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- PDB-1zk3: Triclinic crystal structure of the apo-form of R-specific alcohol... -

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Basic information

Entry
Database: PDB / ID: 1zk3
TitleTriclinic crystal structure of the apo-form of R-specific alcohol dehydrogenase (mutant G37D) from Lactobacillus brevis
ComponentsR-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / short chain reductases/dehydrogenases / magnesium dependence / R-specific alcohol dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
R-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchlieben, N.H. / Niefind, K. / Muller, J. / Riebel, B. / Hummel, W. / Schomburg, D.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Atomic Resolution Structures of R-specific Alcohol Dehydrogenase from Lactobacillus brevis Provide the Structural Bases of its Substrate and Cosubstrate Specificity
Authors: Schlieben, N.H. / Niefind, K. / Muller, J. / Riebel, B. / Hummel, W. / Schomburg, D.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: The crystal structure of R-specific alcohol dehydrogenase from Lactobacillus brevis suggests the structural basis of its metal dependency
Authors: Niefind, K. / Muller, J. / Riebel, B. / Hummel, W. / Schomburg, D.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary characterization of crystals of R-alcohol dehydrogenase from Lactobacills brevis
Authors: Niefind, K. / Riebel, B. / Muller, J. / Hummel, W. / Schomburg, D.
History
DepositionMay 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 600 HETEROGEN Water molecules 253-375 are associated with chain A, 453-575 are associated with chain ... HETEROGEN Water molecules 253-375 are associated with chain A, 453-575 are associated with chain B, 653-775 are associated with chain C, 853-975 are associated with chain D, 1053-1175 are associated with chain E, 1253-1375 are associated with chain F, 1453-1575 are associated with chain G and 1653-1775 are associated with chain H.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
C: R-specific alcohol dehydrogenase
D: R-specific alcohol dehydrogenase
E: R-specific alcohol dehydrogenase
F: R-specific alcohol dehydrogenase
G: R-specific alcohol dehydrogenase
H: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,81012
Polymers213,7138
Non-polymers974
Water21,0051166
1
A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
C: R-specific alcohol dehydrogenase
D: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9056
Polymers106,8564
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint-90 kcal/mol
Surface area31430 Å2
MethodPISA
2
E: R-specific alcohol dehydrogenase
F: R-specific alcohol dehydrogenase
G: R-specific alcohol dehydrogenase
H: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9056
Polymers106,8564
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint-91 kcal/mol
Surface area31720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.632, 72.234, 118.092
Angle α, β, γ (deg.)101.41, 92.78, 114.48
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a tetramer. The asymmetric unit contains eight monomers belonging to two different tetramers.The chains A, B, C, and D form one tetramer and the chains E, F, G, and H the other.

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Components

#1: Protein
R-specific alcohol dehydrogenase


Mass: 26714.098 Da / Num. of mol.: 8 / Mutation: G37D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Plasmid: pkk177-3H / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q84EX5, alcohol dehydrogenase (NADP+)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1166 / 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: 2.25 Å3/Da / Density % sol: 44.8 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→63.8 Å / Num. all: 94706 / Num. obs: 94706

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→63.8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.245 4149 RANDOM
Rwork0.214 --
all0.214 82986 -
obs0.214 78837 -
Refinement stepCycle: LAST / Resolution: 2.2→63.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14992 0 4 1166 16162
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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