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- PDB-8c9i: Cytochrome P450 CYP141A1 (Rv3121) from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8c9i
TitleCytochrome P450 CYP141A1 (Rv3121) from Mycobacterium tuberculosis
ComponentsCytochrome P450 141
KeywordsOXIDOREDUCTASE / Cytochrome P450 Heme-containing
Function / homology
Function and homology information


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 / plasma membrane
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
HEME B/C / Putative cytochrome P450 141
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSelvam, I.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R505870/1, BB/I019669/1, BB/I019227/1, BB/R009775/1 United Kingdom
University of Cambridge United Kingdom
CitationJournal: To Be Published
Title: 2.05 Angstrom structure of cytochrome P450 CYP141A1 (Rv3121) from Mycobacterium tuberculosis
Authors: Selvam, I.R.
History
DepositionJan 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 141
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3942
Polymers43,7761
Non-polymers6191
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, CYP141A1 behaves as a monomer in solution via SAXS, AUC and gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-24 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.019, 95.019, 264.785
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

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Components

#1: Protein Cytochrome P450 141


Mass: 43775.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: cyp141, Rv3121, MTCY164.31 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WPL7, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.94 Å3/Da / Density % sol: 68.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.01 M cobalt (II) chloride hexahydrate 0.2 M magnesium chloride hexahydrate 0.1 M bis-tris propane pH 8.0 22.5% v/v PEG smear medium 2% v/v/ glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→82.3 Å / Num. obs: 45347 / % possible obs: 96 % / Redundancy: 19.3 % / Biso Wilson estimate: 45.55 Å2 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.03 / Rrim(I) all: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 18.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3784 / CC1/2: 0.83 / CC star: 0.95 / Rpim(I) all: 0.36 / Rrim(I) all: 1.58 / % possible all: 85.6

