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- PDB-4kky: Crystal structure of N-(1-Pyrene)acetamide labeled P450cam in sub... -

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Basic information

Entry
Database: PDB / ID: 4kky
TitleCrystal structure of N-(1-Pyrene)acetamide labeled P450cam in substrate bound form.
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / Pyrene Acetamide labeled / Monooxygenase labeled / electrode surface anchor molecule / thiol alkylation.
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
N-(pyren-1-yl)acetamide / CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / : / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, M. / Goodin, D.B.
CitationJournal: To be Published
Title: To be determined.
Authors: Zhang, M. / Goodin, D.B.
History
DepositionMay 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5026
Polymers46,3951
Non-polymers1,1065
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.950, 101.990, 57.350
Angle α, β, γ (deg.)90.00, 101.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules X

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


Mass: 46395.469 Da / Num. of mol.: 1 / Mutation: T2A, C58S, C85S, A113C, C136S, C285S, C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, camC cyp101, cyp101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase

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Non-polymers , 5 types, 184 molecules

#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-1T4 / N-(pyren-1-yl)acetamide


Mass: 259.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13NO
#4: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 8000, 0.2M potassium Chloride, 0.05M Bis-tris Buffer. 1mM camphor., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 287.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→33.273 Å / Num. all: 37270 / Num. obs: 27318 / % possible obs: 73.3 %

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Processing

Software
NameVersionClassification
Web-Icedata collection
CCP4model building
REFMAC5.6.0117refinement
MOSFLMdata reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.82 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.195 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22532 1353 5 %RANDOM
Rwork0.16992 ---
all0.17272 27318 --
obs0.16992 25613 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.06 Å2
2---0.03 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 76 179 3507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193496
X-RAY DIFFRACTIONr_angle_refined_deg2.4031.9954788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0685432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34724.121165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04715578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6591526
X-RAY DIFFRACTIONr_chiral_restr0.1370.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212734
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 94 -
Rwork0.216 1846 -
obs--98.93 %

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