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- PDB-1gs3: High resolution crystal structure of PI delta-5-3-Ketosteroid Iso... -

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Basic information

Entry
Database: PDB / ID: 1gs3
TitleHigh resolution crystal structure of PI delta-5-3-Ketosteroid Isomerase mutants Y30F/Y55F/Y115F/D38N (Y32F/Y57F/Y119F/D40N, PI numbering)complexed with equilenin at 2.1 A resolution
ComponentsSTEROID DELTA-ISOMERASE
KeywordsISOMERASE
Function / homology
Function and homology information


steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process
Similarity search - Function
Ketosteroid isomerase / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShin, S. / Ha, N.-C. / Oh, B.-H.
CitationJournal: To be Published
Title: Contribution of a Low-Barrier Hydrogen Bond to Catalysis by Delta-5-3-Ketosteroid Isomerase is not Extremely High Compared to that of an Ordinary Hydrogen Bond. Low-Barrier Hydrogen Bond of Pi Ksi
Authors: Choi, G. / Shin, S. / Yun, S.-G. / Jang, D.S. / Nam, G.H. / Hong, B.-H. / Lee, H.-C. / Oh, B.-H. / Choi, K.Y.
History
DepositionDec 27, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7662
Polymers14,5001
Non-polymers2661
Water68538
1
A: STEROID DELTA-ISOMERASE
hetero molecules

A: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5324
Polymers28,9992
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)36.319, 96.237, 74.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein STEROID DELTA-ISOMERASE / DELTA-5-3-KETOSTEROID ISOMERASE


Mass: 14499.515 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: BIOTYPE B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION TYR 32 PHE,TYR 57 PHE, TYR 119 PHE,ASP 40 ASN

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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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growpH: 4.6 / Details: pH 4.60

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 121141 / % possible obs: 92.4 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rsym value: 0.143 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.314 / % possible all: 90.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E3N

1e3n
PDB Unreleased entry


Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 -5 %RANDOM
Rwork0.2129 ---
obs0.2129 121141 92.4 %-
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 20 38 1015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007485
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_deg1.25064
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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

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