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- PDB-1fmc: 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE COMPLEX WITH NADH AND 7-OXO ... -

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Basic information

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


bile acid catabolic process / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / 7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase (NAD+) activity / 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 / SYNCHROTRON / Resolution: 1.8 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: Acta Crystallogr.,Sect.D / Year: 1996
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
DepositionApr 26, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 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

Downloads & links

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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
Water4,360242
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 area22690 Å2
ΔGint-135 kcal/mol
Surface area30510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.650, 81.650, 214.600
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: (-0.15963, -0.842545, -0.514428), (-0.846838, -0.150935, 0.509984), (-0.50733, 0.517046, -0.689406)
Vector: 53.163, 53.0755, -0.2978)

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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
Details: LIGANDS ARE NADH AND 7-OXO GLYCOCHENODEOXYCHOLIC ACID (CHO)
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HB101 / Description: COLON BACILLUS / Cell line: CHO / Plasmid: HB101 / Production host: Escherichia coli (E. coli)
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.: 242 / 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: 3.34 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 sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Apr 23, 1995 / Details: BENT CYLINDER
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→76.7 Å / Num. obs: 57290 / % possible obs: 84 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.085
Reflection
*PLUS
Num. measured all: 221323
Reflection shell
*PLUS
% possible obs: 66.1 % / Rmerge(I) obs: 0.397

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.252 -10 %
Rwork0.207 --
obs0.207 56376 83.8 %
Displacement parametersBiso mean: 26.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 144 242 4138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.602
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.472
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: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.472

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