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- PDB-3lc7: Crystal Structure of apo Glyceraldehyde-3-phosphate dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 3lc7
TitleCrystal Structure of apo Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from methicllin resistant Staphylococcus aureus (MRSA252)
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 1Glyceraldehyde 3-phosphate dehydrogenase
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, 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
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
DepositionJan 10, 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_ncs_dom_lim / 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_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_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
O: Glyceraldehyde-3-phosphate dehydrogenase 1
R: Glyceraldehyde-3-phosphate dehydrogenase 1
Q: Glyceraldehyde-3-phosphate dehydrogenase 1
P: Glyceraldehyde-3-phosphate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,5966
Polymers146,4124
Non-polymers1842
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15110 Å2
ΔGint-47 kcal/mol
Surface area44540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.288, 94.937, 86.552
Angle α, β, γ (deg.)90.000, 105.730, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11O
21R
31Q
12O
22P

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALARGARGOA5 - 198 - 22
211VALVALARGARGRB5 - 198 - 22
311VALVALARGARGQC5 - 198 - 22
121VALVALVALVALOA30 - 6033 - 63
221VALVALVALVALRB30 - 6033 - 63
321VALVALVALVALQC30 - 6033 - 63
131ARGARGSERSEROA66 - 7469 - 77
231ARGARGSERSERRB66 - 7469 - 77
331ARGARGSERSERQC66 - 7469 - 77
141GLUGLUILEILEOA95 - 11098 - 113
241GLUGLUILEILERB95 - 11098 - 113
341GLUGLUILEILEQC95 - 11098 - 113
151LYSLYSGLYGLYOA116 - 125119 - 128
251LYSLYSGLYGLYRB116 - 125119 - 128
351LYSLYSGLYGLYQC116 - 125119 - 128
161ILEILEASNASNOA130 - 135133 - 138
261ILEILEASNASNRB130 - 135133 - 138
361ILEILEASNASNQC130 - 135133 - 138
171ASPASPASNASNOA140 - 185143 - 188
271ASPASPASNASNRB140 - 185143 - 188
371ASPASPASNASNQC140 - 185143 - 188
181ARGARGVALVALOA198 - 247201 - 250
281ARGARGVALVALRB198 - 247201 - 250
381ARGARGVALVALQC198 - 247201 - 250
191SERSERTHRTHROA270 - 295273 - 298
291SERSERTHRTHRRB270 - 295273 - 298
391SERSERTHRTHRQC270 - 295273 - 298
1101ALAALATYRTYROA312 - 330315 - 333
2101ALAALATYRTYRRB312 - 330315 - 333
3101ALAALATYRTYRQC312 - 330315 - 333
112VALVALGLUGLUOA5 - 598 - 62
212VALVALGLUGLUPD5 - 598 - 62
122ARGARGSERSEROA66 - 7469 - 77
222ARGARGSERSERPD66 - 7469 - 77
132SERSERASNASNOA120 - 185123 - 188
232SERSERASNASNPD120 - 185123 - 188
142ARGARGGLUGLUOA198 - 275201 - 278
242ARGARGGLUGLUPD198 - 275201 - 278
152VALVALMETMETOA279 - 300282 - 303
252VALVALMETMETPD279 - 300282 - 303
162VALVALTYRTYROA310 - 330313 - 333
262VALVALTYRTYRPD310 - 330313 - 333

NCS ensembles :
ID
1
2

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Components

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


Mass: 36603.047 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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

CrystalMosaicity: 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: 2.494→83.311 Å / Num. all: 34746 / Num. obs: 34746 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.1
Reflection shellResolution: 2.49→2.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.5 / Num. unique all: 4921 / % possible all: 96.7

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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: 2.5→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.163 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.817 / SU B: 17.312 / SU ML: 0.27 / SU R Cruickshank DPI: 0.256 / SU Rfree: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 354 1 %RANDOM
Rwork0.187 ---
obs0.188 34621 99.89 %-
all-34621 --
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: 94.78 Å2 / Biso mean: 40.942 Å2 / Biso min: 3.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20 Å2-0.62 Å2
2---1.03 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10075 0 12 132 10219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210207
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.95713819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01251322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49625.407455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.319151751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.011554
X-RAY DIFFRACTIONr_chiral_restr0.10.21624
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027624
X-RAY DIFFRACTIONr_mcbond_it0.7171.56565
X-RAY DIFFRACTIONr_mcangle_it1.4412.510543
X-RAY DIFFRACTIONr_scbond_it3.80853642
X-RAY DIFFRACTIONr_scangle_it6.45103276
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11O912TIGHT POSITIONAL0.110.05
12R912TIGHT POSITIONAL0.080.05
13Q912TIGHT POSITIONAL0.080.05
11O792MEDIUM POSITIONAL0.110.5
12R792MEDIUM POSITIONAL0.080.5
13Q792MEDIUM POSITIONAL0.080.5
11O912TIGHT THERMAL0.220.5
12R912TIGHT THERMAL0.160.5
13Q912TIGHT THERMAL0.150.5
11O792MEDIUM THERMAL0.222
12R792MEDIUM THERMAL0.172
13Q792MEDIUM THERMAL0.172
21O1000TIGHT POSITIONAL0.080.05
21O878MEDIUM POSITIONAL0.10.5
21O1000TIGHT THERMAL0.160.5
21O878MEDIUM THERMAL0.192
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 31 -
Rwork0.194 2472 -
all-2503 -
obs--99.21 %
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)
10.8914-0.4702-0.13830.86-0.08250.4066-0.00520.032-0.0581-0.0007-0.02320.02560.0858-0.05310.02840.0223-0.01580.00680.0159-0.01090.0139-6.8793-9.118333.71
20.8683-0.27470.01360.48110.18960.46620.0551-0.0975-0.12210.0594-0.0031-0.0239-0.02260.0654-0.0520.029-0.0262-0.0130.04180.0290.066928.698-22.635638.4984
30.7120.2162-0.2170.4556-0.00741.2366-0.06790.0874-0.1912-0.07550.02860.01060.3643-0.14310.03930.1357-0.05370.01310.0933-0.05090.09494.6013-34.86628.237
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1O1 - 334
2X-RAY DIFFRACTION2R1 - 334
3X-RAY DIFFRACTION3Q-2 - 334

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