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- PDB-5wp2: 1.44 Angstrom crystal structure of CYP121 from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 5wp2
Title1.44 Angstrom crystal structure of CYP121 from Mycobacterium tuberculosis in complex with substrate and CN
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / complex / P450
Function / homology
Function and homology information


mycocyclosin synthase / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Chem-YTT / Cytochrome P450 121 CYP121 / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.439 Å
AuthorsFielding, A. / Dornevil, K. / Liu, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108988 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107529 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Probing Ligand Exchange in the P450 Enzyme CYP121 from Mycobacterium tuberculosis: Dynamic Equilibrium of the Distal Heme Ligand as a Function of pH and Temperature.
Authors: Fielding, A.J. / Dornevil, K. / Ma, L. / Davis, I. / Liu, A.
History
DepositionAug 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5288
Polymers43,1751
Non-polymers1,3537
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-78 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.856, 77.856, 263.615
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-880-

HOH

21A-896-

HOH

31A-942-

HOH

41A-1004-

HOH

51A-1085-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mycocyclosin synthase / Cytochrome P450 121 / Cytochrome P450 MT2


Mass: 43174.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp121, MT2336 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WPP6, UniProt: A0A0T9WNE5*PLUS, EC: 1.14.21.9

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Non-polymers , 5 types, 597 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-YTT / (3S,6S)-3,6-bis(4-hydroxybenzyl)piperazine-2,5-dione / cyclo(tyrosyl-tyrosyl) / Cyclo(tyr-tyr)


Mass: 326.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O4
#4: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES, pH 6, 2 M ammonium sulfate / PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 86668 / % possible obs: 100 % / Redundancy: 19.5 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.022 / Rrim(I) all: 0.108 / Χ2: 0.929 / Net I/σ(I): 6.9 / Num. measured all: 1690455
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.44-1.4917.20.96184510.8480.230.990.5699.9
1.49-1.5519.60.76285240.9330.1720.7820.582100
1.55-1.62200.59885290.9540.1340.6140.606100
1.62-1.7118.70.43385180.9740.10.4450.659100
1.71-1.8119.80.30985610.9860.0690.3170.751100
1.81-1.9518.80.21785900.9920.0490.2230.915100
1.95-2.1516.80.15186190.9930.0370.1561.065100
2.15-2.4618.30.11287170.9970.0260.1151.141100
2.46-3.118.70.08288090.9980.0190.0841.047100
3.1-5026.60.08793500.9990.0160.0881.59899.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N40

1n40


Resolution: 1.439→22.581 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1949 4338 5.02 %
Rwork0.1794 82147 -
obs0.1802 86485 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.67 Å2 / Biso mean: 22.9722 Å2 / Biso min: 10.22 Å2
Refinement stepCycle: final / Resolution: 1.439→22.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 137 590 3737
Biso mean--18.33 33.3 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073307
X-RAY DIFFRACTIONf_angle_d0.9064526
X-RAY DIFFRACTIONf_chiral_restr0.075521
X-RAY DIFFRACTIONf_plane_restr0.006581
X-RAY DIFFRACTIONf_dihedral_angle_d23.4191254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4395-1.45580.27651290.267726542783
1.4558-1.47290.30391260.254127402866
1.4729-1.49090.29981350.24326482783
1.4909-1.50980.29271500.24226982848
1.5098-1.52960.25771400.229826912831
1.5296-1.55060.25231480.236626882836
1.5506-1.57270.23981190.217927202839
1.5727-1.59620.26571510.223826672818
1.5962-1.62110.26851510.220527142865
1.6211-1.64770.25671570.222626792836
1.6477-1.67610.25331420.219626772819
1.6761-1.70660.25691470.214227082855
1.7066-1.73940.24421450.207626912836
1.7394-1.77490.24031250.204627592884
1.7749-1.81340.2531460.205226852831
1.8134-1.85560.24551370.207227342871
1.8556-1.9020.24131640.198626872851
1.902-1.95340.21981580.191827092867
1.9534-2.01080.21731580.189626912849
2.0108-2.07570.21161390.188127322871
2.0757-2.14980.211570.178227252882
2.1498-2.23580.21461570.178427402897
2.2358-2.33750.19121330.174227602893
2.3375-2.46060.18441360.172427732909
2.4606-2.61450.18581530.177427682921
2.6145-2.81610.20851280.182628032931
2.8161-3.09880.18451440.17628082952
3.0988-3.54570.1891490.161628452994
3.5457-4.46160.12741560.13928663022
4.4616-22.58380.1521580.164230873245

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