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- PDB-1vlj: Crystal structure of NADH-dependent butanol dehydrogenase A (TM08... -

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Basic information

Entry
Database: PDB / ID: 1vlj
TitleCrystal structure of NADH-dependent butanol dehydrogenase A (TM0820) from Thermotoga maritima at 1.78 A resolution
ComponentsNADH-dependent butanol dehydrogenase
KeywordsOXIDOREDUCTASE / TM0820 / NADH-DEPENDENT BUTANOL DEHYDROGENASE A / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


alcohol dehydrogenase [NAD(P)+] activity / butanol dehydrogenase (NAD+) activity / methylglyoxal reductase (NADPH) (acetol producing) activity / alcohol dehydrogenase (NADP+) activity / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
Butanol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle ...Butanol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / 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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADH-dependent butanol dehydrogenase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NADH-dependent butanol dehydrogenase A (TM0820) from Thermotoga maritima at 1.78 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH-dependent butanol dehydrogenase
B: NADH-dependent butanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3506
Polymers89,7512
Non-polymers1,5994
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-51 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.691, 129.699, 55.234
Angle α, β, γ (deg.)90.00, 103.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NADH-dependent butanol dehydrogenase


Mass: 44875.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0820 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZS7, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.7
Details: 0.2M NaCl, 0.2% PEG-1000, 0.1M Na,K-Phosphate pH 5.7 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.000034
DetectorType: ADSC / Detector: CCD / Date: Sep 11, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000034 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 65785 / % possible obs: 93.95 % / Redundancy: 2.85 % / Biso Wilson estimate: 36.93 Å2 / Rsym value: 0.041 / Net I/σ(I): 21.67
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 1.87 % / Mean I/σ(I) obs: 1.94 / Num. unique all: 4773 / Rsym value: 0.338 / % possible all: 68.72

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMAC5.1.9999refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TM0820 has been phased with EPMR program (500 generations, default low and high resolution limits) using a model based on the template 1o2d (TM0920)

1o2d


Resolution: 1.78→49.6 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.628 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE MODEL OF THE ACTIVE SITE AROUND THE METAL (FE) IS APPARENTLY STILL INCOMPLETE, AND POSSIBLY A SUPERPOSITION OF STATES: THE METAL (FE) ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE MODEL OF THE ACTIVE SITE AROUND THE METAL (FE) IS APPARENTLY STILL INCOMPLETE, AND POSSIBLY A SUPERPOSITION OF STATES: THE METAL (FE) AND THE NAP ARE PARTIALLY OCCUPIED. OMIT DENSITY FOR THE NICOTINAMIDE RING IS WEAK. RESIDUAL DIFFERENCE DENSITY PEAKS PERSIST NEAR NICOTINAMIDE NC5 ATOM AND H272 IN BOTH CHAINS (WEAKER IN B). ONLY ONE STATE, THE MOST DEFENSIBLE ONE, HAS BEEN MODELLED. UNACCOUNTED TUBULAR DENSITY NEXT TO RESIDUES 222 AND 311 IN BOTH CHAINS. UNACCOUNTED STRONG POSITIVE DENSITY NEAR A7/B20 AND B7/A20
RfactorNum. reflection% reflectionSelection details
Rfree0.19265 3343 5.1 %RANDOM
Rwork0.14224 ---
obs0.14475 62407 93.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.944 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å21.73 Å2
2---0.47 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.78→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6078 0 98 480 6656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226331
X-RAY DIFFRACTIONr_bond_other_d0.0010.025827
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9628592
X-RAY DIFFRACTIONr_angle_other_deg1313524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.724.444252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.591151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3071526
X-RAY DIFFRACTIONr_chiral_restr0.0990.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021216
X-RAY DIFFRACTIONr_nbd_refined0.2340.21362
X-RAY DIFFRACTIONr_nbd_other0.180.25966
X-RAY DIFFRACTIONr_nbtor_other0.0870.23503
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2386
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0610.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.220
X-RAY DIFFRACTIONr_mcbond_it2.24934272
X-RAY DIFFRACTIONr_mcbond_other0.61731648
X-RAY DIFFRACTIONr_mcangle_it2.96256342
X-RAY DIFFRACTIONr_scbond_it5.53882673
X-RAY DIFFRACTIONr_scangle_it7.306112250
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 180 5.4 %
Rwork0.234 3155 -
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)
10.80330.0598-0.13930.37270.20490.32590.0174-0.03520.03140.0915-0.01870.0357-0.03830.02990.0013-0.08930.00050.0053-0.16970.0075-0.188514.075144.910749.0548
20.89890.2444-0.01720.36780.01510.3341-0.03720.1976-0.0401-0.00670.0461-0.0519-0.01640.0452-0.0089-0.1668-0.0040.002-0.08740.0074-0.208225.193238.475927.1235
30.773-0.06070.13550.9913-0.25550.2951-0.0252-0.0407-0.08770.1980.02650.0133-0.0317-0.0226-0.0012-0.08110.02260.0204-0.172-0.0123-0.13329.14289.67252.5694
41.0045-0.26580.07340.5057-0.08530.04680.03470.1796-0.235-0.0153-0.04790.084-0.0088-0.01690.0132-0.15860.0288-0.0015-0.0931-0.0705-0.1238-1.684311.498529.6976
57.9466-7.1836-0.53926.8608-0.26721.58880.3058-0.13580.0602-0.1-0.0038-0.2813-0.0749-0.1291-0.302-0.0701-0.0634-0.0205-0.11930.0572-0.078716.540548.28737.9177
69.4973-1.63164.82066.3627-1.92282.6438-0.20480.2906-1.41141.02670.25841.2288-0.48410.1775-0.0536-0.0499-0.02110.1104-0.0887-0.04550.0466.96613.954742.4205
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 18513 - 197
22AA186 - 394198 - 406
33BB1 - 18513 - 197
44BB186 - 394198 - 406
55AC - E400 - 8001
66BD - F400 - 8001

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