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- PDB-5hh3: OxyA from Actinoplanes teichomyceticus -

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Basic information

Entry
Database: PDB / ID: 5hh3
TitleOxyA from Actinoplanes teichomyceticus
ComponentsOxyA protein
KeywordsOXIDOREDUCTASE / Cytochrome P450 monooxygenase / phenolic coupling enzyme / biosynthesis of glycopeptide antibiotics / peptide cyclase
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Oxidation protein CepE
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHaslinger, K. / Cryle, M.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCR 392/1-1 Germany
CitationJournal: Febs Lett. / Year: 2016
Title: Structure of OxyAtei : completing our picture of the glycopeptide antibiotic producing Cytochrome P450 cascade.
Authors: Haslinger, K. / Cryle, M.J.
History
DepositionJan 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OxyA protein
C: OxyA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,19016
Polymers88,9512
Non-polymers2,23914
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-63 kcal/mol
Surface area33390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.490, 103.060, 152.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein OxyA protein / P450 monooxygenase


Mass: 44475.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: tcp18 / Plasmid: pET151TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q6ZZI8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Mes/ NaOH pH 6.5, 14.4% (w/ v) PEG 8,000, 20% (v/ v) glycerol, 0.16 M calcium acetate
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.07169 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07169 Å / Relative weight: 1
ReflectionResolution: 2.1→48.85 Å / Num. obs: 54785 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 20
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 4.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EX8

5ex8


Resolution: 2.1→48.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.674 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22859 2742 5 %RANDOM
Rwork0.19817 ---
obs0.19969 52043 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.104 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å2-0 Å20 Å2
2--1.99 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 152 193 6429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196426
X-RAY DIFFRACTIONr_bond_other_d0.0020.026077
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9818737
X-RAY DIFFRACTIONr_angle_other_deg0.956313890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6435781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.56121.897311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.871151003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8841585
X-RAY DIFFRACTIONr_chiral_restr0.0820.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217259
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021556
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_it1.013.0543109
X-RAY DIFFRACTIONr_mcbond_other1.0073.0493105
X-RAY DIFFRACTIONr_mcangle_it1.6714.5663878
X-RAY DIFFRACTIONr_mcangle_other1.6714.5653879
X-RAY DIFFRACTIONr_scbond_it1.2153.2783317
X-RAY DIFFRACTIONr_scbond_other1.2153.2793318
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.974.8364855
X-RAY DIFFRACTIONr_long_range_B_refined5.06624.6457182
X-RAY DIFFRACTIONr_long_range_B_other5.06624.657183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 198 -
Rwork0.24 3769 -
obs--99.97 %
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)
11.77330.1455-1.50971.5151-0.4462.87160.1672-0.20760.21620.0276-0.0169-0.0132-0.57560.1564-0.15030.2117-0.0789-0.06250.24790.14050.1808-6.817345.756127.8031
21.38470.42150.01482.66181.09341.0732-0.01210.1825-0.2076-0.1029-0.07680.1120.0455-0.11450.08890.0187-0.0016-0.00460.0433-0.04160.0456-11.3526.025139.9896
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 391
2X-RAY DIFFRACTION2C-5 - 391

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