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- PDB-1h2b: Crystal Structure of the Alcohol Dehydrogenase from the Hyperther... -

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Basic information

Entry
Database: PDB / ID: 1h2b
TitleCrystal Structure of the Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Aeropyrum pernix at 1.65A Resolution
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ARCHAEA / HYPERTHERMOPHILE / ALCOHOL DEHYDROGENASE OXIDOREDUCTASE / ZINC
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / OCTANOIC ACID (CAPRYLIC ACID) / NAD-dependent alcohol dehydrogenase
Similarity search - Component
Biological speciesAEROPYRUM PERNIX (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.62 Å
AuthorsGuy, J.E. / Isupov, M.N. / Littlechild, J.A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The structure of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.
Authors: Guy, J.E. / Isupov, M.N. / Littlechild, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Novel Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Aeropyrum Pernix.
Authors: Guy, J.E. / Isupov, M.N. / Littlechild, J.A.
History
DepositionAug 2, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _pdbx_database_status.status_code_sf
Revision 1.6Dec 13, 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.ptnr3_symmetry / _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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALCOHOL DEHYDROGENASE
B: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,18411
Polymers79,2412
Non-polymers1,9429
Water11,890660
1
A: ALCOHOL DEHYDROGENASE
B: ALCOHOL DEHYDROGENASE
hetero molecules

A: ALCOHOL DEHYDROGENASE
B: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,36822
Polymers158,4834
Non-polymers3,88518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.661, 103.186, 67.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.11131, 0.99372, 0.0112), (0.99378, -0.11132, 0.00044), (0.00169, 0.01108, -0.99994)
Vector: 89.60703, -99.9311, -39.25529)

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Components

#1: Protein ALCOHOL DEHYDROGENASE


Mass: 39620.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEROPYRUM PERNIX (archaea) / Plasmid: PTRC 99 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q9Y9P9, alcohol dehydrogenase
#2: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2
#3: Chemical ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBIOLOGICALLY ACTIVE UNIT IS TETRAMERIC. REQUIRES ZN COFACTOR FOR ENZYMATIC ACTIVITY.
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 6.75 / Details: pH 6.75
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMPIPES1reservoirpH6.75
213-16 %(w/v)PEG6001reservoir
30.5 mMNADH1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0704
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0704 Å / Relative weight: 1
ReflectionResolution: 1.62→15 Å / Num. obs: 1008062 / % possible obs: 97.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 28.9
Reflection shellResolution: 1.62→1.65 Å / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.52 / % possible all: 95.6
Reflection
*PLUS
Highest resolution: 1.62 Å / Lowest resolution: 15 Å / Num. obs: 88078 / Redundancy: 11.7 % / Rmerge(I) obs: 0.054

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
MOLREPphasing
SHELXSphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1HSZ

1hsz


Resolution: 1.62→15 Å / SU B: 1.546 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.088
RfactorNum. reflection% reflectionSelection details
Rfree0.20334 1759 2 %RANDOM
Rwork0.16757 ---
obs0.16829 86079 99.73 %-
Displacement parametersBiso mean: 25.697 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.62→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5302 0 113 660 6075
Refinement
*PLUS
Rfactor Rfree: 0.2033 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.015
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.746
X-RAY DIFFRACTIONplane_restr0.009

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