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Processing

Software
NameVersionClassification
DIALSdata reduction
DIALSdata scaling
Cootmodel building
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→82.29 Å / SU ML: 0.2146 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 23.3299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 2187 5.01 %
Rwork0.2066 41435 -
obs0.2078 43622 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.32 Å2
Refinement stepCycle: LAST / Resolution: 2.05→82.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 43 174 3255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213170
X-RAY DIFFRACTIONf_angle_d0.61584346
X-RAY DIFFRACTIONf_chiral_restr0.0391496
X-RAY DIFFRACTIONf_plane_restr0.0032573
X-RAY DIFFRACTIONf_dihedral_angle_d7.1419436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.28641390.26912179X-RAY DIFFRACTION83.96
2.09-2.140.29991460.24842299X-RAY DIFFRACTION88.24
2.14-2.20.2471170.22482436X-RAY DIFFRACTION91.31
2.2-2.260.27871300.23172432X-RAY DIFFRACTION92.22
2.26-2.320.28531230.26212479X-RAY DIFFRACTION93.73
2.32-2.40.36891300.26572527X-RAY DIFFRACTION95.47
2.4-2.480.26181340.21722588X-RAY DIFFRACTION97.25
2.48-2.580.23271260.20372602X-RAY DIFFRACTION97.74
2.58-2.70.24361260.21382648X-RAY DIFFRACTION98.61
2.7-2.840.25031210.23012671X-RAY DIFFRACTION99.08
2.84-3.020.33971490.27012661X-RAY DIFFRACTION99.47
3.02-3.250.30221260.23482698X-RAY DIFFRACTION99.58
3.25-3.580.23811400.20782732X-RAY DIFFRACTION99.97
3.58-4.10.20721270.17982761X-RAY DIFFRACTION100
4.1-5.160.16751760.14752754X-RAY DIFFRACTION100
5.16-82.290.20481770.21652968X-RAY DIFFRACTION99.59
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)
12.317511317930.01455220201760.5458031148071.751098459110.4095986292711.61325273381-0.1346684915310.1172880160640.584959613488-0.0055630391952-0.0394975136893-0.0302421135192-0.873972463586-0.1152328558630.1535881195150.7610167801740.16129302134-0.132800746350.5162485425220.0140018261990.6685186966977.7836993865671.4612278935148.515408266
22.804888707890.0240682932625-0.04734864391711.682654389590.3212708070752.12859965352-0.1224503229730.447899779194-0.0986295336267-0.194541704967-0.08494364499180.174030172566-0.35554071308-0.1935375552150.212599939490.3987905516920.0303210402878-0.08010509010110.633154429736-0.04192768462540.3644780347935.6339784723950.8908859693136.122706228
33.596734417811.29893472215-0.341893675692.56292405558-0.178438187111.42662946915-0.2567274794630.585747955076-0.151307034959-0.555043221110.0503164823066-0.0653314915084-0.3347941350670.308068491390.1620148856260.452303037951-0.0620559772010.01814240142080.7390112701260.00813786686870.35814862466721.087475313950.5674387344128.419629355
41.85903856272-0.88260003083-0.0590500218775.703796128310.4236728132271.17929463104-0.2759212493460.700611807450.533467602808-0.03447767376180.590773389692-0.888084261017-0.5787964180640.481399101475-0.03785527455190.670171735331-0.0211121487089-0.08993327731730.7966862300340.1105233641850.50113883021710.9267723461.4247607316125.899842061
54.150029125672.673796314140.2303105476152.580789696890.7180698409031.41334695684-0.6364962156390.9550423781360.435470990228-1.254910681540.5530238758670.742668109606-0.5323709299220.08124823717280.1078212563760.7514678376340.0042766051774-0.1493419358120.8974155284720.08824845901290.4490484095971.8271973502157.750952827121.501244575
66.671092875671.51602023095-3.22043590289E-52.71297581051-0.8054755771883.81938618831-0.09390094123810.604868184432-0.718345320451-0.05910761755660.167840595698-0.03400524179010.485205752037-0.31716274894-0.07082938363660.3148799499570.0163838203028-0.07743689864110.767719779933-0.1445443723940.482313764218-4.6184935886842.2044142736129.594387299
74.54550795395-0.2445730359121.046370729921.698345973980.3405887945582.04123007302-0.0153206694625-0.06574193860440.446865592149-0.144206236542-0.1108642208550.448421112356-0.27595116904-0.5789157252630.07413339490810.293427390096-0.0135712092835-0.03597213180690.3391254940370.02470277727110.25048722174811.626717362955.6404857952135.47054432
82.735436086790.129936265087-0.7076087378272.407675888271.12735023642.7522437721-0.254936561067-0.5446962022820.1942727855080.2252129530230.315875007379-0.3806465135430.05669066159880.657022417448-0.03396182278550.436772511479-0.0469520141773-0.05477793546230.609397542864-0.04398755250950.48707185129726.934969380150.437509465149.583999603
91.14191943470.26136129311.079410719211.39515524738-0.4183317187051.53268748638-0.243751439713-0.1790767929010.449754973637-0.007984432341570.1261327990870.0681387745867-0.654465968475-0.482194741660.07752730960890.624084007990.191575996295-0.1472600523590.562956906702-0.02623430341240.569631420713.3598363890468.4762595545149.134856747
101.972597794-0.03821331835680.1151617142830.7141921651430.3919136228433.16247825782-0.2038840411960.06836301459790.1304685914810.05355878652390.107188012737-0.122686480393-0.2889617016140.1365029997260.1225571925860.351156690970.0275340530723-0.04935828374840.436755750973-0.03364818088360.44735571859117.291180706852.3906960866149.29961269
113.32817218782-0.0598597216794-0.4492664398373.81829301467-0.5552624436332.27532183929-0.2340679256170.575610078140.791662828243-0.3553913191020.044209983125-0.754291987387-0.6223255693050.5967712052280.09402768413820.469435128735-0.186531575347-0.03070476234540.6085441991890.04723330299640.47545701270329.121734958660.9854622417135.900054832
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 68 )6 - 681 - 63
22chain 'A' and (resid 69 through 129 )69 - 12964 - 124
33chain 'A' and (resid 130 through 156 )130 - 156125 - 151
44chain 'A' and (resid 157 through 177 )157 - 177152 - 172
55chain 'A' and (resid 178 through 201 )178 - 201173 - 196
66chain 'A' and (resid 202 through 222 )202 - 222197 - 217
77chain 'A' and (resid 223 through 254 )223 - 254218 - 249
88chain 'A' and (resid 255 through 279 )255 - 279250 - 274
99chain 'A' and (resid 280 through 317 )280 - 317275 - 312
1010chain 'A' and (resid 318 through 367 )318 - 367313 - 362
1111chain 'A' and (resid 368 through 401 )368 - 401363 - 396

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