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- PDB-1bxz: CRYSTAL STRUCTURE OF A THERMOPHILIC ALCOHOL DEHYDROGENASE SUBSTRA... -

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Basic information

Entry
Database: PDB / ID: 1bxz
TitleCRYSTAL STRUCTURE OF A THERMOPHILIC ALCOHOL DEHYDROGENASE SUBSTRATE COMPLEX FROM THERMOANAEROBACTER BROCKII
ComponentsNADP-DEPENDENT ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / THERMOPHILIC ALCOHOL DEHYDROGENASE
Function / homology
Function and homology information


isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / 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
2-BUTANOL / NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesThermoanaerobacter brockii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsLi, C. / Heatwole, J. / Soelaiman, S. / Shoham, M.
Citation
Journal: Proteins / Year: 1999
Title: Crystal structure of a thermophilic alcohol dehydrogenase substrate complex suggests determinants of substrate specificity and thermostability.
Authors: Li, C. / Heatwole, J. / Soelaiman, S. / Shoham, M.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal Parameters of an Alcohol Dehydrogenase from the Extreme Thermophile Thermoanaerobium Brockii
Authors: Zhang, Z. / Djebli, A. / Shoham, M. / Frolow, F. / Peretz, M. / Burstein, Y.
History
DepositionOct 9, 1998Processing site: BNL
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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_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.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 / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-DEPENDENT ALCOHOL DEHYDROGENASE
B: NADP-DEPENDENT ALCOHOL DEHYDROGENASE
C: NADP-DEPENDENT ALCOHOL DEHYDROGENASE
D: NADP-DEPENDENT ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,57720
Polymers150,7794
Non-polymers79716
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17530 Å2
ΔGint-271 kcal/mol
Surface area43750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.450, 123.080, 168.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.999884, 0.012955, -0.008011), (0.004585, 0.75756, 0.65275), (0.014525, 0.652637, -0.757531)-36.6749, -9.2315, 25.5537
2given(0.531379, 0.300113, -0.792192), (0.296637, -0.941857, -0.157837), (-0.7935, -0.151122, -0.589508)2.6799, 2.6689, 6.2178
3given(-0.526449, -0.285158, 0.80096), (-0.300185, -0.81906, -0.488906), (0.79545, -0.49782, 0.345593)-39.3488, -3.5795, 22.3549

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
NADP-DEPENDENT ALCOHOL DEHYDROGENASE


Mass: 37694.871 Da / Num. of mol.: 4 / Fragment: NUCLEOTIDE-BINDING DOMAIN, CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter brockii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P14941, alcohol dehydrogenase (NADP+)

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Non-polymers , 5 types, 264 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SBT / 2-BUTANOL


Mass: 74.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.77 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.8 / Details: pH 5.8
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG80001reservoir
25.8 %(v/v)MPD1reservoir
32.5 %(v/v)sec-butanol1reservoir
450 mMmagnesium acetate1reservoir
50.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1996
RadiationMonochromator: CRYSTAL MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 30323 / % possible obs: 86.3 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.083 / Rsym value: 0.079 / Net I/σ(I): 12.1
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.278 / % possible all: 89
Reflection shell
*PLUS
% possible obs: 89 % / Mean I/σ(I) obs: 4.6

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.3Crefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEV

1kev


Resolution: 2.99→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2986 10 %RANDOM
Rwork0.2142 ---
obs0.2142 29742 86.3 %-
Displacement parametersBiso mean: 41.89 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--7.064 Å20 Å2
3----7.237 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.54 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.99→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10572 0 20 248 10840
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.4
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.08
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.15
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.6
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDWeight position
11RESTRAINTSX-RAY DIFFRACTION20
22X-RAY DIFFRACTION20
33X-RAY DIFFRACTION20
44X-RAY DIFFRACTION20
LS refinement shellResolution: 2.99→3.01 Å / Num. reflection Rwork: 604 / Total num. of bins used: 50
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19.SBTTOPH19.SBT
X-RAY DIFFRACTION3ION_MOD.PARAMION_MOD.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 29745 / Num. reflection Rfree: 2575 / Rfactor obs: 0.214 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.69
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.15
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.6

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