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- PDB-3hja: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 3hja
TitleCrystal structure of glyceraldehyde-3-phosphate dehydrogenase from Borrelia burgdorferi
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / NIAID / SSGCID / deCODE / UW / SBRI / Lyme disease / non-Hodgkin lymphomas / Cytoplasm / Glycolysis / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / cytosol
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesBorrelia burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB entry 3CMC / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Borrelia burgdorferi
Authors: Edwards, T.E. / Abendroth, J.A. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,18320
Polymers154,3774
Non-polymers3,80616
Water16,268903
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14710 Å2
ΔGint-95.1 kcal/mol
Surface area44340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.080, 122.330, 143.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 38594.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal hexahis tag and 3C protease cleavage site. Expression tag was not removed prior to crystallization.
Source: (gene. exp.) Borrelia burgdorferi B31 (bacteria) / Strain: B31 / CIP 102532 / DSM 4680 / Gene: gap, BB_0057 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: P46795, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#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.: 903 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: JCSG+ sparse matrix screen condition f2: 0.1 M Na citrate pH 5.0, 3.2 M ammonium sulfate, 30 mg/mL protein, crystal tracking ID 202701f2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2009 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 82007 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.228 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 15.38
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 4.3 / Num. unique all: 5995 / Num. unique obs: 5995 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.46 Å47.92 Å
Translation2.46 Å47.92 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: PDB entry 3CMC / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.14 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.894 / SU B: 3.842 / SU ML: 0.1 / SU R Cruickshank DPI: 0.203 / SU Rfree: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4108 5 %RANDOM
Rwork0.154 ---
obs0.156 82007 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 83.27 Å2 / Biso mean: 21.59 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10177 0 236 903 11316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210589
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.99914445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17851379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43824.821392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.465151834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1781551
X-RAY DIFFRACTIONr_chiral_restr0.0840.21746
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217653
X-RAY DIFFRACTIONr_mcbond_it0.5711.56695
X-RAY DIFFRACTIONr_mcangle_it1.098210849
X-RAY DIFFRACTIONr_scbond_it1.86133894
X-RAY DIFFRACTIONr_scangle_it3.1064.53573
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 285 -
Rwork0.171 5702 -
all-5987 -
obs--99.92 %

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