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- PDB-1ahi: 7 ALPHA-HYDROXYSTEROID DEHYDROGENASE COMPLEXED WITH NADH AND 7-OX... -

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Basic information

Entry
Database: PDB / ID: 1ahi
Title7 ALPHA-HYDROXYSTEROID DEHYDROGENASE COMPLEXED WITH NADH AND 7-OXO GLYCOCHENODEOXYCHOLIC ACID
Components7 ALPHA-HYDROXYSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE
Function / homology
Function and homology information


chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / 7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase activity / bile acid catabolic process / lipid catabolic process / NAD binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
: / short chain dehydrogenase / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 7alpha-hydroxysteroid dehydrogenase / 7alpha-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsTanaka, N. / Nonaka, T. / Mitsui, Y.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structures of the binary and ternary complexes of 7 alpha-hydroxysteroid dehydrogenase from Escherichia coli.
Authors: Tanaka, N. / Nonaka, T. / Tanabe, T. / Yoshimoto, T. / Tsuru, D. / Mitsui, Y.
#1: Journal: To be Published
Title: Crystallization and Preliminary X-Ray Crystallographic Studies of 7Alpha-Hydroxysteroid Dehydrogenase from Escherichia Coli
Authors: Tanaka, N. / Nonaka, T. / Yoshimoto, T. / Tsuru, D. / Mitsui, Y.
#2: Journal: J.Bacteriol. / Year: 1991
Title: Cloning and Sequencing of the 7 Alpha-Hydroxysteroid Dehydrogenase Gene from Escherichia Coli Hb101 and Characterization of the Expressed Enzyme
Authors: Yoshimoto, T. / Higashi, H. / Kanatani, A. / Lin, X.S. / Nagai, H. / Oyama, H. / Kurazono, K. / Tsuru, D.
History
DepositionAug 25, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2013Group: Non-polymer description
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7 ALPHA-HYDROXYSTEROID DEHYDROGENASE
B: 7 ALPHA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8336
Polymers53,6032
Non-polymers2,2304
Water1,874104
1
A: 7 ALPHA-HYDROXYSTEROID DEHYDROGENASE
B: 7 ALPHA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules

A: 7 ALPHA-HYDROXYSTEROID DEHYDROGENASE
B: 7 ALPHA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,66612
Polymers107,2064
Non-polymers4,4608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area22600 Å2
ΔGint-135 kcal/mol
Surface area30320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.590, 81.590, 214.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.154685, -0.844779, -0.51227), (-0.850344, -0.150135, 0.504355), (-0.502979, 0.513622, -0.695129)
Vector: 53.0572, 53.0648, -0.3404)

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Components

#1: Protein 7 ALPHA-HYDROXYSTEROID DEHYDROGENASE


Mass: 26801.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HB101 / Cell line: HB101 / Plasmid: HB101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1
References: UniProt: P25529, UniProt: P0AET8*PLUS, 7alpha-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-CHO / GLYCOCHENODEOXYCHOLIC ACID


Mass: 449.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H43NO5 / Comment: detergent*YM
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 62 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: drop solution was prepared by mixing the protein, reservoir and detergent solutions, buffered by 100mM Tris, at the ratio of 4:3:1.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
24 mg/mlNAD+1drop
328 %(w/v)PEG60001reservoir
4200 mMsodium acetate1reservoir
50.8 %(w/v)beta-octylglucoside1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 19, 1994 / Details: SUPPER LONG MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→76.7 Å / Num. obs: 28878 / % possible obs: 86.9 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.089
Reflection
*PLUS
Num. measured all: 86785
Reflection shell
*PLUS
% possible obs: 64.6 % / Rmerge(I) obs: 0.263

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.25 -10 %
Rwork0.18 --
obs0.18 27967 86.6 %
Displacement parametersBiso mean: 32.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 144 104 4000
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.582
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.382
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.382

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