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- PDB-6p44: Crystal Structure of Ketosteroid Isomerase D38N mutant from Mycob... -

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Basic information

Entry
Database: PDB / ID: 6p44
TitleCrystal Structure of Ketosteroid Isomerase D38N mutant from Mycobacterium hassiacum (mhKSI) bound to 3,4-dinitrophenol
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
3,4-dinitrophenol / GUANIDINE / SnoaL-like domain protein
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.251 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 25, 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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)28,1618
Polymers27,4832
Non-polymers6786
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-22 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.193, 116.193, 116.193
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-202-

SO4

21A-202-

SO4

31A-396-

HOH

41A-411-

HOH

51A-416-

HOH

61A-436-

HOH

71B-340-

HOH

81B-366-

HOH

91B-370-

HOH

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Components

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


Mass: 13741.282 Da / Num. of mol.: 2 / Mutation: D38N
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-DNX / 3,4-dinitrophenol


Mass: 184.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N2O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GAI / GUANIDINE


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


Mass: 18.015 Da / Num. of mol.: 281 / 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
Temp details: Room temperature

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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: Feb 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.25→38.731 Å / Num. obs: 74115 / % possible obs: 100 % / Redundancy: 77.518 % / Biso Wilson estimate: 14.09 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.212 / Rrim(I) all: 0.213 / Χ2: 1.004 / Net I/σ(I): 20.38 / Num. measured all: 5745249 / Scaling rejects: 1325
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
1.25-1.2876.3755.9890.55410746538353780.3326.02999.9
1.28-1.3277.3875.0520.77406436525552520.4765.08599.9
1.32-1.3676.864.2871.01394139512851280.5254.315100
1.36-1.476.0933.5341.37378181497349700.6363.55799.9
1.4-1.4471.3062.8931.74344339483048290.7362.913100
1.44-1.4980.9492.2812.48379815469246920.852.295100
1.49-1.5580.4681.6783.54362590450745060.9021.688100
1.55-1.6180.0571.2325.02349851437143700.9461.24100
1.61-1.6979.2541.026.21330488417141700.9641.027100
1.69-1.7774.3220.7328.58299371402940280.9810.737100
1.77-1.8677.3020.51212.43294599381138110.9910.515100
1.86-1.9882.4030.34119.52299040363136290.9970.34399.9
1.98-2.1181.220.23428.22278584343034300.9980.236100
2.11-2.2879.620.17536.83254705319931990.9990.176100
2.28-2.573.2140.14542.65216128295229520.9990.146100
2.5-2.876.4870.1155.91206132269526950.9990.11100
2.8-3.2380.6460.07283.61938722404240410.072100
3.23-3.9577.4260.049113.261594202059205910.049100
3.95-5.5969.6090.039122.551136721633163310.04100
5.59-38.73174.6340.036132.27314198598010.03799.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P3L

6p3l


Resolution: 1.251→38.731 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1793 3565 4.86 %
Rwork0.1529 69762 -
obs0.1541 73327 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.43 Å2 / Biso mean: 21.6715 Å2 / Biso min: 9.89 Å2
Refinement stepCycle: final / Resolution: 1.251→38.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 92 308 2228
Biso mean--27.2 30.87 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062532
X-RAY DIFFRACTIONf_angle_d0.8553476
X-RAY DIFFRACTIONf_chiral_restr0.078357
X-RAY DIFFRACTIONf_plane_restr0.006514
X-RAY DIFFRACTIONf_dihedral_angle_d13.51971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2505-1.26770.30211150.28382273238882
1.2677-1.28580.29241350.27692648278396
1.2858-1.3050.28391560.26662736289298
1.305-1.32540.30281310.26172748287999
1.3254-1.34710.28961320.250227682900100
1.3471-1.37030.27881480.246827502898100
1.3703-1.39530.29061600.239927522912100
1.3953-1.42210.26491370.222627862923100
1.4221-1.45110.27331670.204827512918100
1.4511-1.48270.22231430.189527912934100
1.4827-1.51720.23161450.169427732918100
1.5172-1.55510.20361400.151728062946100
1.5551-1.59720.17431280.139728112939100
1.5972-1.64420.19231460.134527962942100
1.6442-1.69720.16881360.132228072943100
1.6972-1.75790.16251620.126628042966100
1.7579-1.82830.16751440.128128062950100
1.8283-1.91150.15041600.124427982958100
1.9115-2.01220.15291240.12228342958100
2.0122-2.13830.16041530.116928432996100
2.1383-2.30340.1271460.116328472993100
2.3034-2.53510.14191220.12628783000100
2.5351-2.90190.14451590.142528753034100
2.9019-3.65560.17211220.141929663088100
3.6556-38.74960.18651540.173931153269100

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