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- PDB-3lc2: Crystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrog... -

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Basic information

Entry
Database: PDB / ID: 3lc2
TitleCrystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from methicillin resistant Staphylococcus aureus MRSA252
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1
KeywordsOXIDOREDUCTASE / glycolysis / thioacyl intermediate
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
GLYCERALDEHYDE-3-PHOSPHATE / Glyceraldehyde-3-phosphate dehydrogenase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 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_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase 1
Q: Glyceraldehyde-3-phosphate dehydrogenase 1
R: Glyceraldehyde-3-phosphate dehydrogenase 1
P: Glyceraldehyde-3-phosphate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,34614
Polymers145,2834
Non-polymers1,06310
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15800 Å2
ΔGint-59 kcal/mol
Surface area45400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.057, 103.025, 90.303
Angle α, β, γ (deg.)90.00, 109.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11O
21Q
31R
41P

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 2 - 334 / Label seq-ID: 2 - 334

Dom-IDAuth asym-IDLabel asym-ID
1OA
2QB
3RC
4PD

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Components

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


Mass: 36320.762 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-G3H / GLYCERALDEHYDE-3-PHOSPHATE


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.02 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 32% (w/v) PEG 3350 , 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: Dec 19, 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: 2.793→85.178 Å / Num. all: 29489 / Num. obs: 29489 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 46 Å2 / Rsym value: 0.134
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4196 / % possible all: 96.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H48

3h48
PDB Unreleased entry


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.152 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.853 / SU B: 33.943 / SU ML: 0.299 / SU R Cruickshank DPI: 0.315 / SU Rfree: 0.417 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1492 5.1 %RANDOM
Rwork0.181 ---
obs0.184 29373 99.82 %-
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: 70.61 Å2 / Biso mean: 37.376 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-1.33 Å2
2--2.33 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10124 0 61 147 10332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210315
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.96213963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24251332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14725.391460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.302151772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6441556
X-RAY DIFFRACTIONr_chiral_restr0.0850.21636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027688
X-RAY DIFFRACTIONr_mcbond_it0.6261.56596
X-RAY DIFFRACTIONr_mcangle_it1.312.510604
X-RAY DIFFRACTIONr_scbond_it3.72253719
X-RAY DIFFRACTIONr_scangle_it6.637103359
Refine LS restraints NCS

Ens-ID: 1 / Number: 2523 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1OTIGHT POSITIONAL0.050.05
2QTIGHT POSITIONAL0.060.05
3RTIGHT POSITIONAL0.070.05
4PTIGHT POSITIONAL0.050.05
1OTIGHT THERMAL0.531.5
2QTIGHT THERMAL0.551.5
3RTIGHT THERMAL0.581.5
4PTIGHT THERMAL0.541.5
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 119 -
Rwork0.257 2025 -
all-2144 -
obs--99.77 %
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)
11.00640.36640.27940.85060.55982.2759-0.11670.08090.1665-0.11160.0402-0.0568-0.29470.22990.07640.0454-0.0316-0.01590.03920.04930.114823.4276-0.84126.5627
21.542-0.12020.00170.43850.04561.36970.0374-0.1061-0.03790.1403-0.0391-0.09210.15970.11250.00170.088-0.0246-0.05440.03870.03960.082427.3241-19.698439.8017
30.821-0.34970.08770.63650.16571.6640.0312-0.0896-0.0301-0.0087-0.09810.0459-0.065-0.21260.06690.034-0.02830.01790.0924-0.03830.0696-7.6172-4.627733.1188
40.86020.2205-0.3110.90110.04753.0957-0.05540.0376-0.0774-0.0122-0.05910.03410.4965-0.28050.11450.0874-0.04530.0250.0298-0.01410.06142.6032-33.29759.2947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1O1 - 334
2X-RAY DIFFRACTION2Q1 - 334
3X-RAY DIFFRACTION3R1 - 334
4X-RAY DIFFRACTION4P1 - 334

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