.29710.0479-0.0543-0.1030.0617-0.0099-0.01290.29390.1396-0.0380.0890.0315-0.00750.03440.02280.043416.2785-11.828433.7017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1P-1 - 336
2X-RAY DIFFRACTION2R2 - 336
3X-RAY DIFFRACTION3O2 - 335
4X-RAY DIFFRACTION4Q2 - 335

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