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- PDB-3ox4: Structures of iron-dependent alcohol dehydrogenase 2 from Zymomon... -

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Basic information

Entry
Database: PDB / ID: 3ox4
TitleStructures of iron-dependent alcohol dehydrogenase 2 from Zymomonas mobilis ZM4 complexed with NAD cofactor
ComponentsAlcohol dehydrogenase 2
KeywordsOXIDOREDUCTASE / Alcohol Dehydrogenase / Iron / NAD
Function / homology
Function and homology information


ethanol dehydrogenase (NAD+) activity / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / metal ion binding
Similarity search - Function
Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Iron-containing alcohol dehydrogenases signature 1. / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase ...Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Iron-containing alcohol dehydrogenases signature 1. / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase 2 / Alcohol dehydrogenase 2
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMoon, J.H. / Lee, H.J. / Song, J.M. / Park, S.Y. / Park, M.Y. / Park, H.M. / Sun, J. / Park, J.H. / Kim, J.S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structures of iron-dependent alcohol dehydrogenase 2 from Zymomonas mobilis ZM4 with and without NAD+ cofactor
Authors: Moon, J.H. / Lee, H.J. / Park, S.Y. / Song, J.M. / Park, M.Y. / Park, H.M. / Sun, J. / Park, J.H. / Kim, B.Y. / Kim, J.S.
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_label_asym_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 2
B: Alcohol dehydrogenase 2
C: Alcohol dehydrogenase 2
D: Alcohol dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,62112
Polymers160,7444
Non-polymers2,8778
Water9,998555
1
A: Alcohol dehydrogenase 2
B: Alcohol dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8116
Polymers80,3722
Non-polymers1,4394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-17 kcal/mol
Surface area27500 Å2
MethodPISA
2
C: Alcohol dehydrogenase 2
D: Alcohol dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8116
Polymers80,3722
Non-polymers1,4394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-15 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.514, 86.965, 124.475
Angle α, β, γ (deg.)90.00, 94.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alcohol dehydrogenase 2 / Alcohol dehydrogenase II / ADH II


Mass: 40186.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Strain: ZM4 / Gene: adhB, ZMO1596 / Production host: Escherichia coli (E. coli)
References: UniProt: P06758, UniProt: P0DJA2*PLUS, 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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 4000, 0.15M Magnesium Chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 84735 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rsym value: 0.071 / Net I/σ(I): 15.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.37 / Num. unique all: 4206 / Rsym value: 0.404 / % possible all: 97

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Processing

Software
NameClassification
HKL-2000data collection
PHASESphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OWO

3owo


Resolution: 2→28.75 Å / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4199 -RANDOM
Rwork0.212 ---
all0.262 86912 --
obs0.24 82507 94.9 %-
Refinement stepCycle: LAST / Resolution: 2→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11188 0 180 555 11923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005925
X-RAY DIFFRACTIONc_angle_deg1.34911

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