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- PDB-5ex9: Structure of P450 StaF from glycopeptide antibiotic A47934 biosyn... -

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Basic information

Entry
Database: PDB / ID: 5ex9
TitleStructure of P450 StaF from glycopeptide antibiotic A47934 biosynthesis; glycerol cryo
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / monooxygenase / phenolic coupling / glycopeptide antibiotic biosynthesis
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 speciesStreptomyces toyocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCryle, M.J. / Ulrich, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCR 392/1-1 Germany
CitationJournal: Beilstein J Org Chem / Year: 2016
Title: Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934.
Authors: Ulrich, V. / Brieke, C. / Cryle, M.J.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,69110
Polymers47,3381
Non-polymers1,3539
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-27 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.700, 109.700, 93.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cytochrome P450 / StaF


Mass: 47337.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Gene: BU52_01275 / Plasmid: pET151 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KLL7
#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.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 1.2 M NH4PO4, 0.3 M K2HPO4, 0.1 M NH4PO4 citrate (pH 4.2)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 33006 / % possible obs: 98.4 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.09 / Rsym value: 0.062 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.5 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
Cootmodel building
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O1A

3o1a


Resolution: 2.2→47.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.055 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22011 1656 4.9 %RANDOM
Rwork0.19076 ---
obs0.1922 31857 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.062 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.2→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 91 216 3546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0712.0084680
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0835423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.04923.006163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42715547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261535
X-RAY DIFFRACTIONr_chiral_restr0.0720.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212655
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3811.52080
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74723355
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.23631359
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0324.51320
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 108 -
Rwork0.218 2339 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.26060.5456-1.73120.4686-0.01324.7270.2206-0.02070.25290.0798-0.04020.1645-0.2838-0.192-0.18040.0904-0.0331-0.02850.21460.03380.180921.2321-47.283114.8902
23.18261.3143-0.53655.2054-1.84334.41120.07310.12990.38750.0190.09910.6481-0.1803-0.6245-0.17220.0954-0.0647-0.08880.22580.08930.225517.1144-46.8059-1.0717
37.4897-0.75540.69533.1478-1.64774.8016-0.02320.11250.1086-0.21480.18710.30370.027-0.2857-0.16390.1462-0.0782-0.05430.06720.06030.101432.6947-32.6515-9.9214
41.4514-0.7830.84883.4872-1.29491.9896-0.03160.0650.1105-0.08420.0949-0.2213-0.10260.1637-0.06340.0281-0.0456-0.00180.0909-0.01050.100250.608-37.27851.5661
50.8972-0.053-0.01171.9269-0.70591.48370.02970.1965-0.0807-0.22880.09910.07080.2689-0.0836-0.12880.1177-0.05-0.05370.0798-0.00410.045935.3362-49.692-4.4746
64.4431-1.35820.61212.3522-0.41771.73180.05640.1807-0.3388-0.20120.1215-0.02350.45980.1609-0.17780.16540.0055-0.01360.0528-0.05130.057144.0254-55.8417-0.5076
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-22 - 25
2X-RAY DIFFRACTION2A26 - 75
3X-RAY DIFFRACTION3A76 - 107
4X-RAY DIFFRACTION4A108 - 206
5X-RAY DIFFRACTION5A207 - 320
6X-RAY DIFFRACTION6A321 - 391

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