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- PDB-3k9q: Crystal structure of C151G mutant of Glyceraldehyde 3-phosphate d... -

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Basic information

Entry
Database: PDB / ID: 3k9q
TitleCrystal structure of C151G mutant of Glyceraldehyde 3-phosphate dehydrogenase 1 from Methicillin resistant Staphylococcus aureus (MRSA252) at 2.5 angstrom resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1
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, 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: 2.5 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
DepositionOct 16, 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 4, 2013Group: Database references
Revision 1.3Jan 23, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Sep 9, 2020Group: Derived calculations / Structure summary / Category: struct / struct_site
Item: _struct.title / _struct_site.pdbx_auth_asym_id ..._struct.title / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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


Theoretical massNumber of molelcules
Total (without water)148,06412
Polymers145,0994
Non-polymers2,9658
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21560 Å2
ΔGint-100 kcal/mol
Surface area44120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.933, 105.142, 90.760
Angle α, β, γ (deg.)90.00, 107.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Q
21O
31P
41R

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 1 - 335 / Label seq-ID: 1 - 335

Dom-IDAuth asym-IDLabel asym-ID
1QA
2OB
3PC
4RD

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase 1 / 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(pREP4)
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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 42.27 % / Mosaicity: 0.389 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1M TRIS-HCl pH8.2, 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: Jul 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: 2.5→86.57 Å / Num. obs: 42157 / % possible obs: 100 % / Redundancy: 3.72 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1 / Net I/σ(I): 9.9 / Scaling rejects: 1187
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.7 / Num. measured all: 14800 / Num. unique all: 4213 / Χ2: 1.23 / % possible all: 100

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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: 2.5→27.24 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.861 / SU B: 19.79 / SU ML: 0.205 / SU R Cruickshank DPI: 0.243 / SU Rfree: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2130 5.1 %RANDOM
Rwork0.183 ---
obs0.185 42155 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.17 Å2 / Biso mean: 23.495 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0.19 Å2
2--0.88 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.5→27.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10140 0 195 356 10691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210540
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9814315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51351352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92325.375467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.329151789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2231558
X-RAY DIFFRACTIONr_chiral_restr0.0980.21672
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027850
X-RAY DIFFRACTIONr_mcbond_it0.6521.56636
X-RAY DIFFRACTIONr_mcangle_it1.299210672
X-RAY DIFFRACTIONr_scbond_it2.24733904
X-RAY DIFFRACTIONr_scangle_it3.8654.53635
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
Q1333TIGHT POSITIONAL0.070.05
O1333TIGHT POSITIONAL0.080.05
P1333TIGHT POSITIONAL0.060.05
R1333TIGHT POSITIONAL0.070.05
Q1161MEDIUM POSITIONAL0.080.5
O1161MEDIUM POSITIONAL0.080.5
P1161MEDIUM POSITIONAL0.090.5
R1161MEDIUM POSITIONAL0.080.5
Q1333TIGHT THERMAL0.150.5
O1333TIGHT THERMAL0.140.5
P1333TIGHT THERMAL0.140.5
R1333TIGHT THERMAL0.140.5
Q1161MEDIUM THERMAL0.172
O1161MEDIUM THERMAL0.172
P1161MEDIUM THERMAL0.172
R1161MEDIUM THERMAL0.152
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 168 -
Rwork0.248 2962 -
all-3130 -
obs--99.97 %
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)
10.2711-0.0391-0.17681.06920.36480.94720.00530.00130.0376-0.02110.0094-0.0721-0.01280.0774-0.01470.00150.0049-0.00020.04870.01390.053823.708-1.04987.9374
20.4723-0.1504-0.1020.53360.2081.22960.0041-0.0951-0.01160.0103-0.012-0.08970.05680.13930.00790.0377-0.0037-0.01680.05460.01820.073128.0127-21.426540.2753
30.4818-0.1401-0.04460.631-0.33381.22560.00530.01170.0325-0.02770.01580.0863-0.0224-0.1445-0.02110.0064-0.00860.00050.061-0.02140.0611-6.472-6.078634.7723
40.69830.22830.16520.76860.02541.9192-0.0217-0.0084-0.1195-0.02090.0240.03080.3759-0.1288-0.00230.1217-0.02330.00210.0592-0.02740.093.6512-33.46729.5942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Q1 - 335
2X-RAY DIFFRACTION2O1 - 335
3X-RAY DIFFRACTION3P1 - 335
4X-RAY DIFFRACTION4R1 - 335

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