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- PDB-4j6b: The 2.2 A crystal structure of CYP154C5 from Nocardia farcinica i... -

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Basic information

Entry
Database: PDB / ID: 4j6b
TitleThe 2.2 A crystal structure of CYP154C5 from Nocardia farcinica in complex with pregnenolone
ComponentsCytochrome P450 monooxygenaseCytochrome P450
Keywordsoxidoreductase/substrate / Cytochrom 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 / 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
FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / : / (3BETA)-3-HYDROXYPREGN-5-EN-20-ONE / Cytochrome P450 monooxygenase
Similarity search - Component
Biological speciesNocardia farcinica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsHerzog, K. / Hoffmann, K.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Enzyme-substrate complex structures of CYP154C5 shed light on its mode of highly selective steroid hydroxylation.
Authors: Herzog, K. / Bracco, P. / Onoda, A. / Hayashi, T. / Hoffmann, K. / Schallmey, A.
History
DepositionFeb 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Sep 20, 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_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 monooxygenase
B: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,89113
Polymers90,7542
Non-polymers2,13811
Water8,827490
1
A: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4196
Polymers45,3771
Non-polymers1,0425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4196
Polymers45,3771
Non-polymers1,0425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cytochrome P450 monooxygenase
hetero molecules

B: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,89113
Polymers90,7542
Non-polymers2,13811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6570 Å2
ΔGint-64 kcal/mol
Surface area31420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.120, 103.120, 217.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
Detailsbiological unit is one chain of the dimer in the asym. unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450 monooxygenase / Cytochrome P450


Mass: 45376.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia farcinica (bacteria) / Strain: IFM 10152 / Gene: NFA_53110 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: Q5YNS8

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Non-polymers , 6 types, 501 molecules

#2: Chemical ChemComp-PLO / (3BETA)-3-HYDROXYPREGN-5-EN-20-ONE / PREGNENOLONE / Pregnenolone


Mass: 316.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H32O2 / Comment: medication, hormone*YM
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.3 M MgCHO2 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 9, 2011
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→82.63 Å / Num. all: 43848 / Num. obs: 43848 / % possible obs: 100 % / Redundancy: 5.9 % / Rsym value: 0.139 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.325.70.5593.33663663810.559100
2.32-2.465.80.4111.93563160970.411100
2.46-2.635.90.3372.33358456920.337100
2.63-2.845.90.2592.93133453050.259100
2.84-3.1160.184.32910548630.18100
3.11-3.4860.1216.12646644190.121100
3.48-4.0260.0828.52332438850.082100
4.02-4.926.10.05911.12005732880.059100
4.92-6.966.10.0738.61557325340.073100
6.96-43.7436.10.03614.6846113840.03699.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB-entry 1GWI

1gwi


Resolution: 2.2→82.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.1889 / WRfactor Rwork: 0.1429 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8893 / SU B: 9.457 / SU ML: 0.134 / SU R Cruickshank DPI: 0.2445 / SU Rfree: 0.1844 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 2204 5 %RANDOM
Rwork0.1557 ---
obs0.1581 43846 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 101.47 Å2 / Biso mean: 42.2999 Å2 / Biso min: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-0.61 Å20 Å2
2---1.22 Å20 Å2
3---1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→82.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6215 0 147 490 6852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196558
X-RAY DIFFRACTIONr_bond_other_d0.0020.024329
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9998984
X-RAY DIFFRACTIONr_angle_other_deg0.762310536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4515816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28623.03264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.349151025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6271556
X-RAY DIFFRACTIONr_chiral_restr0.060.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217299
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021334
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2783MEDIUM POSITIONAL0.090.5
2359TIGHT THERMAL2.320.5
2783MEDIUM THERMAL2.592
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 192 -
Rwork0.215 3025 -
all-3217 -
obs--99.97 %
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)
10.4560.2020.75892.7512-0.03791.3158-0.0211-0.09070.00750.08430.03680.1774-0.0495-0.1614-0.01570.04730.05170.03590.0690.01880.140720.3878.161-9.022
20.45320.35710.19410.65510.2140.53810.07580.01320.0614-0.00120.0432-0.0135-0.09820.0433-0.1190.08440.00930.04550.0437-0.00140.082238.2927.029-15.343
33.72633.03191.56873.74992.77762.4189-0.20190.27050.1201-0.03110.3138-0.0430.0810.2162-0.11190.097-0.01670.00350.13320.01540.031942.925-8.256-31.765
40.18050.2157-0.00970.46950.11150.14250.0185-0.0428-0.0279-0.0054-0.0199-0.02530.03240.00640.00140.0740.0066-0.00310.08990.00110.042635.441-19.358-12.596
55.18441.224-0.43770.2894-0.10480.0424-0.12920.3162-0.3417-0.03190.0848-0.08460.0061-0.04870.04440.0710.01710.02560.1118-0.06210.059853.565-15.944-24.331
60.01460.01560.02540.25680.08480.21340.01750.01780.0156-0.0475-0.00520.0625-0.0207-0.0227-0.01230.06610.0227-0.00760.07630.02640.086623.511-6.852-21.893
70.29910.9155-0.14352.8751-0.52810.20860.0176-0.0240.12190.0399-0.05030.2918-0.0285-0.04220.03270.05170.01060.03330.0653-0.03330.147318.991-14.706-8.519
81.6966-0.4304-0.50460.4351-0.55311.5765-0.08490.0626-0.2218-0.0506-0.02470.04030.1555-0.00290.10970.18860.0401-0.02360.0135-0.01110.078817.4613.6338.894
90.69460.1279-0.36510.29270.11940.74080.0871-0.0845-0.05890.0073-0.0397-0.0865-0.10080.2134-0.04740.0584-0.0041-0.0110.12270.00570.037523.82532.10818.434
100.54920.1397-0.04070.0757-0.03970.11990.03390.01370.0689-0.02310.00830.0443-0.0543-0.0228-0.04220.1112-0.00940.01690.04940.01130.05941.19140.3313.371
115.06411.4833-0.42712.2474-0.83120.31150.228-0.36520.2684-0.0055-0.18060.15470.01610.0557-0.04750.1296-0.07230.09310.0589-0.06480.078111.63254.70824.753
120.1212-0.0167-0.12610.01870.08660.4258-0.0061-0.05920.00080.02610.0009-0.00220.10730.03490.00520.10540.0053-0.01230.05550.03580.07039.33523.44621.473
131.25780.09450.39920.01010.05710.65830.067-0.1091-0.11680.0204-0.0145-0.01290.1096-0.0225-0.05250.1299-0.0184-0.00360.04070.03580.0360.18726.31119.361
1410.2489-2.80551.15771.0035-0.01270.53240.4706-0.0583-0.8985-0.1288-0.09920.04760.0303-0.1279-0.37140.0999-0.0565-0.02430.08580.08270.2505-8.52325.4299.128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 34
2X-RAY DIFFRACTION2A35 - 97
3X-RAY DIFFRACTION3A98 - 113
4X-RAY DIFFRACTION4A114 - 204
5X-RAY DIFFRACTION5A205 - 231
6X-RAY DIFFRACTION6A232 - 386
7X-RAY DIFFRACTION7A387 - 410
8X-RAY DIFFRACTION8B4 - 34
9X-RAY DIFFRACTION9B35 - 111
10X-RAY DIFFRACTION10B112 - 204
11X-RAY DIFFRACTION11B205 - 227
12X-RAY DIFFRACTION12B228 - 345
13X-RAY DIFFRACTION13B346 - 399
14X-RAY DIFFRACTION14B400 - 410

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