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- PDB-2z36: Crystal structure of cytochrome P450 MoxA from Nonomuraea rectica... -

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Basic information

Entry
Database: PDB / ID: 2z36
TitleCrystal structure of cytochrome P450 MoxA from Nonomuraea recticatena (CYP105)
ComponentsCytochrome P450 type compactin 3'',4''-hydroxylase
KeywordsOXIDOREDUCTASE / P450 / CYP105
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
: / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 type compactin 3'',4''-hydroxylase
Similarity search - Component
Biological speciesNonomuraea recticatena (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYasutake, Y. / Fujii, Y. / Fujii, T. / Arisawa, A. / Tamura, T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Crystal structure of cytochrome P450 MoxA from Nonomuraea recticatena (CYP105)
Authors: Yasutake, Y. / Imoto, N. / Fujii, Y. / Fujii, T. / Arisawa, A. / Tamura, T.
History
DepositionJun 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif
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.ptnr1_symmetry / _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_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 type compactin 3'',4''-hydroxylase
B: Cytochrome P450 type compactin 3'',4''-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5148
Polymers91,7792
Non-polymers1,7356
Water1,22568
1
A: Cytochrome P450 type compactin 3'',4''-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7574
Polymers45,8891
Non-polymers8683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 type compactin 3'',4''-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7574
Polymers45,8891
Non-polymers8683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.557, 83.256, 175.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological unit is a monomer. Asymmetric unit contains two monomers.

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Components

#1: Protein Cytochrome P450 type compactin 3'',4''-hydroxylase / MoxA


Mass: 45889.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonomuraea recticatena (bacteria) / Strain: IFO 14525 / Gene: moxA / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q2L6S8, Oxidoreductases
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.25 Å3/Da / Density % sol: 62.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 8% ethyleneglycol, 4% PEG 8000, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97898 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 29919 / Num. obs: 29919 / % possible obs: 99.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 46.711 Å2 / Rsym value: 0.097 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 4351 / Rsym value: 0.364 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JIN

1jin


Resolution: 2.8→47.6 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1414 -RANDOM
Rwork0.23 ---
obs-28248 93.4 %-
Displacement parametersBiso mean: 48.7695 Å2
Baniso -1Baniso -2Baniso -3
1--9.851 Å20 Å20 Å2
2---2.259 Å20 Å2
3---12.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 112 68 6480
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005788
X-RAY DIFFRACTIONc_angle_deg1.2494
X-RAY DIFFRACTIONc_improper_angle_d21.49227
X-RAY DIFFRACTIONc_dihedral_angle_d0.80047
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.4618 128 -
Rwork0.4129 --
obs-2556 85.7 %

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