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- PDB-6fsh: Crystal structure of hybrid P450 OxyBtei(BC/FGvan) -

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Basic information

Entry
Database: PDB / ID: 6fsh
TitleCrystal structure of hybrid P450 OxyBtei(BC/FGvan)
ComponentsOxyB protein
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / PHENOLIC COUPLING ENZYME / TEICOPLANIN BIOSYNTHESIS
Function / homology
Function and homology information


glycosyltransferase activity / 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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / : / Oxidation protein CepF/oxidation protein CepG
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBrieke, C. / Tarnawski, M. / Greule, A. / Cryle, M.J.
Funding support Germany, Australia, 2items
OrganizationGrant numberCountry
German Research FoundationCR 392/1-1 Germany
Australian Research CouncilDP170102220 Australia
CitationJournal: J. Inorg. Biochem. / Year: 2018
Title: Investigating Cytochrome P450 specificity during glycopeptide antibiotic biosynthesis through a homologue hybridization approach.
Authors: Brieke, C. / Tarnawski, M. / Greule, A. / Cryle, M.J.
History
DepositionFeb 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OxyB protein
B: OxyB protein
C: OxyB protein
D: OxyB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,65112
Polymers176,0094
Non-polymers2,6428
Water2,540141
1
A: OxyB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6974
Polymers44,0021
Non-polymers6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OxyB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6583
Polymers44,0021
Non-polymers6562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: OxyB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6192
Polymers44,0021
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: OxyB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6783
Polymers44,0021
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.270, 83.160, 92.220
Angle α, β, γ (deg.)85.20, 101.98, 97.83
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
OxyB protein


Mass: 44002.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: tcp20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70AY8
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES-NaOH pH 7.5, 0.2 M potassium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99991 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99991 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 57549 / % possible obs: 97.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3 / Num. unique obs: 6375 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(dev_2645: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVF

4tvf


Resolution: 2.5→48.257 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.78
RfactorNum. reflection% reflection
Rfree0.2462 2877 5 %
Rwork0.1875 --
obs0.1904 57545 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11503 0 179 141 11823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911940
X-RAY DIFFRACTIONf_angle_d1.02416312
X-RAY DIFFRACTIONf_dihedral_angle_d11.8627120
X-RAY DIFFRACTIONf_chiral_restr0.0521842
X-RAY DIFFRACTIONf_plane_restr0.0072139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5410.37231370.28492594X-RAY DIFFRACTION97
2.541-2.58480.36121390.25482639X-RAY DIFFRACTION97
2.5848-2.63180.33171330.23352539X-RAY DIFFRACTION98
2.6318-2.68240.28981380.22262624X-RAY DIFFRACTION97
2.6824-2.73720.27881350.21742561X-RAY DIFFRACTION97
2.7372-2.79670.29191390.21212641X-RAY DIFFRACTION98
2.7967-2.86170.25691370.2052594X-RAY DIFFRACTION98
2.8617-2.93330.28271350.21062582X-RAY DIFFRACTION97
2.9333-3.01260.27891370.2132594X-RAY DIFFRACTION98
3.0126-3.10120.29491390.20382635X-RAY DIFFRACTION98
3.1012-3.20130.27341370.19932602X-RAY DIFFRACTION98
3.2013-3.31570.27321390.18952643X-RAY DIFFRACTION98
3.3157-3.44840.24561350.19572579X-RAY DIFFRACTION98
3.4484-3.60530.2521380.18082611X-RAY DIFFRACTION98
3.6053-3.79530.25191370.17092597X-RAY DIFFRACTION97
3.7953-4.0330.20951360.16782599X-RAY DIFFRACTION97
4.033-4.34420.22481360.1642575X-RAY DIFFRACTION97
4.3442-4.7810.22131380.15362619X-RAY DIFFRACTION98
4.781-5.4720.18461380.16792617X-RAY DIFFRACTION98
5.472-6.89090.25491360.2082590X-RAY DIFFRACTION98
6.8909-48.26570.21141380.17722633X-RAY DIFFRACTION98
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)
11.513-1.12990.58823.9185-0.06531.6343-0.03290.0282-0.07850.32410.1046-0.19540.00770.0615-0.0820.48-0.03160.00820.21070.00010.2709-11.97543.6259-18.6141
23.6968-3.8647-0.67555.2296-0.39925.1462-0.8703-1.2727-0.12551.6111.150.45860.2027-0.5114-0.05560.89430.3160.18990.73860.03090.6596-23.844-0.6185-3.7059
32.3684-1.36710.40723.4218-0.9211.7755-0.01640.11690.05880.06650.0169-0.1467-0.13580.0318-0.00040.399-0.0177-0.03780.2136-0.01540.2974-13.87618.5954-26.5971
41.31210.91120.31814.58331.3711.6612-0.02190.1027-0.1155-0.30250.0560.2323-0.0639-0.1132-0.03090.50330.0591-0.05490.26170.05540.3173-19.2859-39.4339-37.0131
50.781.9334-1.21815.1147-3.52473.9303-0.9090.75880.0229-2.09411.1275-0.5906-0.25290.68520.59861.2493-0.25840.1430.42720.01780.6901-6.7806-40.3997-51.3212
61.51021.04220.22774.65561.17091.79590.0267-0.08640.05670.0054-0.07920.3332-0.1415-0.09470.03370.43620.0491-0.07260.23810.01970.335-19.161-34.1304-28.7024
71.40850.02210.22013.2942-1.07541.96430.07570.0865-0.1524-0.354-0.05190.08380.0076-0.0242-0.04480.46840.0267-0.11790.2434-0.07560.34324.4894-35.01786.1608
86.16982.4171.46864.45220.27881.5581-0.1850.3082-0.2466-1.70270.76831.49620.646-0.9899-0.19460.8006-0.1506-0.30140.58620.21160.8294-14.5001-34.71585.9113
90.7954-0.52840.53543.8169-1.9852.15340.00530.0144-0.0174-0.1367-0.0351-0.18130.08260.0650.01940.47880.0331-0.04460.3077-0.04540.343710.9446-39.495512.3411
101.7227-0.7633-0.03263.21890.63391.7296-0.1437-0.03570.08380.44710.15-0.26840.073-0.0424-0.02090.3918-0.0019-0.10420.24680.00850.37484.3246.798228.3528
112.5368-1.2366-1.05325.80292.56121.2552-0.5591-0.94710.75770.43441.3938-1.37230.22131.0543-0.35170.66210.1074-0.39630.6953-0.3071.615722.750812.128228.9383
122.0156-1.1236-0.74293.40841.43081.63440.00420.0234-0.02520.17320.0306-0.05720.1947-0.0507-0.00510.48610.0261-0.08350.28730.01130.2995-0.43340.88122.0503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:157)
2X-RAY DIFFRACTION2(chain A and resid 158:221)
3X-RAY DIFFRACTION3(chain A and resid 222:398)
4X-RAY DIFFRACTION4(chain B and resid 7:159)
5X-RAY DIFFRACTION5(chain B and resid 160:221)
6X-RAY DIFFRACTION6(chain B and resid 222:398)
7X-RAY DIFFRACTION7(chain C and resid 7:159)
8X-RAY DIFFRACTION8(chain C and resid 160:221)
9X-RAY DIFFRACTION9(chain C and resid 222:398)
10X-RAY DIFFRACTION10(chain D and resid 7:159)
11X-RAY DIFFRACTION11(chain D and resid 160:221)
12X-RAY DIFFRACTION12(chain D and resid 222:398)

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