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- PDB-3r64: Crystal structure of a NAD-dependent benzaldehyde dehydrogenase f... -

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Basic information

Entry
Database: PDB / ID: 3r64
TitleCrystal structure of a NAD-dependent benzaldehyde dehydrogenase from Corynebacterium glutamicum
ComponentsNAD dependent benzaldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / NAD binding site
Function / homologyAldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsAgarwal, R. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a NAD-dependent benzaldehyde dehydrogenase from Corynebacterium glutamicum
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD dependent benzaldehyde dehydrogenase
B: NAD dependent benzaldehyde dehydrogenase
C: NAD dependent benzaldehyde dehydrogenase
D: NAD dependent benzaldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)216,6424
Polymers216,6424
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-47 kcal/mol
Surface area62390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.920, 99.826, 160.975
Angle α, β, γ (deg.)90.00, 113.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
NAD dependent benzaldehyde dehydrogenase


Mass: 54160.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032 / Gene: xylC, cg2953 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL
References: UniProt: Q6M2H6, benzaldehyde dehydrogenase (NAD+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Li2SO4, 0.1M Bis tris pH 5.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.28 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2011 / Details: mirrors
RadiationMonochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. all: 65060 / Num. obs: 65060 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5 / Num. unique all: 6429 / % possible all: 99.4

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Processing

Software
NameClassification
CNSrefinement
MOLREPphasing
CCP4refinement
REFMACrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BXS

1bxs


Resolution: 2.57→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 104471.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1933 3 %RANDOM
Rwork0.235 ---
obs0.235 63629 97.2 %-
all-65060 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.6293 Å2 / ksol: 0.314273 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.15 Å20 Å26.64 Å2
2--3.89 Å20 Å2
3---0.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13387 0 0 287 13674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.99
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.56→2.72 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 297 3.1 %
Rwork0.312 9362 -
obs-9362 88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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