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- PDB-2xaa: Alcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541 at... -

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Basic information

Entry
Database: PDB / ID: 2xaa
TitleAlcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541 at pH 8.5 in complex with NAD and butane-1,4-diol
ComponentsSECONDARY ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CARBONYL REDUCTASE / KETOREDUCTASE
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / nucleotide binding / 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
1,4-BUTANEDIOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / alcohol dehydrogenase
Similarity search - Component
Biological speciesRHODOCOCCUS RUBER (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKroutil, W. / Gruber, K. / Grogan, G.
CitationJournal: Chem.Commun.(Camb.) / Year: 2010
Title: Structural Insights Into Substrate Specificity and Solvent Tolerance in Alcohol Dehydrogenase Adh-'A' from Rhodococcus Ruber Dsm 44541.
Authors: Karabec, M. / Lyskowski, A. / Tauber, K.C. / Steinkellner, G. / Kroutil, W. / Grogan, G. / Gruber, K.
History
DepositionMar 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: SECONDARY ALCOHOL DEHYDROGENASE
B: SECONDARY ALCOHOL DEHYDROGENASE
C: SECONDARY ALCOHOL DEHYDROGENASE
D: SECONDARY ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,33219
Polymers140,8844
Non-polymers3,44715
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16010 Å2
ΔGint-256 kcal/mol
Surface area44340 Å2
MethodPISA
2
A: SECONDARY ALCOHOL DEHYDROGENASE
D: SECONDARY ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1219
Polymers70,4422
Non-polymers1,6797
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-116.2 kcal/mol
Surface area24160 Å2
MethodPISA
3
B: SECONDARY ALCOHOL DEHYDROGENASE
C: SECONDARY ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,21110
Polymers70,4422
Non-polymers1,7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-119.9 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.674, 105.100, 109.176
Angle α, β, γ (deg.)90.00, 91.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 1 - 345 / Label seq-ID: 1 - 345

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(0.982, -0.1585, 0.1031), (-0.157, -0.9873, -0.023), (0.1054, 0.006406, -0.9944)-2.518, 1.592, 51.24
2given(-0.9822, 0.1531, -0.1085), (0.1557, 0.342, -0.9267), (-0.1048, -0.9271, -0.3598)31.02, 21.83, 36.94
3given(-1, -0.002726, 0.0049), (0.00555, -0.3561, 0.9344), (0.000802, 0.9344, 0.3561)28.23, -25.58, 17.63

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Components

#1: Protein
SECONDARY ALCOHOL DEHYDROGENASE / ADH-'A'


Mass: 35221.113 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS RUBER (bacteria) / Strain: DSM 44541 / Description: DSM / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER (DE3) / References: UniProt: Q8KLT9, alcohol dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.68 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 8.5
Details: 100 MM BISTRIS PROPANE BUFFER PH 8.5, 20% (W/V) PEG MW 4000, 5 MM CDCL2, 6% V/V 2-PROPANOL, 5% (V/V) 1, 4-BUTANEDIOL. PROTEIN AT 10 MG/ML

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9789
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.8→109.5 Å / Num. obs: 34356 / % possible obs: 9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.5
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 87.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JV7

3jv7


Resolution: 2.8→109.15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.893 / SU B: 15.282 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25756 1807 5 %RANDOM
Rwork0.18816 ---
obs0.1916 34356 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å20.94 Å2
2--3.02 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.8→109.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9731 0 202 142 10075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210136
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9913859
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40351354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41322.65351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.195151379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2641571
X-RAY DIFFRACTIONr_chiral_restr0.0920.21621
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217683
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5031.56708
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.947210665
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4233428
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4224.53193
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2341 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.380.5
2Bmedium positional0.330.5
3Cmedium positional0.320.5
4Dmedium positional0.310.5
1Amedium thermal1.012
2Bmedium thermal0.812
3Cmedium thermal0.952
4Dmedium thermal0.862
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 101 -
Rwork0.239 2238 -
obs--87.28 %

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