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- PDB-3gaz: Crystal structure of an alcohol dehydrogenase superfamily protein... -

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Basic information

Entry
Database: PDB / ID: 3gaz
TitleCrystal structure of an alcohol dehydrogenase superfamily protein from Novosphingobium aromaticivorans
ComponentsAlcohol dehydrogenase superfamily protein
KeywordsOXIDOREDUCTASE / PSI-II / 11160o / Alcohol dehydrogenase superfamily / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / New York Structural GenomiX Research Consortium
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alcohol dehydrogenase superfamily, zinc-containing
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsDamodharan, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of alcohol dehydrogenase superfamily protein from Novosphingobium aromaticivorans
Authors: Damodharan, L. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Alcohol dehydrogenase superfamily protein
B: Alcohol dehydrogenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4714
Polymers72,3902
Non-polymers802
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-8.3 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.328, 80.694, 110.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alcohol dehydrogenase superfamily protein


Mass: 36195.246 Da / Num. of mol.: 2 / Fragment: UNP residues 2-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_2768 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G4L9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 0.2 M Calcium chloride dihydrate, 20% w/v PEG 3350, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2009 / Details: mirrors
RadiationMonochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 45614 / Num. obs: 45614 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14
Reflection shellResolution: 1.87→1.96 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2 / Num. unique all: 4598 / % possible all: 80

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.96→43.32 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 105539.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1991 4.9 %RANDOM
Rwork0.225 ---
obs0.225 40883 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9491 Å2 / ksol: 0.342121 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1--4.11 Å20 Å20 Å2
2--8.12 Å20 Å2
3----4.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.96→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 2 697 5552
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.742
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 1.96→2.08 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 271 4.5 %
Rwork0.254 5737 -
obs--80.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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