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- PDB-3r9c: Crystal structure of Mycobacterium smegmatis CYP164A2 with Econaz... -

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Basic information

Entry
Database: PDB / ID: 3r9c
TitleCrystal structure of Mycobacterium smegmatis CYP164A2 with Econazole bound
ComponentsCytochrome P450 164A2
KeywordsOXIDOREDUCTASE / Cytochrome P450 / monooxygenase
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
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
Chem-ECL / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 107B1
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å
AuthorsAgnew, C.R.J. / Kelly, S.L. / Brady, R.L.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2012
Title: An enlarged, adaptable active site in CYP164 family P450 enzymes, the sole P450 in Mycobacterium leprae.
Authors: Agnew, C.R. / Warrilow, A.G. / Burton, N.M. / Lamb, D.C. / Kelly, S.L. / Brady, R.L.
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Non-polymer description
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 164A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,33111
Polymers45,5561
Non-polymers1,77510
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.790, 85.790, 121.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 164A2


Mass: 45555.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Genus: MSMEG_6312 / Strain: ATCC 700084 / Production host: Escherichia coli (E. coli)
References: UniProt: A0R5U2, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 5 types, 125 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-ECL / 1-[(2R)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole / R-Econazole


Mass: 381.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H15Cl3N2O
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.23 Å3/Da / Density % sol: 44.75 % / Mosaicity: 0.95 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M Potassium thiocyanate, 30% w/v PEG 2000MME, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.14→70.16 Å / Num. all: 22538 / Num. obs: 22538 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Rsym value: 0.109 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.14-2.2611.70.5220.5011.53556830410.1430.5220.5015.792.1
2.26-2.3911.40.3860.372.13394229850.1070.3860.377.295.4
2.39-2.5611.20.2980.2852.73248228910.0830.2980.2858.896.9
2.56-2.7611.40.2120.2033.83072426990.0590.2120.20311.697.1
2.76-3.0311.50.1510.1455.32876025070.0430.1510.14515.198.5
3.03-3.3811.80.1030.0987.52721023130.0290.1030.09821.199.3
3.38-3.9112.40.0770.0749.32601921040.0220.0770.07429.799.9
3.91-4.7911.80.0610.05811.22067217470.0170.0610.0583698.8
4.79-6.7713.30.0620.0610.41877314100.0170.0620.0637.699.8
6.77-40.63712.30.0370.03517.4103798410.010.0370.03544.799.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.67 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.73 Å
Translation2.5 Å36.73 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
GDAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R9B

3r9b


Resolution: 2.14→70.16 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.263 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1154 5.1 %RANDOM
Rwork0.2003 ---
obs0.202 22446 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.08 Å2 / Biso mean: 25.7285 Å2 / Biso min: 8.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.83 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.14→70.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 116 115 3286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223269
X-RAY DIFFRACTIONr_angle_refined_deg0.9312.0554458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2565407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.95422.899138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62115513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5911534
X-RAY DIFFRACTIONr_chiral_restr0.0580.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212508
X-RAY DIFFRACTIONr_mcbond_it0.1941.52017
X-RAY DIFFRACTIONr_mcangle_it0.37723247
X-RAY DIFFRACTIONr_scbond_it0.63431252
X-RAY DIFFRACTIONr_scangle_it1.1094.51207
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 71 -
Rwork0.212 1448 -
all-1519 -
obs--90.58 %
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)
126.1912-4.083720.4324.034-2.0419.80430.4791.2991-0.1038-0.5803-0.4063-0.18610.39260.6248-0.07270.16920.12240.04960.2219-0.01550.107716.673716.268219.2865
22.9071-1.72493.35993.617-2.92754.77130.08780.28520.1837-0.4253-0.1511-0.24590.24490.18360.06330.12550.02940.02780.10680.04080.104911.789622.697423.4913
33.02772.78632.29789.23572.71241.9087-0.10590.06270.1561-0.67590.11230.0604-0.1805-0.0428-0.00640.12720.07620.01140.11470.06150.1573-0.849516.740423.4395
46.7164-8.3273-7.030510.77918.60847.4658-0.8726-0.2235-0.72240.94290.12370.86631.05050.12820.74890.304-0.06220.01340.34110.01890.228-3.36473.649624.5964
50.6474-1.0045-1.96081.5663.05335.95490.05090.03750.0282-0.0841-0.0358-0.0024-0.1541-0.0953-0.01510.29220.0118-0.01750.20490.0160.29592.6774-6.703226.2797
64.2191.52141.96952.03161.26051.57930.0432-0.2133-0.02920.3194-0.12730.19410.1835-0.08060.08410.1303-0.01050.04540.10550.03220.04397.50078.146252.8662
76.25686.9112-1.76149.1034-0.87822.10540.1915-0.1287-0.24320.2804-0.0744-0.37320.1440.0448-0.11710.05520.0151-0.02720.06550.03750.055420.64068.775348.8181
85.6222-0.81012.69686.2482-3.981611.50120.0503-0.2148-0.06030.0094-0.0713-0.40910.2669-0.0740.0210.06750.00060.00140.0242-0.03060.157217.0499-0.457337.5853
90.1383-1.47141.785516.2906-19.785224.03760.0730.08230.0019-1.3389-0.3674-0.21321.5980.40450.29440.5535-0.1215-0.02960.5605-0.11350.44716.1164-1.302224.5448
104.9957-2.6982-3.33563.7783-0.38658.7016-0.12750.046-0.44540.22610.1304-0.1210.55760.0728-0.00290.2696-0.0529-0.10140.1445-0.03250.20666.57-11.008248.2697
119.2076.76551.065713.35382.76484.82070.3713-0.4235-0.35140.1886-0.2710.0140.4562-0.1482-0.10030.1238-0.0235-0.07130.12350.00750.05420.6392-6.362442.7459
121.2820.20860.00971.21590.40250.9790.0501-0.05140.08720.0225-0.0037-0.0275-0.09340.0152-0.04640.05580.00120.00260.06120.01340.073713.832321.093242.3484
133.70280.65241.76514.04657.57496.34540.0460.29340.4416-1.2512-0.4810.9172-0.7809-0.32410.43490.19960.0596-0.13050.1726-0.01390.2841-7.336313.035118.254
141.44080.61470.84811.5368-0.13360.706-0.1832-0.00210.0806-0.09750.1136-0.0624-0.1303-0.06220.06960.08520.02940.01060.0630.00350.09886.531926.100632.6187
151.52210.67780.21531.78430.36381.65640.0815-0.07680.06680.0665-0.005-0.0299-0.0599-0.0008-0.07650.04440.00080.00050.03180.02660.048415.39117.716143.1199
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 26
2X-RAY DIFFRACTION2A27 - 46
3X-RAY DIFFRACTION3A47 - 65
4X-RAY DIFFRACTION4A66 - 79
5X-RAY DIFFRACTION5A80 - 103
6X-RAY DIFFRACTION6A104 - 140
7X-RAY DIFFRACTION7A141 - 164
8X-RAY DIFFRACTION8A165 - 188
9X-RAY DIFFRACTION9A189 - 205
10X-RAY DIFFRACTION10A206 - 236
11X-RAY DIFFRACTION11A237 - 254
12X-RAY DIFFRACTION12A255 - 309
13X-RAY DIFFRACTION13A310 - 324
14X-RAY DIFFRACTION14A325 - 352
15X-RAY DIFFRACTION15A353 - 414

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