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- PDB-3bdz: The Role of Asn 242 in P450cin -

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Basic information

Entry
Database: PDB / ID: 3bdz
TitleThe Role of Asn 242 in P450cin
ComponentsP450cin1,8-Cineole 2-endo-monooxygenase
KeywordsUNKNOWN FUNCTION / Protein in the absence of substrate
Function / homology
Function and homology information


1,8-cineole 2-endo-monooxygenase / carbazole catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / 1,8-cineole 2-endo-monooxygenase
Similarity search - Component
Biological speciesCitrobacter braakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMeharenna, Y.T. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The critical role of substrate-protein hydrogen bonding in the control of regioselective hydroxylation in p450cin
Authors: Meharenna, Y.T. / Slessor, K.E. / Cavaignac, S.M. / Poulos, T.L. / De Voss, J.J.
History
DepositionNov 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P450cin
B: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6646
Polymers89,2272
Non-polymers1,4374
Water9,494527
1
A: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3323
Polymers44,6141
Non-polymers7192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3323
Polymers44,6141
Non-polymers7192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.330, 68.230, 103.560
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein P450cin / 1,8-Cineole 2-endo-monooxygenase / Cytochrome P450cin


Mass: 44613.660 Da / Num. of mol.: 2 / Fragment: UNP residues 8-404 / Mutation: N242A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter braakii (bacteria) / Gene: cinA / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: Q8VQF6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.8M Sodium malonate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2006 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 56425 / % possible obs: 78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.2 / Rsym value: 0.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.5 % / % possible all: 78

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T2B

1t2b


Resolution: 2→46.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1767900.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2831 5 %RANDOM
Rwork0.181 ---
obs-56399 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.1842 Å2 / ksol: 0.55 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.08 Å20 Å21.69 Å2
2---4.92 Å20 Å2
3----2.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6292 0 114 527 6933
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.227 225 5 %
Rwork0.181 4290 -
obs--76.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.param
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3hetero.paramhetero.top

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