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- PDB-3jv7: Structure of ADH-A from Rhodococcus ruber -

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Basic information

Entry
Database: PDB / ID: 3jv7
TitleStructure of ADH-A from Rhodococcus ruber
ComponentsADH-A
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / NUCLEOTIDE BINDING / ROSSMANN-FOLD
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
ACETIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / alcohol dehydrogenase
Similarity search - Component
Biological speciesRhodococcus ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKarabec, M. / Lyskowski, A. / Gruber, K.
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
DepositionSep 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADH-A
B: ADH-A
C: ADH-A
D: ADH-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,77424
Polymers140,8844
Non-polymers3,89020
Water21,3301184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16610 Å2
ΔGint-207 kcal/mol
Surface area43700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.822, 106.119, 109.097
Angle α, β, γ (deg.)90.000, 91.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ADH-A


Mass: 35221.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus ruber (bacteria) / Strain: DSM 44541 / Gene: ADH-A / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KLT9*PLUS, alcohol dehydrogenase

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Non-polymers , 5 types, 1204 molecules

#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.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1184 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 298 K / pH: 5.5
Details: 0.1M AMMONIUM ACETATE, 0.1M BIS-TRIS, 17% PEG-10000, pH5.5, batch crystallization, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0815 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0815 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 99524 / Num. obs: 99524 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 31.821 Å2 / Rsym value: 0.075 / Net I/σ(I): 11.87
Reflection shellResolution: 2→2.17 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.6 / Num. measured obs: 80219 / Num. unique all: 21640 / Num. unique obs: 21640 / Rsym value: 0.334 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EER, 1JVB, 2H6E, 1RJW, 2HCY

2eer

1jvb

2h6e

1rjw

2hcy
PDB Unreleased entry


Resolution: 2→38.453 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.875 / SU ML: 0.24 / Isotropic thermal model: ISOTROPIC/TLS / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4985 5.01 %RANDOM
Rwork0.159 ---
obs0.162 99493 98.4 %-
all-99493 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.324 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 132.6 Å2 / Biso mean: 29.825 Å2 / Biso min: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1--3.482 Å20 Å2-0.386 Å2
2--2.786 Å20 Å2
3---0.695 Å2
Refinement stepCycle: LAST / Resolution: 2→38.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9892 0 232 1184 11308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01610392
X-RAY DIFFRACTIONf_angle_d1.09514184
X-RAY DIFFRACTIONf_chiral_restr0.0651658
X-RAY DIFFRACTIONf_plane_restr0.0051846
X-RAY DIFFRACTIONf_dihedral_angle_d14.5633616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0230.2541600.2022968312894
2.023-2.0460.2551740.18131843358100
2.046-2.0720.2131430.17132043347100
2.072-2.0980.2381670.16831683335100
2.098-2.1250.2331640.17532413405100
2.125-2.1540.2361920.17431323324100
2.154-2.1850.2291640.16631863350100
2.185-2.2180.2421640.1973173333799
2.218-2.2530.3051720.2563116328898
2.253-2.2890.3751560.2863104326097
2.289-2.3290.2771700.2093113328398
2.329-2.3710.2581520.1732203372100
2.371-2.4170.2211830.15431873370100
2.417-2.4660.2291790.1493155333499
2.466-2.520.2021460.1523201334799
2.52-2.5780.2321690.15231793348100
2.578-2.6430.2141630.15532013364100
2.643-2.7140.2221780.15731733351100
2.714-2.7940.2031520.1493185333799
2.794-2.8840.1941580.1493182334099
2.884-2.9870.2031620.1493191335399
2.987-3.1070.1981670.163135330299
3.107-3.2480.1931560.1553151330798
3.248-3.4190.221660.1593132329898
3.419-3.6330.2081750.1563082325797
3.633-3.9140.1881650.153049321495
3.914-4.3070.1621700.1283047321795
4.307-4.9290.1381690.113089325896
4.929-6.2060.1541680.1233148331697
6.206-38.460.1451810.1293212339398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.69030.3305-0.02551.0030.11210.70140.0946-0.15280.13810.1812-0.04570.0215-0.18890.0405-0.04680.1927-0.03240.00160.1264-0.03080.105558.880115.806893.0304
20.3877-0.0857-0.5761.6914-1.24842.29840.10780.03490.0816-0.2248-0.0467-0.2330.21770.2218-0.0220.094200.02530.10750.01160.120870.6676.139468.3658
30.72620.1645-0.03530.2681-0.02660.70170.06650.00810.1570.0516-0.0228-0.0043-0.10840.0383-0.02460.1243-0.0287-0.00080.0836-0.00630.127562.023112.410679.3187
40.6706-0.1235-0.00660.99210.27571.04160.00130.0636-0.1766-0.0718-0.01640.03520.16770.00350.0170.1348-0.00420.0190.0781-0.0110.10956.3697-29.427270.0297
50.7342-0.06280.05232.3921-0.99080.76470.0382-0.2762-0.05970.39570.0244-0.2165-0.16390.2969-0.00470.1369-0.0284-0.02380.14430.03590.100366.8942-21.386295.8807
60.7051-0.1767-0.13390.32470.15540.77950.0076-0.0614-0.1650.0494-0.0110.0140.09610.03370.00680.1253-0.00130.00610.07340.02750.112958.5585-26.441584.0347
71.55390.3447-0.07961.3382-0.36980.44910.1128-0.6698-0.00360.4935-0.0470.1888-0.163-0.1172-0.05330.2848-0.00630.08560.42610.00820.152433.001-3.3856105.5687
80.86461.22130.02152.8047-0.94711.19350.0659-0.1242-0.0322-0.25580.09580.18710.2785-0.3761-0.19290.1413-0.0733-0.01630.20150.05130.165421.1134-21.975387.1329
90.6470.17090.31210.7236-0.4030.50010.0469-0.2344-0.12210.15080.05330.2166-0.0085-0.2347-0.0950.1454-0.03330.0610.25060.07260.172229.8887-14.651496.9931
101.0934-0.45660.19861.0801-0.05390.56340.1470.38-0.018-0.2998-0.1360.1080.03440.01420.00950.15750.0252-0.04290.2493-0.00140.123935.5834-6.241955.0202
110.3906-0.3628-0.39471.967-0.44721.11210.11660.10220.20660.1574-0.06280.2854-0.1923-0.2732-0.08220.09710.02350.02260.14810.0340.169124.852914.045572.6883
120.7-0.3296-0.05070.61290.14510.20470.09060.20780.0947-0.0682-0.05630.0887-0.046-0.0587-0.0290.11740.0215-0.02470.18480.0430.124233.38415.330663.3647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A 1-197, 501,502A1 - 197
2X-RAY DIFFRACTION2chain A 198-239A198 - 239
3X-RAY DIFFRACTION3chain A 240-345A240 - 345
4X-RAY DIFFRACTION4chain B 1-197, 501,502B1 - 197
5X-RAY DIFFRACTION5chain B 198-239B198 - 239
6X-RAY DIFFRACTION6chain B 240-345B240 - 345
7X-RAY DIFFRACTION7chain C 1-197, 501,502C1 - 197
8X-RAY DIFFRACTION8chain C 198-239C198 - 239
9X-RAY DIFFRACTION9chain C 240-345C240 - 345
10X-RAY DIFFRACTION10chain D 1-197, 501,502D1 - 197
11X-RAY DIFFRACTION11chain D 198-239D198 - 239
12X-RAY DIFFRACTION12chain D 240-345D240 - 345

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