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- PDB-4dib: The crystal structure of glyceraldehyde-3-phosphate dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 4dib
TitleThe crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bacillus anthracis str. Sterne
ComponentsGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / NIAID / structural genomics / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / Rossmann fold / CSGID
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glucose metabolic process / NAD binding / NADP binding / protease binding / membrane / 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
Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsNocek, B. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bacillus anthracis str. Sterne
Authors: Nocek, B. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Advisory / Database references / Category: citation_author / pdbx_unobs_or_zero_occ_atoms / Item: _citation_author.name
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / 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
E: Glyceraldehyde 3-phosphate dehydrogenase
F: Glyceraldehyde 3-phosphate dehydrogenase
G: Glyceraldehyde 3-phosphate dehydrogenase
H: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,30615
Polymers302,6348
Non-polymers6727
Water4,648258
1
A: Glyceraldehyde 3-phosphate dehydrogenase
D: Glyceraldehyde 3-phosphate dehydrogenase
E: Glyceraldehyde 3-phosphate dehydrogenase
F: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,7018
Polymers151,3174
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-139 kcal/mol
Surface area45690 Å2
MethodPISA
2
B: Glyceraldehyde 3-phosphate dehydrogenase
C: Glyceraldehyde 3-phosphate dehydrogenase
G: Glyceraldehyde 3-phosphate dehydrogenase
H: Glyceraldehyde 3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6057
Polymers151,3174
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-128 kcal/mol
Surface area45570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.347, 102.044, 102.144
Angle α, β, γ (deg.)90.32, 73.99, 68.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glyceraldehyde 3-phosphate dehydrogenase / GAPDH


Mass: 37829.246 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: gap1, BA_4827, BAS4478, GBAA_4827 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q81L07, UniProt: A0A348AAL1*PLUS, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M lithium sulfate, 25.5% PEG3350, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2011 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. all: 90350 / Num. obs: 87718 / % possible obs: 97.2 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 2.1 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 2.55→2.59 Å / % possible all: 89.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CMC
Resolution: 2.55→40 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.861 / SU B: 12 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 3500 5 %RANDOM
Rwork0.20796 ---
obs0.213 66018 76.81 %-
all-69520 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.473 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å2-0.28 Å20.29 Å2
2---0.5 Å2-0.2 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19171 0 35 258 19464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01919467
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212445
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.95426494
X-RAY DIFFRACTIONr_angle_other_deg2.613330616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70152530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38124.586761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.994153217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.16415102
X-RAY DIFFRACTIONr_chiral_restr0.0760.23283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221609
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023681
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 79 -
Rwork0.255 1550 -
obs--24.34 %

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