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- PDB-3nm2: Crystal Structure of Ketosteroid Isomerase D38EP39GV40GS42G from ... -

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Basic information

Entry
Database: PDB / ID: 3nm2
TitleCrystal Structure of Ketosteroid Isomerase D38EP39GV40GS42G from Pseudomonas Testosteroni (tKSI)
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


steroid Delta-isomerase / steroid Delta-isomerase activity / steroid metabolic process
Similarity search - Function
Steroid delta5-4-isomerase / Ketosteroid isomerase / Nuclear transport factor 2 (NTF2) domain / 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
Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.887 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: To be Published
Title: Crystal Structure of Ketosteroid Isomerase D38EP39GV40GS42G from Pseudomonas Testosteroni (tKSI)
Authors: Schwans, J. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 6, 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_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: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8907
Polymers13,3141
Non-polymers5766
Water1,53185
1
A: Steroid Delta-isomerase
hetero molecules

A: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,78114
Polymers26,6282
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area4070 Å2
ΔGint-143 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.356, 59.356, 141.974
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Steroid Delta-isomerase / Delta(5)-3-ketosteroid isomerase


Mass: 13313.960 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: ATC 11996 / Gene: ksi / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00947, steroid Delta-isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 1 mM DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97946
SYNCHROTRONSSRL BL9-220.97946
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDMar 25, 2010
MARMOSAIC 325 mm CCD2CCDMar 24, 2010
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si double crystalSINGLE WAVELENGTHx-ray1
2Si double crystalSINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.887→29.678 Å / Num. all: 12614 / Num. obs: 12614 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 29.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 21.6
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.887-1.9910.80.9830.81882917410.98397.2
1.99-2.1114.10.6821.12374016870.682100
2.11-2.25140.411.92240616050.41100
2.25-2.44140.2772.82100615020.277100
2.44-2.6713.90.1764.41922713870.176100
2.67-2.9813.70.1047.31756812790.104100
2.98-3.4413.50.05912.11535711380.059100
3.44-4.2213.20.03817.6130709900.038100
4.22-5.9712.60.03220.399777920.032100
5.97-29.678110.0292154014930.02999.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.15 Å29.68 Å
Translation2.15 Å29.68 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
Web-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8CHO

8cho


Resolution: 1.887→29.678 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2559 / WRfactor Rwork: 0.1919 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8112 / SU B: 8.536 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1527 / SU Rfree: 0.1605 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 610 4.9 %RANDOM
Rwork0.2024 ---
all0.2048 12563 --
obs0.2048 12563 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 151.45 Å2 / Biso mean: 37.019 Å2 / Biso min: 17.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.71 Å20 Å2
2--1.41 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 1.887→29.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 30 85 1053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221028
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.9691403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9525134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21523.7548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21115156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.854158
X-RAY DIFFRACTIONr_chiral_restr0.1520.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021798
X-RAY DIFFRACTIONr_mcbond_it1.391.5647
X-RAY DIFFRACTIONr_mcangle_it2.30121034
X-RAY DIFFRACTIONr_scbond_it3.8583381
X-RAY DIFFRACTIONr_scangle_it6.0854.5369
LS refinement shellResolution: 1.887→1.936 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 54 -
Rwork0.291 791 -
all-845 -
obs--94.52 %
Refinement TLS params.Method: refined / Origin x: 5.2532 Å / Origin y: 45.773 Å / Origin z: 10.4249 Å
111213212223313233
T0.0694 Å20.0059 Å2-0.0079 Å2-0.0144 Å20.0131 Å2--0.016 Å2
L0.9329 °20.8057 °2-0.2519 °2-2.1381 °2-0.6934 °2--2.0741 °2
S0.0331 Å °-0.0727 Å °-0.0862 Å °0.229 Å °-0.1089 Å °-0.1629 Å °-0.1203 Å °0.0031 Å °0.0758 Å °

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