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- PDB-5xw2: Crystal structure of the Hydroxylase HmtN in C 1 2 1 crystal form -

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Basic information

Entry
Database: PDB / ID: 5xw2
TitleCrystal structure of the Hydroxylase HmtN in C 1 2 1 crystal form
ComponentsCytochrome P450 107B1 (P450CVIIB1)
KeywordsBIOSYNTHETIC PROTEIN / himastatin / hydroxylase / cytochrome P450
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 107B1 (P450CVIIB1)
Similarity search - Component
Biological speciesStreptomyces himastatinicus ATCC 53653 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.298 Å
AuthorsZhang, H.D. / Zhang, H.J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Molecular characterization of the hydroxylase HmtN at 1.3 angstrom resolution.
Authors: Zhang, H. / Chen, J. / Zhang, H.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 107B1 (P450CVIIB1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0276
Polymers47,1101
Non-polymers9175
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-25 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.130, 72.840, 53.750
Angle α, β, γ (deg.)90.00, 107.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cytochrome P450 107B1 (P450CVIIB1) / HmtN / p450-like enzyme


Mass: 47109.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces himastatinicus ATCC 53653 (bacteria)
Strain: ATCC 53653 / Gene: hmtN, SSOG_07636 / Production host: Escherichia coli (E. coli) / References: UniProt: D9WMQ6
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 50.8 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG 8000, 0.2M magnesium chloride, 0.1M Tris, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979228 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979228 Å / Relative weight: 1
ReflectionResolution: 1.298→60.171 Å / Num. obs: 111281 / % possible obs: 97.39 % / Redundancy: 3.6 % / Biso Wilson estimate: 16.723 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 18.79
Reflection shellHighest resolution: 1.298 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.88 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GGV

4ggv


Resolution: 1.298→46.508 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.68 / Phase error: 17.25
RfactorNum. reflection% reflection
Rfree0.1848 5569 5 %
Rwork0.1679 --
obs0.1688 111281 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.298→46.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 62 508 3535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133101
X-RAY DIFFRACTIONf_angle_d1.2824215
X-RAY DIFFRACTIONf_dihedral_angle_d11.6961151
X-RAY DIFFRACTIONf_chiral_restr0.091453
X-RAY DIFFRACTIONf_plane_restr0.01545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2982-1.3130.20671390.23222768X-RAY DIFFRACTION76
1.313-1.32840.22351760.20913284X-RAY DIFFRACTION92
1.3284-1.34470.21871750.20453480X-RAY DIFFRACTION97
1.3447-1.36170.2331770.20513593X-RAY DIFFRACTION100
1.3617-1.37960.27341930.22273510X-RAY DIFFRACTION97
1.3796-1.39850.22021760.19813586X-RAY DIFFRACTION100
1.3985-1.41850.19221860.19363594X-RAY DIFFRACTION100
1.4185-1.43960.22981840.18853562X-RAY DIFFRACTION100
1.4396-1.46210.19171910.18733588X-RAY DIFFRACTION99
1.4621-1.48610.20671790.18433619X-RAY DIFFRACTION99
1.4861-1.51170.1851740.17463570X-RAY DIFFRACTION100
1.5117-1.53920.20561850.17913499X-RAY DIFFRACTION97
1.5392-1.56880.20131690.1673594X-RAY DIFFRACTION100
1.5688-1.60090.16562050.16543600X-RAY DIFFRACTION100
1.6009-1.63570.19511940.17013593X-RAY DIFFRACTION100
1.6357-1.67370.18162030.16023577X-RAY DIFFRACTION100
1.6737-1.71560.18391860.16213581X-RAY DIFFRACTION100
1.7156-1.7620.18381740.16613624X-RAY DIFFRACTION99
1.762-1.81380.18432180.16683578X-RAY DIFFRACTION100
1.8138-1.87240.18582150.16193600X-RAY DIFFRACTION100
1.8724-1.93930.18481800.16483489X-RAY DIFFRACTION97
1.9393-2.01690.1711730.16113627X-RAY DIFFRACTION99
2.0169-2.10870.16831990.16053498X-RAY DIFFRACTION98
2.1087-2.21990.17742080.14973608X-RAY DIFFRACTION100
2.2199-2.3590.16171760.15353569X-RAY DIFFRACTION98
2.359-2.54110.15091870.15553620X-RAY DIFFRACTION100
2.5411-2.79680.1671800.15643621X-RAY DIFFRACTION99
2.7968-3.20140.17332040.16073598X-RAY DIFFRACTION100
3.2014-4.03310.16531800.15263559X-RAY DIFFRACTION97
4.0331-46.53830.23251830.19173123X-RAY DIFFRACTION84

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