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- PDB-1zk2: Orthorhombic crystal structure of the apo-form of R-specific alco... -

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Basic information

Entry
Database: PDB / ID: 1zk2
TitleOrthorhombic 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: 1.55 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: Derived calculations / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.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_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.ptnr1_symmetry / _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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7382
Polymers26,7141
Non-polymers241
Water7,728429
1
A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9548
Polymers106,8564
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area14600 Å2
ΔGint-114 kcal/mol
Surface area32470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.830, 79.887, 113.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1252-

MG

21A-1390-

HOH

31A-1465-

HOH

41A-1538-

HOH

DetailsThe biological assembly is a tetramer generated form the monomer in the asymmetric unit by the following operations: x, y, z; -x, -y, z; -x, y, -z; x, -y, -z

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Components

#1: Protein R-specific alcohol dehydrogenase


Mass: 26714.098 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.4 Å3/Da / Density % sol: 47.5 %

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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: 1.55→65.3 Å / Num. all: 37100 / Num. obs: 36602

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→65.3 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.185 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17177 1421 3.9 %RANDOM
Rwork0.14772 ---
all0.14868 36669 --
obs0.14868 35181 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.55→65.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 1 429 2305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212102
X-RAY DIFFRACTIONr_bond_other_d0.0020.021884
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9492855
X-RAY DIFFRACTIONr_angle_other_deg0.79234407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022424
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02410
X-RAY DIFFRACTIONr_nbd_refined0.2190.2445
X-RAY DIFFRACTIONr_nbd_other0.2450.22274
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21139
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3730.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.271
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.561.51362
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03822192
X-RAY DIFFRACTIONr_scbond_it1.9183740
X-RAY DIFFRACTIONr_scangle_it3.1334.5663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 97
Rwork0.307 2376

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