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- PDB-6p3l: Crystal Structure of Ketosteroid Isomerase from Mycobacterium has... -

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Basic information

Entry
Database: PDB / ID: 6p3l
TitleCrystal Structure of Ketosteroid Isomerase from Mycobacterium hassiacum (mhKSI)
ComponentsSnoaL-like domain protein
KeywordsISOMERASE / Thermophile
Function / homology
Function and homology information


steroid Delta-isomerase activity / identical protein binding
Similarity search - Function
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
GUANIDINE / SnoaL-like domain protein
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.571 Å
AuthorsYabukarski, F. / Doukov, T. / Pinney, M. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
CitationJournal: Science / Year: 2021
Title: Parallel molecular mechanisms for enzyme temperature adaptation.
Authors: Pinney, M.M. / Mokhtari, D.A. / Akiva, E. / Yabukarski, F. / Sanchez, D.M. / Liang, R. / Doukov, T. / Martinez, T.J. / Babbitt, P.C. / Herschlag, D.
History
DepositionMay 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: SnoaL-like domain protein
B: SnoaL-like domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6995
Polymers27,4852
Non-polymers2143
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-11 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.899, 115.899, 115.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-201-

SO4

31A-353-

HOH

41A-364-

HOH

51B-235-

HOH

61B-246-

HOH

71B-262-

HOH

81B-285-

HOH

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Components

#1: Protein SnoaL-like domain protein / Steroid Delta-isomerase


Mass: 13742.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: ksi, C731_3354, MHAS_03236 / Production host: Escherichia coli (E. coli) / References: UniProt: K5BJ73, steroid Delta-isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.4 to 2 M ammonium sulfate, 10 mM potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.57→38.633 Å / Num. obs: 37638 / % possible obs: 99.9 % / Redundancy: 154.658 % / Biso Wilson estimate: 24.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.262 / Rrim(I) all: 0.262 / Χ2: 0.975 / Net I/σ(I): 29.89 / Num. measured all: 5821036 / Scaling rejects: 4140
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.57-1.61151.42611.2040.51412031272927210.36811.24199.7
1.61-1.65153.4649.6430.68408522266226620.4669.674100
1.65-1.7140.0187.5990.97361666259025830.5887.62699.7
1.7-1.75161.2575.4651.51405885252225170.7595.48199.8
1.75-1.81162.0764.2952.03394816243724360.8214.309100
1.81-1.88161.0572.9753.07380577236923630.8892.98499.7
1.88-1.95160.5842.0674.73368701229622960.9572.074100
1.95-2.03158.3891.4576.96349722220822080.9721.462100
2.03-2.12151.5591.0749.4321760212621230.9841.07799.9
2.12-2.22146.2310.77712.83298896204520440.990.779100
2.22-2.34165.0440.62716.81319031193419330.9950.62999.9
2.34-2.48162.9050.48321.72301049185018480.9970.48599.9
2.48-2.65160.1910.35829.04278573173917390.9980.359100
2.65-2.86156.3440.24741.13254371162716270.9990.247100
2.86-3.14137.7050.15460.382073841507150610.15499.9
3.14-3.51157.8530.09796.952184691384138410.097100
3.51-4.05157.7490.063138.991940311230123010.063100
4.05-4.96149.7510.044175.511590361062106210.045100
4.96-7.02134.540.047157.1111287983983910.047100
7.02-38.633142.4310.025244.647363752251710.02599

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.571→38.633 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.24
RfactorNum. reflection% reflection
Rfree0.2113 1757 4.76 %
Rwork0.1692 --
obs0.1711 36950 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.62 Å2 / Biso mean: 35.906 Å2 / Biso min: 8.59 Å2
Refinement stepCycle: final / Resolution: 1.571→38.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 23 207 2044
Biso mean--56.51 38.47 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062144
X-RAY DIFFRACTIONf_angle_d0.8312935
X-RAY DIFFRACTIONf_chiral_restr0.056316
X-RAY DIFFRACTIONf_plane_restr0.005400
X-RAY DIFFRACTIONf_dihedral_angle_d12.051281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5712-1.61370.2884950.24842183227881
1.6137-1.66120.3221440.25552627277198
1.6612-1.71480.33161310.23392688281999
1.7148-1.77610.24231550.219326822837100
1.7761-1.84720.27181380.181627072845100
1.8472-1.93130.22681480.169127162864100
1.9313-2.03310.20741300.151627172847100
2.0331-2.16050.19931430.140627232866100
2.1605-2.32730.17551350.133527482883100
2.3273-2.56140.17181210.139427772898100
2.5614-2.9320.20651520.153627682920100
2.932-3.69350.2041130.163828582971100
3.6935-38.64470.21011520.185729993151100

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