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- PDB-6uad: Ketosteroid isomerase (C. testosteroni) with truncated & designed... -

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Basic information

Entry
Database: PDB / ID: 6uad
TitleKetosteroid isomerase (C. testosteroni) with truncated & designed loop for precise positioning of a catalytic E38
ComponentsKetosteroid isomerase with truncated and designed loop
KeywordsISOMERASE / computational protein design / Rosetta / kinematic closure
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 / NTF2-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKundert, K. / Thompson, M.C. / Liu, L. / Fraser, J.S. / Kortemme, T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM110089 United States
National Science Foundation (NSF, United States)DBI-1564692 United States
CitationJournal: To Be Published
Title: Ketosteroid isomerase (C. testosteroni) with truncated & designed loop for precise positioning of a catalytic E38
Authors: Kundert, K. / Thompson, M.C. / Liu, L. / Fraser, J.S. / Kortemme, T.
History
DepositionSep 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketosteroid isomerase with truncated and designed loop
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4135
Polymers13,4381
Non-polymers9754
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.150, 53.150, 178.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

#1: Protein Ketosteroid isomerase with truncated and designed loop


Mass: 13438.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00947*PLUS
#2: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 1.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2016
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.75→46.03 Å / Num. obs: 15833 / % possible obs: 99.2 % / Redundancy: 9.7 % / Biso Wilson estimate: 19.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.013 / Net I/σ(I): 34.2
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4 / Num. unique obs: 1048 / CC1/2: 0.939 / Rpim(I) all: 0.159 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
xia2data reduction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.03 Å / SU ML: 0.1592 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.4302
RfactorNum. reflection% reflection
Rfree0.2095 1577 10.01 %
Rwork0.1742 --
obs0.1778 15756 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.79 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 66 163 1161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421114
X-RAY DIFFRACTIONf_angle_d1.22961540
X-RAY DIFFRACTIONf_chiral_restr0.0787176
X-RAY DIFFRACTIONf_plane_restr0.0076198
X-RAY DIFFRACTIONf_dihedral_angle_d20.6288633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.28521300.20831172X-RAY DIFFRACTION92.21
1.81-1.870.23351380.21041233X-RAY DIFFRACTION97.86
1.87-1.950.28021410.19551256X-RAY DIFFRACTION99.86
1.95-2.040.23631400.19171268X-RAY DIFFRACTION99.86
2.04-2.140.21271410.16561266X-RAY DIFFRACTION100
2.14-2.280.20261390.16261280X-RAY DIFFRACTION99.86
2.28-2.450.21421440.17291288X-RAY DIFFRACTION100
2.45-2.70.24091470.17321299X-RAY DIFFRACTION99.93
2.7-3.090.20661430.18171311X-RAY DIFFRACTION100
3.09-3.890.1961510.15951338X-RAY DIFFRACTION99.93
3.89-46.030.17791630.17141468X-RAY DIFFRACTION99.94
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)
13.178575532060.4156549113152.144403547450.8511227845321.381124434232.995733600140.09023645670340.1711139667510.320613642185-0.638456574527-0.169012570410.175289008085-0.2553122402810.08916889338870.0474940289640.429851025007-0.0173978924095-0.02879077200780.1114210823280.01675278523630.215374355162-21.793124450123.5852523353.0313583678
20.598480544902-0.1430927024840.07859083100061.382813671541.011025196171.66711272613-0.0174063200430.0263659471522-0.0389843871014-0.584677288144-0.03489005642080.00289482503066-0.4537063597590.002780721667310.02777590128170.314131960755-0.01610853582430.00156909629780.0986174104302-0.004442409875920.1607262402-23.746266716212.35530761670.716947643396
32.871319500561.818293308631.969464413721.34081058361.719789763152.523548660850.02547377586730.162166970237-0.387059984749-0.275379804231-0.4004265351790.513157760181-0.113878670334-0.453680156779-0.2627706820060.2293549445050.0798621661339-0.1619730480830.298531060037-0.1612804738140.403000964401-41.74919800987.26870767713-0.768174803527
45.283425876031.80272974348-0.6323145329051.81626413827-0.05176184799371.46204105118-0.3072387006710.0429866116243-0.19012293623-0.5278154638840.130149127882-0.215241781359-0.1847292087820.1784347603490.06648824702310.21956915285-0.03645905780780.03707283062820.092667353813-0.01223129979850.16699505753-18.257392880413.75669069358.09226157179
57.774517388510.5762430256183.549506005925.27970042806-2.875724447628.01268604817-0.306331318109-0.258466488712-0.149936254766-0.2056006417840.08563583954810.60938157133-0.0885623643886-1.077397028570.06726483286920.13282390428-0.00512169986762-0.04819426284230.197740058627-0.06929646003730.231460003315-36.71883152085.998670221889.86341637066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 94 )
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 114 )
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 122 )

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