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- PDB-5ex8: Structure of P450 StaF from glycopeptide antibiotic A47934 biosyn... -

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Basic information

Entry
Database: PDB / ID: 5ex8
TitleStructure of P450 StaF from glycopeptide antibiotic A47934 biosynthesis; ethylene glycol 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: 2.1 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)48,94718
Polymers47,3381
Non-polymers1,61017
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint21 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.050, 110.050, 93.650
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 3.46 Å3/Da / Density % sol: 64.43 %
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: 2.1→50 Å / Num. obs: 36757 / % possible obs: 95.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.072 / Rsym value: 0.063 / Net I/σ(I): 19.8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 4.2 / % possible all: 91.6

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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: 2.1→47.67 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.68 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1906 5 %RANDOM
Rwork0.19392 ---
obs0.19565 36206 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: 35.928 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 107 268 3614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1932.0044757
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.565436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86522.899169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30615559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6991537
X-RAY DIFFRACTIONr_chiral_restr0.0820.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212714
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_it0.4371.52101
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84323398
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.44131401
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3464.51347
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: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 142 -
Rwork0.225 2696 -
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)
10.5903-0.60711.99842.0573-2.53116.9453-0.0384-0.1401-0.0192-0.21320.26730.4924-0.1043-0.5669-0.22890.26220.04910.03980.19440.02440.249849.05055.374-16.2113
23.4829-0.2805-1.13422.7067-0.26973.41950.09410.14450.37430.14570.09960.5551-0.4416-0.3364-0.19380.2476-0.00160.09480.05660.00860.215251.96177.74150.3234
35.5665-0.891-2.92891.46810.79622.83870.094-0.2366-0.13380.2874-0.0120.10410.16180.1753-0.0820.1435-0.0291-0.03440.02280.00630.072858.0749-19.25264.978
42.687-0.0747-2.94541.49370.56025.64250.07270.1956-0.1471-0.05010.0432-0.01080.2277-0.2216-0.11590.0947-0.035-0.00550.07070.00180.128647.6776-25.2578-0.4751
52.2666-0.5974-0.49332.7664-0.00421.69220.0725-0.2320.19820.37330.0429-0.0442-0.22490.2413-0.11540.1674-0.07120.03030.0642-0.03550.02364.8726-2.53083.3787
64.2318-1.6592-1.25362.54870.39312.39770.1197-0.21440.06710.20220.0418-0.2039-0.13950.5064-0.16150.0855-0.0485-0.03560.115-0.02840.057369.8562-11.17640.1014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-22 - 18
2X-RAY DIFFRACTION2A19 - 75
3X-RAY DIFFRACTION3A76 - 152
4X-RAY DIFFRACTION4A153 - 225
5X-RAY DIFFRACTION5A226 - 326
6X-RAY DIFFRACTION6A327 - 391

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