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- PDB-2lqd: Reduced and CO-bound cytochrome P450cam (CYP101A1) -

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Basic information

Entry
Database: PDB / ID: 2lqd
TitleReduced and CO-bound cytochrome P450cam (CYP101A1)
ComponentsCamphor 5-monooxygenase
KeywordsHYDROLASE / metalloenzyme / monooxygenase
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / : / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 1
AuthorsPochapsky, T.C. / Pochapsky, S.S. / Asciutto, E. / Madura, J. / Young, M.J.
Citation
Journal: Biochemistry / Year: 2012
Title: Solution Structural Ensembles of Substrate-Free Cytochrome P450(cam).
Authors: Asciutto, E.K. / Young, M.J. / Madura, J. / Pochapsky, S.S. / Pochapsky, T.C.
#1: Journal: Biochemistry / Year: 2011
Title: Experimentally Restrained Molecular Dynamics Simulations for Characterizing the Open States of Cytochrome P450(cam).
Authors: Asciutto, E.K. / Dang, M. / Pochapsky, S. / Madura, J.D. / Pochapsky, T.C.
History
DepositionMar 2, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Structure summary
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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_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

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Assembly

Deposited unit
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1714
Polymers46,4881
Non-polymers6843
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 46487.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Production host: Escherichia coli (E. coli) / References: UniProt: P00183, camphor 5-monooxygenase
#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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CO)CA
1313D HN(CA)CB
1413D 1H-15N NOESY
1522D 1H-15N TROSY-semiTROSY
1632D 1H-15N TROSY-semiTROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 13C; U-100% 15N; U-80% 2H] cytochrome P450cam, 90 % H2O, 10 % D2O, 0.4 mM CYP101A1, 3 mM CAM, 100 mM KCl, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-15N] cytochrome P450cam, 90 % H2O, 10 % D2O, 0.4 mM CYP101A1, 3 mM CAM, 100 mM KCl, 5 % C12E5/hexanol, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-15N] cytochrome P450cam, 90 % H2O, 10 % D2O, 0.4 mM CYP101A1, 3 mM CAM, 100 mM KCl, 8 mg/mL pf1, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMcytochrome P450cam-1[U-100% 13C; U-100% 15N; U-80% 2H]1
90 %H2O-21
10 %D2O-31
0.4 mMCYP101A1-41
3 mMCAM-51
100 mMKCl-61
0.4 mMcytochrome P450cam-7[U-15N]2
90 %H2O-82
10 %D2O-92
0.4 mMCYP101A1-102
3 mMCAM-112
100 mMKCl-122
5 %C12E5/hexanol-132
0.4 mMcytochrome P450cam-14[U-15N]3
90 %H2O-153
10 %D2O-163
0.4 mMCYP101A1-173
3 mMCAM-183
100 mMKCl-193
8 mg/mLpf1-203
Sample conditionsIonic strength: 100 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: Amber / Version: 10
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 1

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