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- PDB-3nuv: Crystal structure of ketosteroid isomerase D38ND99N from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 3nuv
TitleCrystal structure of ketosteroid isomerase D38ND99N 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 (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
4-ANDROSTENE-3-17-DIONE / Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Ketosteroid Isomerase D38ND99N from Pseudomonas testosteroni (tKSI) with 4-Androstene-3,17-dione Bound
Authors: Schwans, J. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionJul 7, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8739
Polymers26,8202
Non-polymers1,0537
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-101 kcal/mol
Surface area12050 Å2
MethodPISA
2
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules

A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,74718
Polymers53,6414
Non-polymers2,10614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z+1/31
Buried area11610 Å2
ΔGint-227 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.785, 59.785, 144.499
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-150-

HOH

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Components

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


Mass: 13410.133 Da / Num. of mol.: 2 / Mutation: D38N, 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


Mass: 286.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 1.8 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
111.000H, 1.000K, L10.832
11-1.000H-1.000K, 1.000K, -L20.168
ReflectionResolution: 1.758→29.627 Å / Num. obs: 29522 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.096 / Net I/σ(I): 12.1
Reflection shellResolution: 1.758→1.85 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 0.5 / Rsym value: 1.047 / % possible all: 93.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8CHO

8cho


Resolution: 1.76→29.627 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.037 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1499 5.1 %RANDOM
Rwork0.176 ---
obs0.177 29405 99 %-
all-29405 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--0.86 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.76→29.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 66 178 2126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222163
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9922978
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08923.87898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.415318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7971516
X-RAY DIFFRACTIONr_chiral_restr0.1060.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211680
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_it0.9981.51333
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67522145
X-RAY DIFFRACTIONr_scbond_it2.7583830
X-RAY DIFFRACTIONr_scangle_it4.0634.5833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 110 -
Rwork0.281 1808 -
obs--89.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79860.38460.10480.5331-0.37130.59010.01590.07170.043-0.0271-0.00330.01140.06280.0395-0.01250.0226-0.00670.00910.01830.00260.031434.3064.96613.2698
20.4452-0.2218-0.11580.5434-0.02530.8072-0.0122-0.04070.02930.0408-0.0145-0.05870.00260.03940.02670.029-0.0160.00720.0155-0.00280.036434.3171-4.470425.3127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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