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- PDB-7jj1: Crystal structure of the sterol 14alpha-demethylase-ferredoxin (C... -

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Basic information

Entry
Database: PDB / ID: 7jj1
TitleCrystal structure of the sterol 14alpha-demethylase-ferredoxin (CYP51-fx) heme domain and architectural comparison to the whole fusion protein
ComponentsCytochrome P450 51
KeywordsOXIDOREDUCTASE / cytochrome P450 / CYP51 / sterol biosynthesis / ferredoxin
Function / homology
Function and homology information


sterol 14alpha-demethylase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
4Fe-4S single cluster domain / Cytochrome P450, E-class, group IV / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
CETYL-TRIMETHYL-AMMONIUM / PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Cytochrome P450 51
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhao, B. / Lamb, D.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the sterol 14alpha-demethylase-ferredoxin (CYP51-fx) heme domain and architectural comparison to the whole fusion protein
Authors: Zhao, B. / Lamb, D.C.
History
DepositionJul 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Cytochrome P450 51
B: Cytochrome P450 51
C: Cytochrome P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,57115
Polymers155,4543
Non-polymers3,11812
Water75742
1
A: Cytochrome P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9266
Polymers51,8181
Non-polymers1,1085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7884
Polymers51,8181
Non-polymers9703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8575
Polymers51,8181
Non-polymers1,0394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.682, 164.755, 187.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 49 or resid 51...
21(chain C and (resid 7 through 15 or (resid 16...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 7 through 49 or resid 51...A7 - 49
121(chain A and (resid 7 through 49 or resid 51...A51 - 66
131(chain A and (resid 7 through 49 or resid 51...A6 - 474
141(chain A and (resid 7 through 49 or resid 51...A80
151(chain A and (resid 7 through 49 or resid 51...A6 - 474
161(chain A and (resid 7 through 49 or resid 51...A6 - 474
171(chain A and (resid 7 through 49 or resid 51...A6 - 474
181(chain A and (resid 7 through 49 or resid 51...A6 - 474
191(chain A and (resid 7 through 49 or resid 51...A6 - 474
1101(chain A and (resid 7 through 49 or resid 51...A6 - 474
211(chain C and (resid 7 through 15 or (resid 16...C7 - 15
221(chain C and (resid 7 through 15 or (resid 16...C16
231(chain C and (resid 7 through 15 or (resid 16...C7 - 466
241(chain C and (resid 7 through 15 or (resid 16...C7 - 466
251(chain C and (resid 7 through 15 or (resid 16...C7 - 466
261(chain C and (resid 7 through 15 or (resid 16...C7 - 466
271(chain C and (resid 7 through 15 or (resid 16...C7 - 466

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Components

#1: Protein Cytochrome P450 51 /


Mass: 51817.840 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Gene: cyp51 / Production host: Escherichia coli (E. coli) / References: UniProt: Q603T8, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-16A / CETYL-TRIMETHYL-AMMONIUM


Mass: 284.543 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H42N
#4: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, SODIUM CLORIDE, Cetrimide, Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 49452 / % possible obs: 99.2 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.13 / Rsym value: 0.12 / Net I/σ(I): 18.7
Reflection shellResolution: 3→3.05 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1541 / Rsym value: 0.55 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P99

