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- PDB-1rjw: CRYSTAL STRUCTURE OF NAD(+)-DEPENDENT ALCOHOL DEHYDROGENASE FROM ... -

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Basic information

Entry
Database: PDB / ID: 1rjw
TitleCRYSTAL STRUCTURE OF NAD(+)-DEPENDENT ALCOHOL DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS STRAIN LLD-R
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / NAD / ZINC / ALCOHOL / DEHYDROGENASE / TETRAMER
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / 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 ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / 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
TRIFLUOROETHANOL / Alcohol dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCeccarelli, C. / Bahnson, B.J.
Citation
Journal: Biochemistry / Year: 2004
Title: Crystal Structure and Amide H/D Exchange of Binary Complexes of Alcohol Dehydrogenase from Bacillus stearothermophilus: Insight into Thermostability and Cofactor Binding
Authors: Ceccarelli, C. / Liang, Z.X. / Strickler, M. / Prehna, G. / Goldstein, B.M. / Klinman, J.P. / Bahnson, B.J.
#1: Journal: Eur.J.Biochem. / Year: 1994
Title: A few amino acid substitutions are responsible for the higher thermostability of a novel NAD(+)-dependent bacillar alcohol dehydrogenase
Authors: Cannio, R. / Rossi, M. / Bartolucci, S.
History
DepositionNov 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
C: Alcohol dehydrogenase
D: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,36025
Polymers145,5374
Non-polymers1,82421
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.322, 138.222, 158.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.982286, -0.164488, -0.089765), (-0.173641, 0.618904, 0.766033), (-0.070447, 0.768051, -0.636502)10.98921, -15.75665, 35.37394
2given(-0.934762, 0.163742, -0.315293), (0.154038, -0.612913, -0.77499), (-0.320145, -0.772998, 0.547705)6.72099, 97.63541, 50.185
3given(0.910476, 0.028885, 0.412553), (0.033038, -0.99945, -0.002936), (0.412241, 0.016303, -0.910929)-17.92798, 81.60631, 77.342

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Components

#1: Protein
Alcohol dehydrogenase / / ADH-HT


Mass: 36384.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: LLD-R / Gene: ADH-HT / Plasmid: PRC17 / Production host: Escherichia coli (E. coli) / Strain (production host): RB791 / References: UniProt: P42328, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3F3O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.51 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20MG/ML PROTEIN, 100MM HEPES, 12% TRIFLUOROETHANOL, 12% PEG 4000, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 / Wavelength: 0.908 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.35→41.44 Å / Num. all: 55369 / Num. obs: 55369 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.769 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.2
Reflection shellResolution: 2.35→2.37 Å / Redundancy: 4.696 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 6.3 / % possible all: 90.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CCP4SUITEmodel building
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: E. COLI NAD(+)-DEPENDENT TETRAMERIC ALCOHOL DEHYDROGENASE

Resolution: 2.35→41.44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 398738.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESTRAINTS FOR 222 NON-CRYSTALLOGRAPHIC SYMMETRY WERE APPLIED TO 2238 OF 2554 ATOMS IN EACH PROTEIN SUBUNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2596 5 %RANDOM
Rwork0.214 ---
obs0.214 51591 81.1 %-
all-51591 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.6042 Å2 / ksol: 0.353307 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1--12.71 Å20 Å20 Å2
2--4.31 Å20 Å2
3---8.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.35→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10216 0 86 332 10634
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.982.5
Refine LS restraints NCSNCS model details: RESTRAINED / Rms dev Biso : 1.718 Å2 / Rms dev position: 0.107 Å / Weight Biso : 2 / Weight position: 50
LS refinement shellResolution: 2.35→2.49 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 390 5.1 %
Rwork0.256 7239 -
obs-390 72.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ETF.PARAMETF.TOP

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