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- PDB-3nhx: Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3nhx
TitleCrystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound
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 domain / Nuclear transport factor 2 (NTF2) 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
4-ANDROSTENE-3-17-DIONE / Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Ruben, E. / Sunden, F. / Herschlag, D.
CitationJournal: To be Published
Title: Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound
Authors: Schwans, J. / Ruben, E. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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

Downloads & links

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Assembly

Deposited unit
A: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,65812
Polymers13,4111
Non-polymers1,24711
Water2,576143
1
A: Steroid Delta-isomerase
hetero molecules

A: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,31624
Polymers26,8222
Non-polymers2,49422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5960 Å2
ΔGint-303 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.280, 61.280, 142.861
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 13411.117 Da / Num. of mol.: 1 / Mutation: D99N
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-ASD / 4-ANDROSTENE-3-17-DIONE / Androstenedione


Mass: 286.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O2 / Comment: hormone*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 2 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
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: 1.59→28.572 Å / Num. obs: 22234 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.072 / Net I/σ(I): 19.9
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 14 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1 / Rsym value: 0.744 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.86 Å28.16 Å
Translation1.86 Å28.16 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M8C

3m8c


Resolution: 1.59→28.57 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.282 / SU ML: 0.053 / SU R Cruickshank DPI: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1133 5.1 %RANDOM
Rwork0.183 ---
obs0.185 22163 100 %-
all-22163 --
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 mean: 24.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.26 Å20 Å2
2--0.51 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.59→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 71 143 1159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0221155
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6152.0081588
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43624.23152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49315176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.608158
X-RAY DIFFRACTIONr_chiral_restr0.2050.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021885
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5481.5703
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39421134
X-RAY DIFFRACTIONr_scbond_it3.8323452
X-RAY DIFFRACTIONr_scangle_it5.5484.5454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 83 -
Rwork0.284 1498 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: 26.2755 Å / Origin y: -5.4454 Å / Origin z: -10.6495 Å
111213212223313233
T0.0338 Å20.0183 Å2-0.0025 Å2-0.027 Å2-0.0116 Å2--0.0144 Å2
L0.7548 °2-0.0737 °2-0.1558 °2-1.1787 °20.3879 °2--1.1262 °2
S0.0488 Å °0.0999 Å °0.0036 Å °-0.098 Å °-0.1353 Å °0.1098 Å °-0.0245 Å °-0.0749 Å °0.0865 Å °

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