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- PDB-4cpd: Alcohol dehydrogenase TADH from Thermus sp. ATN1 -

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Basic information

Entry
Database: PDB / ID: 4cpd
TitleAlcohol dehydrogenase TADH from Thermus sp. ATN1
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / THERMOPHILE / MEDIUM CHAIN REDUCTASE / MDR
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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase
Similarity search - Component
Biological speciesTHERMUS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsMan, H. / Gargulio, S. / Frank, A. / Hollmann, F. / Grogan, G.
CitationJournal: J.Mol.Catal., B Enzym. / Year: 2014
Title: Structure of the Nadh-Dependent Thermostable Alcohol Dehydrogenase Tadh from Thermus Sp. Atn1 Provides a Platform for Engineering Specificity and Improved Compatibility with Inorganic Cofactor- ...Title: Structure of the Nadh-Dependent Thermostable Alcohol Dehydrogenase Tadh from Thermus Sp. Atn1 Provides a Platform for Engineering Specificity and Improved Compatibility with Inorganic Cofactor-Regeneration Catalysts
Authors: Man, H. / Gargulio, S. / Frank, A. / Hollmann, F. / Grogan, G.
History
DepositionFeb 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 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_asym_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_asym_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.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: ALCOHOL DEHYDROGENASE
B: ALCOHOL DEHYDROGENASE
C: ALCOHOL DEHYDROGENASE
D: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,43315
Polymers148,9204
Non-polymers2,51411
Water2,972165
1
A: ALCOHOL DEHYDROGENASE
D: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0488
Polymers74,4602
Non-polymers1,5886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-108.8 kcal/mol
Surface area24670 Å2
MethodPISA
2
B: ALCOHOL DEHYDROGENASE
C: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3857
Polymers74,4602
Non-polymers9255
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-95.4 kcal/mol
Surface area25300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.367, 87.367, 337.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
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: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 1 - 346 / Label seq-ID: 1 - 346

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

NCS oper:
IDCodeMatrixVector
1given(-0.06497, -0.347, 0.9356), (-0.3669, -0.8636, -0.3458), (0.928, -0.3657, -0.0712)-41, 99.44, 79
2given(-0.2982, -0.406, -0.8639), (-0.4382, -0.7458, 0.5018), (-0.848, 0.5281, 0.04452)119.7, 25.09, 86.26
3given(-0.6524, 0.7522, -0.09268), (0.7533, 0.6302, -0.1883), (-0.08324, -0.1927, -0.9777)25.62, 8.664, 176.7
4given(1), (1), (1)
5given(-0.065072, -0.346938, 0.935628), (-0.366973, -0.863591, -0.345749), (0.927953, -0.365849, -0.071121)-41.00352, 99.43887, 79.00057
6given(-0.298141, -0.406076, -0.863837), (-0.438155, -0.745794, 0.501809), (-0.848017, 0.528104, 0.044427)119.70823, 25.08451, 86.27495
7given(-0.652453, 0.752147, -0.092624), (0.753255, 0.630245, -0.188147), (-0.083139, -0.192527, -0.977763)25.61495, 8.6522, 176.72943

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Components

#1: Protein
ALCOHOL DEHYDROGENASE


Mass: 37229.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS SP. (bacteria) / Strain: ATN1 / Description: ENVIRONMENTAL ISOLATE / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2ZRE3, 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6.5
Details: 1 M SODIUM CHLORIDE AND 1.5 M AMMONIUM SULPHATE IN 0.1 M BIS-TRIS BUFFER AT PH 6.5.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91999 Å / Relative weight: 1
ReflectionResolution: 2.74→48.22 Å / Num. obs: 40559 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.2
Reflection shellResolution: 2.74→2.91 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D8A

2d8a


Resolution: 2.74→112.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.236 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24758 2045 5 %RANDOM
Rwork0.19157 ---
obs0.19431 38461 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.545 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.74→112.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10065 0 140 165 10370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910496
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210124
X-RAY DIFFRACTIONr_angle_refined_deg1.5082.00114350
X-RAY DIFFRACTIONr_angle_other_deg0.835323160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39251378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35223.516401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.167151527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5771572
X-RAY DIFFRACTIONr_chiral_restr0.0770.21668
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112031
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022292
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_it3.9835.5225530
X-RAY DIFFRACTIONr_mcbond_other3.9825.5225529
X-RAY DIFFRACTIONr_mcangle_it6.0138.2746902
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8435.8854966
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 4848 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.280.5
2Bmedium positional0.670.5
3Cmedium positional0.440.5
4Dmedium positional0.460.5
1Amedium thermal9.712
2Bmedium thermal6.052
3Cmedium thermal7.712
4Dmedium thermal12.672
LS refinement shellResolution: 2.74→2.811 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 162 -
Rwork0.292 2777 -
obs--100 %

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