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- PDB-6to2: Crystal structure of CYP154C5 from Nocardia farcinica in complex ... -

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Basic information

Entry
Database: PDB / ID: 6to2
TitleCrystal structure of CYP154C5 from Nocardia farcinica in complex with 5alpha-Androstan-3-one
ComponentsCytochrome P450 monooxygenase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / steroid hydroxylating monooxygenase / steroid binding / oxidoreductase-substrate complex
Function / homology
Function and homology information


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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-NQ8 / Cytochrome P450 monooxygenase
Similarity search - Component
Biological speciesNocardia farcinica IFM 10152 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsRodriguez, A. / Kluenemann, T. / Blankenfeldt, W. / Schallmey, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation2223 Germany
CitationJournal: Chembiochem / Year: 2021
Title: CYP154C5 Regioselectivity in Steroid Hydroxylation Explored by Substrate Modifications and Protein Engineering*.
Authors: Bracco, P. / Wijma, H.J. / Nicolai, B. / Buitrago, J.A.R. / Klunemann, T. / Vila, A. / Schrepfer, P. / Blankenfeldt, W. / Janssen, D.B. / Schallmey, A.
History
DepositionDec 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 monooxygenase
B: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2928
Polymers90,4392
Non-polymers1,8536
Water9,062503
1
A: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1464
Polymers45,2201
Non-polymers9263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1464
Polymers45,2201
Non-polymers9263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.411, 103.411, 218.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Cytochrome P450 monooxygenase


Mass: 45219.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia farcinica IFM 10152 (bacteria)
Gene: NFA_53110 / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5YNS8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NQ8 / (5~{S},8~{S},9~{S},10~{S},13~{S},14~{S})-10,13-dimethyl-1,2,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydrocyclopenta[a]phenanthren-3-one


Mass: 274.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H30O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-TRIS pH 6.5 0.2M ammonium sulfate 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→82.85 Å / Num. obs: 58738 / % possible obs: 99.9 % / Redundancy: 10.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.077 / Rrim(I) all: 0.252 / Net I/σ(I): 6.2 / Num. measured all: 618378 / Scaling rejects: 250
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.059.72.8944168343060.5470.9673.0551.299.9
8.94-82.8511.30.10875156660.9960.0330.11318.299.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIXdev-3707refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
DIALSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4j6d