3p99


Resolution: 3→29.52 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 4927 10.06 %
Rwork0.1961 44048 -
obs0.2002 48975 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.3 Å2 / Biso mean: 46.6563 Å2 / Biso min: 6.61 Å2
Refinement stepCycle: final / Resolution: 3→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10377 0 219 42 10638
Biso mean--40.09 28.14 -
Num. residues----1316
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2530X-RAY DIFFRACTION12.148TORSIONAL
12C2530X-RAY DIFFRACTION12.148TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.030.35821440.29011397154197
3.03-3.070.36371770.29214561633100
3.07-3.110.34561670.273514381605100
3.11-3.150.29881510.264614701621100
3.15-3.190.33021480.251214721620100
3.19-3.230.27751620.235914581620100
3.23-3.280.27751730.244214431616100
3.28-3.330.31471580.235614581616100
3.33-3.380.28591670.227714491616100
3.38-3.430.27641650.242714541619100
3.43-3.490.27911710.231314311602100
3.49-3.560.2641730.212514721645100
3.56-3.620.22811460.205914521598100
3.62-3.70.26451680.203914551623100
3.7-3.780.27871770.201414591636100
3.78-3.870.25121650.197514481613100
3.87-3.960.24561800.19314591639100
3.96-4.070.21871720.183414691641100
4.07-4.190.21051700.166114441614100
4.19-4.320.20041380.166514981636100
4.32-4.480.1861860.1514601646100
4.48-4.660.19761580.148914691627100
4.66-4.870.18411670.148514651632100
4.87-5.120.19191700.15914881658100
5.12-5.440.19691520.175614991651100
5.44-5.860.20451450.199114991644100
5.86-6.440.24981870.207714751662100
6.44-7.360.2341760.191414891665100
7.36-9.220.17561530.152915381691100
9.23-29.520.17881610.18461584174599
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)
10.15510.0246-0.29940.1939-0.06940.6705-0.03650.33680.0981-0.29990.00840.21270.0945-0.2745-0.13150.2920.0171-0.08960.26690.05180.2523-7.4264-78.350819.7182
20.46170.0019-0.24770.49240.18610.196-0.08490.0614-0.24680.030.1495-0.19930.41490.1617-0.19640.5690.242-0.08580.2826-0.24130.32418.2581-92.282120.9669
30.12270.0368-0.01250.0217-0.01880.04210.07210.1151-0.03020.0370.2046-0.070.33380.19890.1310.31190.2155-0.12940.4398-0.08860.380522.6608-79.626219.6141
40.59350.39240.30780.56960.12830.3984-0.16120.2124-0.1825-0.18790.145-0.10230.12930.41260.05230.44880.198-0.03530.173-0.13870.227521.7092-89.536615.139
50.830.2339-0.34340.54960.10020.6972-0.19050.1626-0.15580.31750.10740.03950.7668-0.0023-0.22270.69590.0584-0.03980.0824-0.05550.27330.0792-96.039229.4651
60.17890.1764-0.20430.43920.13980.6448-0.1269-0.1938-0.15140.29370.02-0.36010.61260.3684-0.30370.61290.3111-0.10230.04860.01270.227510.5088-92.721733.4639
70.5925-0.3323-0.06680.3618-0.18950.41950.04890.24870.0251-0.0574-0.03240.04990.04570.2970.0180.19880.0144-0.06750.31960.02490.2858-12.0237-46.864411.9695
80.03390.0435-0.02640.2991-0.24610.21510.08370.4558-0.4062-0.3473-0.06370.0610.2852-0.2335-0.03150.36750.0892-0.13560.6463-0.13790.523-4.1975-57.59050.6509
90.37080.12640.41720.81520.66250.81330.08030.32050.3285-0.22670.0798-0.256-0.16640.35350.10670.29520.02640.01490.25450.10110.3962-12.7476-48.2652-0.3297
100.6718-0.2303-0.43170.4034-0.09390.7796-0.0093-0.10610.3022-0.05260.03820.2129-0.1713-0.21750.79560.14430.0516-0.06490.18110.04320.2275-25.3228-42.907714.3779
110.0202-0.0484-0.03320.10980.06520.06570.02160.0925-0.0019-0.2450.0982-0.17310.1484-0.03230.02280.4603-0.0334-0.1880.44080.09690.4452-28.7382-62.158312.8337
120.3576-0.0676-0.13920.03830.07030.22040.0008-0.0211-0.19740.0726-0.0802-0.22950.1276-0.0412-0.05220.2183-0.0323-0.05890.210.1010.355222.4482-63.260136.9945
130.141-0.1352-0.17760.49220.17380.28170.0122-0.2407-0.02230.08930.0192-0.3544-0.04260.30540.01370.2122-0.02990.0330.37720.03150.253334.1254-47.559122.0926
140.71860.4131-0.21330.5549-0.2870.39680.2194-0.20190.29280.2683-0.03810.0816-0.26720.10410.15450.1841-0.1250.1060.24790.03160.30623.1547-32.520723.318
150.580.0685-0.19170.3616-0.10870.98010.1293-0.41440.05320.259-0.0616-0.0889-0.48050.5803-0.09560.1174-0.18320.09750.42460.05230.249528.3853-40.644440.3107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 76 )A6 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 157 )A77 - 157
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 193 )A158 - 193
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 275 )A194 - 275
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 379 )A276 - 379
6X-RAY DIFFRACTION6chain 'A' and (resid 380 through 448 )A380 - 448
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 157 )B5 - 157
8X-RAY DIFFRACTION8chain 'B' and (resid 158 through 215 )B158 - 215
9X-RAY DIFFRACTION9chain 'B' and (resid 216 through 274 )B216 - 274
10X-RAY DIFFRACTION10chain 'B' and (resid 275 through 413 )B275 - 413
11X-RAY DIFFRACTION11chain 'B' and (resid 414 through 450 )B414 - 450
12X-RAY DIFFRACTION12chain 'C' and (resid 7 through 76 )C7 - 76
13X-RAY DIFFRACTION13chain 'C' and (resid 77 through 113 )C77 - 113
14X-RAY DIFFRACTION14chain 'C' and (resid 114 through 219 )C114 - 219
15X-RAY DIFFRACTION15chain 'C' and (resid 220 through 448 )C220 - 448

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