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- PDB-3l4s: Crystal structure of C151G mutant of Glyceraldehyde 3-phosphate d... -

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Basic information

Entry
Database: PDB / ID: 3l4s
TitleCrystal structure of C151G mutant of Glyceraldehyde 3-phosphate dehydrogenase 1 (GAPDH1) from methicillin resistant Staphylococcus aureus MRSA252 complexed with NAD and G3P
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1Glyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / 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, 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
3-PHOSPHOGLYCERIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / 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
DepositionDec 21, 2009Deposition 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
Q: Glyceraldehyde-3-phosphate dehydrogenase 1
P: Glyceraldehyde-3-phosphate dehydrogenase 1
O: Glyceraldehyde-3-phosphate dehydrogenase 1
R: Glyceraldehyde-3-phosphate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,49712
Polymers145,0994
Non-polymers3,3988
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15940 Å2
ΔGint-59 kcal/mol
Surface area45900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.593, 102.936, 90.652
Angle α, β, γ (deg.)90.00, 109.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Q
21P
31O
41R

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Components

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


Mass: 36274.672 Da / Num. of mol.: 4 / Mutation: C151G
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-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE 3PG IS NOT PHOSPHOGLYCERIC ACID STRUCTURALLY. THE LIGAND BOUND IS THE GEM DI-OL FORM OF ...THE 3PG IS NOT PHOSPHOGLYCERIC ACID STRUCTURALLY. THE LIGAND BOUND IS THE GEM DI-OL FORM OF GLYCERALDEHYDE-3-PHOSPHATE (G3H).

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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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 (M) 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: Oct 10, 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→85.55 Å / Num. all: 60084 / Num. obs: 57048 / % possible obs: 94.9 % / Observed criterion σ(I): 5 / Redundancy: 3.63 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.47 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5916 / % possible all: 98.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.5.0095refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H48

3h48
PDB Unreleased entry


Resolution: 2.2→27.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 18.936 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24877 3035 5.1 %RANDOM
Rwork0.19707 ---
obs0.19961 57048 99.55 %-
all-60084 --
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 mean: 45.522 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å2-0.81 Å2
2--3.19 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10106 0 220 263 10589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210480
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.98314234
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87651333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.46725.401461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.727151764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.761556
X-RAY DIFFRACTIONr_chiral_restr0.1070.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027792
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6941.56590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4432.510590
X-RAY DIFFRACTIONr_scbond_it4.21953890
X-RAY DIFFRACTIONr_scangle_it6.974103643
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
Q1303tight positional0.070.05
P1303tight positional0.080.05
O1303tight positional0.070.05
R1303tight positional0.070.05
Q1162medium positional0.070.5
P1162medium positional0.080.5
O1162medium positional0.080.5
R1162medium positional0.070.5
Q1303tight thermal0.180.5
P1303tight thermal0.180.5
O1303tight thermal0.180.5
R1303tight thermal0.170.5
Q1162medium thermal0.212
P1162medium thermal0.212
O1162medium thermal0.192
R1162medium thermal0.192
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 225 -
Rwork0.303 4153 -
obs--98.45 %
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)
11.01530.16880.01140.88670.13630.931-0.02010.28220.2795-0.06690.0129-0.1106-0.07890.16250.00710.18130.00470.02520.11230.09920.2496-11.0154-0.85066.9613
21.3834-0.2621-0.37970.55130.01061.52710.0085-0.22580.0915-0.0073-0.04370.0736-0.1127-0.35690.03520.15310.01310.00110.1853-0.0430.1817-41.3033-4.635733.3159
31.416-0.17260.31030.49730.27611.85260.0342-0.3095-0.10990.0456-0.0279-0.0860.09850.2245-0.00630.1759-0.024-0.0190.15290.07710.1914-7.1086-20.304639.5476
41.55230.33630.34530.83880.31622.21990.05110.0669-0.29510.0099-0.0335-0.02080.3687-0.1791-0.01750.2446-0.009-0.00610.0236-0.01570.2138-31.4502-32.98119.3023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Q1 - 334
2X-RAY DIFFRACTION2P2 - 334
3X-RAY DIFFRACTION3O1 - 334
4X-RAY DIFFRACTION4R2 - 335

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