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- PDB-3myt: Crystal structure of Ketosteroid Isomerase D38HD99N from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 3myt
TitleCrystal structure of Ketosteroid Isomerase D38HD99N from Pseudomonas testosteroni (tKSI)
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / lipid metabolism / steroid metabolism
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
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.961 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: To be Published
Title: Crystal Structure of Ketosteroid Isomerase D38HD99N from Pseudomonas Testosteroni (tKSI)
Authors: Schwans, J. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionMay 11, 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
B: Steroid Delta-isomerase
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,34526
Polymers53,7374
Non-polymers2,60822
Water5,837324
1
A: Steroid Delta-isomerase
C: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,16212
Polymers26,8682
Non-polymers1,29310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-79 kcal/mol
Surface area11940 Å2
MethodPISA
2
B: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,18314
Polymers26,8682
Non-polymers1,31512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-112 kcal/mol
Surface area12030 Å2
MethodPISA
3
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)112,69052
Polymers107,4738
Non-polymers5,21744
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area25000 Å2
ΔGint-425 kcal/mol
Surface area41110 Å2
MethodPISA
4
B: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)56,34526
Polymers53,7374
Non-polymers2,60822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area11010 Å2
ΔGint-199 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.274, 64.274, 504.199
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11D-407-

HOH

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Components

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


Mass: 13434.177 Da / Num. of mol.: 4 / Mutation: D38HD99N
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.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H18O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 298 K / Method: sitting drop / pH: 7.2
Details: 1.2 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2mM DTT, 1.8mM equilenin, pH 7.2, 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 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: 1.961→29.348 Å / Num. all: 45766 / Num. obs: 45766 / % possible obs: 98.6 % / Redundancy: 11.7 % / Rsym value: 0.142 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.961-2.076.80.8650.80214056559460.310.870.8021.991.1
2.07-2.199.30.620.5861.35740861820.190.620.5863.299.7
2.19-2.349.70.590.5571.35685258700.190.590.5573.799.8
2.34-2.5310.70.3710.3532.25888755230.110.370.3536.299.9
2.53-2.7711.80.2670.2553.16035951300.080.270.2559.1100
2.77-3.112.90.1690.1634.86048746720.050.170.16314.8100
3.1-3.5814.70.1030.0997.76128241820.030.10.09925.2100
3.58-4.3816.20.080.0779.25789835770.020.080.07735.6100
4.38-6.218.20.060.05911.85279129030.010.060.05942100
6.2-29.3517.30.0420.04116.93076217810.010.040.04145.899.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.2 Å29.36 Å
Translation2.2 Å29.36 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data 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: 1.961→29.34 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.873 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.504 / SU ML: 0.133 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28184 2219 5 %RANDOM
Rwork0.22336 ---
obs0.2262 41851 95.17 %-
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: 24.452 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å20 Å2
2--0.9 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.961→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 159 324 4259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224173
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9775703
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6955529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00523.333189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29515623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2391533
X-RAY DIFFRACTIONr_chiral_restr0.1350.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213224
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_it1.2311.52580
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0624146
X-RAY DIFFRACTIONr_scbond_it3.1731593
X-RAY DIFFRACTIONr_scangle_it4.7254.51557
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.961→2.012 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 146 -
Rwork0.304 2667 -
obs--84.3 %
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)
10.18790.0782-0.05210.1140.18290.5609-0.0051-0.00770.01440.00710.01710.01340.03270.0464-0.0120.0063-0.0008-0.00640.02290.00730.022222.409117.63032.3946
20.1534-0.0985-0.19820.2179-0.06330.5009-0.0031-0.0130.0261-0.02120.0257-0.01820.0508-0.0054-0.02260.0237-0.00590.0040.0121-0.00040.015913.50812.3761-39.4264
30.23890.06520.03330.0653-0.12640.4391-0.02870.0343-0.0119-0.00130.0195-0.0028-0.00490.02610.00920.01480.01440.00460.04060.0040.004837.778222.8715-15.426
40.2111-0.0359-0.16470.03190.13290.5690.02810.0067-0.0205-0.0104-0.003-0.0099-0.0405-0.0283-0.02510.0095-0.00020.00180.01370.00470.025-4.559227.68-34.6955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 125
2X-RAY DIFFRACTION2B1 - 125
3X-RAY DIFFRACTION3C1 - 125
4X-RAY DIFFRACTION4D1 - 125

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