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- PDB-2hsd: THE REFINED THREE-DIMENSIONAL STRUCTURE OF 3ALPHA,20BETA-HYDROXYS... -

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Basic information

Entry
Database: PDB / ID: 2hsd
TitleTHE REFINED THREE-DIMENSIONAL STRUCTURE OF 3ALPHA,20BETA-HYDROXYSTEROID DEHYDROGENASE AND POSSIBLE ROLES OF THE RESIDUES CONSERVED IN SHORT-CHAIN DEHYDROGENASES
Components3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


C21-steroid hormone metabolic process / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity
Similarity search - Function
short chain dehydrogenase / PKS_KR / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesStreptomyces exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.64 Å
AuthorsGhosh, D. / Duax, W.L.
Citation
Journal: Structure / Year: 1994
Title: The refined three-dimensional structure of 3 alpha,20 beta-hydroxysteroid dehydrogenase and possible roles of the residues conserved in short-chain dehydrogenases.
Authors: Ghosh, D. / Wawrzak, Z. / Weeks, C.M. / Duax, W.L. / Erman, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Three-Dimensional Structure of Holo 3Alpha,20Beta-Hydroxysteroid Dehydrogenase: A Member of a Short-Chain Dehydrogenase Family
Authors: Ghosh, D. / Weeks, C.M. / Grochulski, P. / Duax, W.L. / Erman, M. / Rimsay, R.L. / Orr, J.C.
History
DepositionMar 28, 1994Processing site: BNL
SupersessionAug 31, 1994ID: 1HSD
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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: 3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE
B: 3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE
C: 3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE
D: 3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7608
Polymers105,1064
Non-polymers2,6544
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21000 Å2
ΔGint-133 kcal/mol
Surface area29780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.200, 106.200, 203.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.58331, 0.79126, -0.18345), (0.79184, 0.50364, -0.34544), (-0.18094, -0.34676, -0.92034)141.11292, -43.24774, 134.86388
2given(-0.38575, -0.49491, -0.77863), (-0.50082, -0.59645, 0.62724), (-0.77484, 0.63191, -0.01778)154.58894, -12.6126, 130.38321
3given(-0.03308, -0.29237, 0.95573), (-0.29467, -0.9109, -0.28886), (0.95503, -0.29118, -0.05602)17.2712, 27.73076, -8.88892
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *C*. THE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *D*.

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Components

#1: Protein
3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE


Mass: 26276.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces exfoliatus (bacteria)
References: UniProt: P19992, 3alpha(or 20beta)-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: 2BHD_STREX THE FOLLOWING RESIDUES ARE MISSING FROM THE N-TERMINUS OF A CHAINS; SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY MET 1 RESIDUES OF CHAIN A, B, C, AND D MISSING FROM THE ATOM LIST SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ASN 212 SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 109 GLU A 109 ASP 109 GLU B 109 ASP 109 GLU C 109 ASP 109 GLU D 109

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion, hanging drop / Details: referred to J.Biol.Chem. 261.1306-1308 1986
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.40-1.60 Mphosphate1reservoir
213-15 mg/mlprotein1drop
30.7 Mphosphate1drop

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.64→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.188 28327
Refinement stepCycle: LAST / Resolution: 2.64→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7368 0 176 0 7544
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.035
X-RAY DIFFRACTIONp_planar_d0.05

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