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- PDB-3nbr: Crystal Structure of Ketosteroid Isomerase D38NP39GD99N from Pseu... -

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Basic information

Entry
Database: PDB / ID: 3nbr
TitleCrystal Structure of Ketosteroid Isomerase D38NP39GD99N 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 / 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
4-ANDROSTENE-3-17-DIONE / Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Ruben, E. / Sunden, F. / Herschlag, D.
CitationJournal: To be Published
Title: Crystal Structure of Ketosteroid Isomerase D38NP39GD99N 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 3, 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

Downloads & links

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Assembly

Deposited unit
A: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9455
Polymers13,3701
Non-polymers5754
Water1,24369
1
A: Steroid Delta-isomerase
hetero molecules

A: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,88910
Polymers26,7402
Non-polymers1,1498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area3330 Å2
ΔGint-91 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.168, 60.168, 142.585
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: 13370.069 Da / Num. of mol.: 1 / Mutation: D38NP39GD99N
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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE


Mass: 286.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 2 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, 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 BL9-110.97946
SYNCHROTRONSSRL BL9-220.97946
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMay 14, 2010
MARMOSAIC 325 mm CCD2CCDJan 5, 2010
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si single crystalSINGLE WAVELENGTHx-ray1
2Si double crystalSINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.73→52.107 Å / Num. all: 16748 / Num. obs: 16748 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.2 % / Rsym value: 0.058 / Net I/σ(I): 30.9
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.023 / Mean I/σ(I) obs: 1.4 / Rsym value: 2.265 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.16 Å29.44 Å
Translation2.16 Å29.44 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMAC5.5.0109refinement
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: 1.73→52.107 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.651 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26483 830 5.1 %RANDOM
Rwork0.23252 ---
obs0.23411 15577 98.15 %-
all-16407 --
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: 43.128 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20.73 Å20 Å2
2--1.47 Å20 Å2
3----2.2 Å2
Refinement stepCycle: LAST / Resolution: 1.73→52.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 36 69 1039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221042
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.25821431
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6075129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43823.47846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.52615153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.089158
X-RAY DIFFRACTIONr_chiral_restr0.1440.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021792
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_it1.3251.5632
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21921010
X-RAY DIFFRACTIONr_scbond_it3.4233410
X-RAY DIFFRACTIONr_scangle_it5.3084.5421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.587 62 -
Rwork0.514 1078 -
obs--95.72 %
Refinement TLS params.Method: refined / Origin x: 5.0188 Å / Origin y: 46.5499 Å / Origin z: 10.6441 Å
111213212223313233
T0.1245 Å20.0118 Å20.012 Å2-0.231 Å20.1418 Å2--0.0959 Å2
L0.5175 °20.3292 °2-0.0802 °2-2.0307 °2-0.0112 °2--0.8951 °2
S0.0085 Å °-0.0356 Å °0.005 Å °0.1994 Å °-0.2172 Å °-0.1029 Å °-0.0306 Å °0.2383 Å °0.2087 Å °

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