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- PDB-4g3r: Crystal Structure of Nitrosyl Cytochrome P450cam -

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Basic information

Entry
Database: PDB / ID: 4g3r
TitleCrystal Structure of Nitrosyl Cytochrome P450cam
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / P450 / HEME / MONOOXYGENASE / Putidaredoxin
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm
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
CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / : / NITRIC OXIDE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsMadrona, Y. / Tripathi, S.M. / Li, H. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal structures of substrate-free and nitrosyl cytochrome p450cin: implications for o(2) activation.
Authors: Madrona, Y. / Tripathi, S. / Li, H. / Poulos, T.L.
History
DepositionJul 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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: Camphor 5-monooxygenase
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7599
Polymers93,1142
Non-polymers1,6467
Water7,602422
1
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3654
Polymers46,5571
Non-polymers8083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3955
Polymers46,5571
Non-polymers8384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.553, 62.269, 95.490
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Camphor 5-monooxygenase / Cytochrome P450-cam / Cytochrome P450cam


Mass: 46556.816 Da / Num. of mol.: 2 / Mutation: C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pCWori-P450cam / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: P00183, camphor 5-monooxygenase

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Non-polymers , 5 types, 429 molecules

#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-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 50mM Tris-HCl pH 7.4, 26-32% PEG 4000, 250mM KCl, 1mM D-Camphor, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 11, 2012 / Details: Mirrors
RadiationMonochromator: Cu Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→33.1 Å / Num. all: 40554 / Num. obs: 39581 / % possible obs: 97.6 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.2-2.28192.7
2.28-2.37194.3
2.37-2.48195.9
2.48-2.61197.4
2.61-2.77198.7
2.77-2.99199.1
2.99-3.29199.3
3.29-3.76199.7
3.76-4.74199.7
4.74-33.1199.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.8_1069)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→33.1 Å / SU ML: 0.32 / σ(F): 1.33 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 2001 5.06 %RANDOM
Rwork0.1899 ---
obs0.193 39549 97.55 %-
all-39571 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6427 0 112 422 6961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116726
X-RAY DIFFRACTIONf_angle_d1.0649147
X-RAY DIFFRACTIONf_dihedral_angle_d13.3512514
X-RAY DIFFRACTIONf_chiral_restr0.07985
X-RAY DIFFRACTIONf_plane_restr0.0041205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.38621400.29452529X-RAY DIFFRACTION93
2.255-2.3160.34991240.2782523X-RAY DIFFRACTION93
2.316-2.38410.35641530.26512575X-RAY DIFFRACTION95
2.3841-2.4610.32481320.26062632X-RAY DIFFRACTION97
2.461-2.5490.35881590.25262676X-RAY DIFFRACTION97
2.549-2.6510.36481270.23572687X-RAY DIFFRACTION98
2.651-2.77160.26351440.23362672X-RAY DIFFRACTION98
2.7716-2.91760.31071450.22182707X-RAY DIFFRACTION99
2.9176-3.10030.30431360.2182757X-RAY DIFFRACTION99
3.1003-3.33940.28791400.2052711X-RAY DIFFRACTION99
3.3394-3.67510.24721460.17812782X-RAY DIFFRACTION100
3.6751-4.2060.19371590.14942712X-RAY DIFFRACTION100
4.206-5.29560.17981470.13372778X-RAY DIFFRACTION100
5.2956-33.10.16681490.14462807X-RAY DIFFRACTION99
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)
10.1549-0.0592-0.12980.05880.02190.10090.0545-0.0063-0.02150.1012-0.06990.14250.0617-0.378-00.2437-0.0262-0.00850.22070.00640.24857.1895-2.535863.9671
20.1527-0.08690.11510.14490.09350.1804-0.0226-0.11480.0757-0.03260.1016-0.07050.0033-0.050.00080.2142-0.02320.01310.13510.01260.246926.24234.331658.1315
30.0239-0.06420.03780.1484-0.08690.06680.14560.5537-0.0253-0.282-0.2719-0.1393-0.1508-0.0461-0.00470.37450.0854-0.00880.61340.00230.28520.94621.343225.9383
40.1165-0.0610.04080.1617-0.02320.06990.04030.3218-0.3191-0.1234-0.10810.109-0.07090.0164-0.00090.21220.0021-0.02620.1292-0.07290.291621.2515-10.009538.6079
50.0357-0.0914-0.0620.24140.12680.06220.07890.2787-0.0518-0.1269-0.0049-0.30360.0049-0.00330.00010.2174-0.0060.03640.1753-0.02920.356540.0863-6.055344.6265
60.2942-0.1538-0.14010.54850.04830.14560.06240.1098-0.0154-0.0702-0.0301-0.0091-0.0669-0.1354-00.19940.057-0.0130.19140.00860.200514.46526.496846.3274
70.1498-0.2064-0.03040.2679-0.02050.05960.05430.1181-0.0681-0.0832-0.07370.26120.1589-0.1475-0.00850.2426-0.009-0.10940.3554-0.03540.30284.9513-4.513332.5126
80.1696-0.0953-0.15110.1878-0.04320.19790.0212-0.84390.45430.31760.02270.3518-0.0763-0.41740.0870.4578-0.00770.18640.7802-0.04880.317642.86372.1182105.7713
90.5671-0.16430.31690.34770.05810.18460.0639-0.07570.02410.03710.03650.02860.030.05570.00020.2179-0.0199-0.0070.19360.00070.167861.17930.743184.5909
100.2344-0.4098-0.16540.47170.19850.17570.0908-0.2563-0.0860.10350.0490.08550.05660.0113-00.3061-0.0261-0.02050.32750.06820.241364.341-5.29390.9944
110.66430.2219-0.00520.175-0.015-0.02650.0752-0.22170.16440.00720.0540.1921-0.0975-0.01090.01880.24420.03540.06940.3342-0.04130.248947.401910.363990.182
120.1028-0.0770.03980.34060.11890.0867-0.0192-0.28670.154-0.05080.05710.2334-0.015-0.2025-0.01440.1819-0.1062-0.04980.2360.06850.235842.3783-2.731674.744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 8:60)
2X-RAY DIFFRACTION2chain 'A' and (resseq 61:120)
3X-RAY DIFFRACTION3chain 'A' and (resseq 121:145)
4X-RAY DIFFRACTION4chain 'A' and (resseq 146:192)
5X-RAY DIFFRACTION5chain 'A' and (resseq 193:234)
6X-RAY DIFFRACTION6chain 'A' and (resseq 235:375)
7X-RAY DIFFRACTION7chain 'A' and (resseq 376:414)
8X-RAY DIFFRACTION8chain 'B' and (resseq 10:89)
9X-RAY DIFFRACTION9chain 'B' and (resseq 90:170)
10X-RAY DIFFRACTION10chain 'B' and (resseq 171:266)
11X-RAY DIFFRACTION11chain 'B' and (resseq 267:377)
12X-RAY DIFFRACTION12chain 'B' and (resseq 378:414)

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