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- PDB-5ysm: Crystal Structure Analysis of Rif16 -

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Basic information

Entry
Database: PDB / ID: 5ysm
TitleCrystal Structure Analysis of Rif16
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / rifamycin / METAL BINDING PROTEIN
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
Similarity search - Component
Biological speciesAmycolatopsis mediterranei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsLi, F.W. / Qi, F.F. / Xiao, Y.L. / Zhao, G.P. / Li, S.Y.
CitationJournal: Nat Commun / Year: 2018
Title: Deciphering the late steps of rifamycin biosynthesis.
Authors: Qi, F. / Lei, C. / Li, F. / Zhang, X. / Wang, J. / Zhang, W. / Fan, Z. / Li, W. / Tang, G.L. / Xiao, Y. / Zhao, G. / Li, S.
History
DepositionNov 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4022
Polymers48,7851
Non-polymers6161
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-25 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.105, 70.335, 81.019
Angle α, β, γ (deg.)90.000, 94.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 48785.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis mediterranei (strain U-32) (bacteria)
Strain: U-32 / Gene: AMED_0653 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CVZ6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.04 Å3/Da / Density % sol: 39.83 % / Mosaicity: 0.877 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5 / Details: Magnesium chloride hexahydrate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2017 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 33798 / % possible obs: 94.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 0.966 / Net I/σ(I): 9 / Num. measured all: 213187
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8360.47516350.8950.2060.5190.87590.6
1.83-1.8660.41315120.9040.180.4520.86985.1
1.86-1.96.30.3917010.9270.1660.4250.8794.7
1.9-1.946.40.3117200.9570.1310.3370.84595
1.94-1.986.40.27416820.9660.1160.2980.88497
1.98-2.036.40.23117090.970.0980.2510.90195.7
2.03-2.086.40.19917280.9780.0840.2160.87695.2
2.08-2.136.40.16516980.9820.070.1790.88996.1
2.13-2.26.30.13317320.9890.0570.1450.89295.1
2.2-2.276.40.11516510.990.0490.1250.9394.1
2.27-2.356.20.09316020.9930.040.1020.94288.7
2.35-2.446.40.08916370.9930.0380.0970.93990.8
2.44-2.556.60.08417200.9940.0350.0910.98997.3
2.55-2.696.50.07217780.9950.030.0780.97997.2
2.69-2.866.40.06417220.9940.0270.071.03397.6
2.86-3.086.40.05717200.9970.0240.0611.04695.3
3.08-3.396.10.04816400.9960.0210.0531.08691.2
3.39-3.886.30.04517260.9960.0190.0491.19294.2
3.88-4.886.30.04317530.9970.0180.0461.20697.1
4.88-506.10.04417320.9960.0190.0481.05393.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
REFMACphasing
RefinementResolution: 1.9→40.42 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2293 / WRfactor Rwork: 0.1798 / FOM work R set: 0.8641 / SU B: 3.08 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1553 / SU Rfree: 0.1502 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 1459 4.9 %RANDOM
Rwork0.1831 ---
obs0.1857 28027 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.48 Å2 / Biso mean: 22.621 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20.22 Å2
2---0.18 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 1.9→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 43 149 2986
Biso mean--11.5 27.49 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192906
X-RAY DIFFRACTIONr_bond_other_d0.0010.022771
X-RAY DIFFRACTIONr_angle_refined_deg1.951.9963972
X-RAY DIFFRACTIONr_angle_other_deg0.94536328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88922.558129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75715439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6431530
X-RAY DIFFRACTIONr_chiral_restr0.1260.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213310
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02676
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 116 -
Rwork0.196 2139 -
all-2255 -
obs--95.11 %

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