4j6d


Resolution: 2→82.85 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.32
RfactorNum. reflection% reflection
Rfree0.2488 2989 5.09 %
Rwork0.2073 --
obs0.2094 58679 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.24 Å2 / Biso mean: 41.7707 Å2 / Biso min: 18.17 Å2
Refinement stepCycle: final / Resolution: 2→82.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 248 503 7021
Biso mean--31.43 39.76 -
Num. residues----808
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.030.3871360.31322608274499
2.03-2.070.3181460.283626692815100
2.07-2.110.33211450.275326542799100
2.11-2.150.28541540.266926482802100
2.15-2.190.281290.262426582787100
2.19-2.240.30741480.25226382786100
2.24-2.290.3021600.243526392799100
2.29-2.350.26731270.233926872814100
2.35-2.410.24031340.23626542788100
2.41-2.480.29941390.229826362775100
2.48-2.560.2631390.232926332772100
2.56-2.650.31941450.226926752820100
2.65-2.760.29251540.232326602814100
2.76-2.880.25771210.222726542775100
2.88-3.040.29121460.213826882834100
3.04-3.230.24471280.214226262754100
3.23-3.480.26491640.20226442808100
3.48-3.830.20141430.174326562799100
3.83-4.380.20811500.163426472797100
4.38-5.520.19941450.170926532798100
5.52-82.850.21631360.190126632799100
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)
12.77980.42981.86941.528-0.29151.48820.05150.8124-0.3126-0.2384-0.035-0.31290.07130.68810.01030.31440.04980.05420.5384-0.04270.5599-4.006220.2916.8408
21.1977-0.52740.70332.3117-0.08392.73060.025-0.07510.16460.08070.0541-0.3334-0.23820.1734-0.10830.2778-0.03880.05770.2949-0.04010.3946-7.500834.344916.804
31.21340.0344-0.16192.263-0.11371.06840.0415-0.07230.05870.1403-0.01710.0798-0.1004-0.1519-0.02620.21050.0548-0.01160.25410.00850.234-30.37823.948718.401
44.1497-1.2087-2.95443.04091.60643.20980.10160.04990.0575-0.0387-0.04570.2476-0.1399-0.2343-0.09220.29690.0836-0.03480.29120.06240.2754-34.973333.324912.9927
51.23380.696-0.15481.06160.2430.63760.0129-0.0143-0.21360.09240.0195-0.26430.00630.0317-0.02930.27940.0457-0.02840.2816-0.01780.2951-17.127618.734821.9216
62.19562.5036-0.4984.44720.41920.8057-0.20110.1559-0.3738-0.23470.2017-0.6970.0637-0.0380.03070.25960.03320.02010.25930.02120.3379-22.82310.235610.9856
74.6933-1.20062.8423.41160.67182.34140.1617-0.8292-0.12660.436-0.19650.23670.2857-0.54670.01330.356-0.07880.02850.46110.01650.5213.871920.4152-7.9326
81.44790.76221.24092.53340.7383.97920.04080.03840.1811-0.048-0.00730.5045-0.1886-0.4225-0.03020.24820.03030.02820.32080.05110.48427.221634.4743-17.9764
92.2435-0.3215-0.67461.31080.30223.50160.11010.04380.4426-0.07760.16070.2175-0.3284-0.1317-0.2490.3386-0.04060.02350.2518-0.00250.362718.890638.6299-12.4657
101.3272-1.72671.26137.9204-3.94293.3721-0.03760.26360.0472-0.111-0.2278-0.5719-0.1580.42790.27060.2778-0.08650.01350.3804-0.02570.30433.72422.1508-26.9425
110.25980.6304-0.07912.4089-0.20991.38420.0049-0.0053-0.1583-0.08460.0202-0.40520.08610.2857-0.02250.2433-0.0416-0.0160.3156-0.03060.30833.329119.7167-11.3951
124.93760.4848-4.44541.4585-1.60524.96620.0482-0.1436-0.04370.1391-0.0357-0.2282-0.29790.427-0.02080.4112-0.1561-0.00260.3244-0.06820.384636.15936.9968-16.5079
131.6476-0.65510.08521.7436-0.29321.0279-0.0108-0.0276-0.1904-0.11470.10930.3208-0.0139-0.0292-0.09330.2609-0.0451-0.0210.27590.02930.259715.410220.3615-21.6168
140.5055-0.2204-0.44993.3080.15910.7466-0.00010.05430.0352-0.3298-0.03070.3210.115-0.03880.02090.3044-0.0593-0.05410.30130.00070.25520.745515.1112-27.095
152.229-3.1028-0.27816.44611.3821.0424-0.2065-0.1258-0.00190.14190.3390.08150.05360.0919-0.11680.265-0.02460.02260.28580.00740.381922.83627.5894-10.1669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 28 )A4 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 71 )A29 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 165 )A72 - 165
4X-RAY DIFFRACTION4chain 'A' and (resid 166 through 230 )A166 - 230
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 377 )A231 - 377
6X-RAY DIFFRACTION6chain 'A' and (resid 378 through 409 )A378 - 409
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 28 )B4 - 28
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 71 )B29 - 71
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 96 )B72 - 96
10X-RAY DIFFRACTION10chain 'B' and (resid 97 through 136 )B97 - 136
11X-RAY DIFFRACTION11chain 'B' and (resid 137 through 185 )B137 - 185
12X-RAY DIFFRACTION12chain 'B' and (resid 186 through 230 )B186 - 230
13X-RAY DIFFRACTION13chain 'B' and (resid 231 through 335 )B231 - 335
14X-RAY DIFFRACTION14chain 'B' and (resid 336 through 377 )B336 - 377
15X-RAY DIFFRACTION15chain 'B' and (resid 378 through 409 )B378 - 409

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