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- PDB-6zi3: Crystal structure of OleP-6DEB bound to L-rhamnose -

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Basic information

Entry
Database: PDB / ID: 6zi3
TitleCrystal structure of OleP-6DEB bound to L-rhamnose
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / cytochrome P450 / 8.8a-deoxyoleandolide monooxygenase / 8.8a-deoxyoleandolide
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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
6-DEOXYERYTHRONOLIDE B / FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / alpha-L-rhamnopyranose / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.08 Å
AuthorsMontemiglio, L.C. / Savino, C. / Vallone, B. / Parisi, G. / Freda, I.
Funding support Italy, 1items
OrganizationGrant numberCountry
Pasteur Institute Italy
CitationJournal: Biomolecules / Year: 2020
Title: Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate.
Authors: Parisi, G. / Freda, I. / Exertier, C. / Cecchetti, C. / Gugole, E. / Cerutti, G. / D'Auria, L. / Macone, A. / Vallone, B. / Savino, C. / Montemiglio, L.C.
History
DepositionJun 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 P-450
B: Cytochrome P-450
C: Cytochrome P-450
D: Cytochrome P-450
E: Cytochrome P-450
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,663244
Polymers270,0726
Non-polymers17,590238
Water20,8791159
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23448
Polymers45,0121
Non-polymers3,22247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,40871
Polymers45,0121
Non-polymers4,39670
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,31267
Polymers45,0121
Non-polymers4,30066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,93921
Polymers45,0121
Non-polymers1,92720
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,70916
Polymers45,0121
Non-polymers1,69615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,06121
Polymers45,0121
Non-polymers2,04920
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)247.379, 111.149, 159.144
Angle α, β, γ (deg.)90.00, 129.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 13 molecules ABCDEF

#1: Protein
Cytochrome P-450


Mass: 45012.070 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: oleP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59819
#4: Sugar
ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 1390 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-DEB / 6-DEOXYERYTHRONOLIDE B


Mass: 386.523 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H38O6
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 203 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1159 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.1 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 4.2 M Sodium Formate (HCOONa)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 462663 / % possible obs: 97.7 % / Redundancy: 2.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.8
Reflection shellResolution: 1.96→2.08 Å / Rmerge(I) obs: 1.64 / Num. unique obs: 73872 / CC1/2: 0.362

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5MNS

5mns


Resolution: 2.08→48.09 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.753 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22501 9943 5 %RANDOM
Rwork0.17168 ---
obs0.17438 189127 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.045 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å2-0.55 Å2
2--1.37 Å20 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.08→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18570 0 1173 1159 20902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01322032
X-RAY DIFFRACTIONr_bond_other_d0.0010.01720820
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.68130141
X-RAY DIFFRACTIONr_angle_other_deg1.3411.59748233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80452892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06419.9551339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.351153651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.69415272
X-RAY DIFFRACTIONr_chiral_restr0.0850.22837
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0225521
X-RAY DIFFRACTIONr_gen_planes_other0.0060.025135
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_it2.2914.15410134
X-RAY DIFFRACTIONr_mcbond_other2.2914.15410135
X-RAY DIFFRACTIONr_mcangle_it3.3686.22412806
X-RAY DIFFRACTIONr_mcangle_other3.3686.22412807
X-RAY DIFFRACTIONr_scbond_it2.8174.55111898
X-RAY DIFFRACTIONr_scbond_other2.5194.40411493
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8996.59917065
X-RAY DIFFRACTIONr_long_range_B_refined7.81749.59824655
X-RAY DIFFRACTIONr_long_range_B_other7.79649.51324638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 726 -
Rwork0.427 13994 -
obs--99.94 %
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)
11.7596-0.12710.30230.6882-0.5241.16030.10180.1550.12370.0711-0.10460.0741-0.1130.13270.00290.0475-0.04360.04730.0996-0.02490.1148-68.7548-24.420719.3995
21.7166-0.027-0.00550.6608-0.2310.97460.0409-0.0079-0.1490.0194-0.0193-0.11030.0736-0.0026-0.02160.0474-0.0421-0.03790.06010.06990.140942.88394.781562.2839
31.0155-0.0053-0.00170.4168-0.30340.96610.0575-0.02560.00780.044-0.0215-0.0152-0.10550.0832-0.0360.0595-0.04320.01960.0362-0.00010.07033.8004-22.836281.4402
41.98220.2645-0.19530.5652-0.1251.1890.1606-0.1013-0.25980.05810.0384-0.03370.1416-0.1013-0.19890.0661-0.0897-0.11070.20280.18320.2004-30.6745.75121.3794
51.436-0.06270.38051.8091-0.01521.4978-0.0319-0.09330.1533-0.07360.1190.1878-0.0227-0.2622-0.0870.0083-0.0046-0.02060.05980.0260.1144-21.816714.699141.4193
60.6119-0.19970.58551.4925-0.20711.2247-0.0799-0.4069-0.0410.15340.1220.23580.0064-0.3685-0.04210.04180.0435-0.01060.28420.06740.171950.662622.226102.1864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 601
2X-RAY DIFFRACTION2B5 - 1401
3X-RAY DIFFRACTION3C11 - 1401
4X-RAY DIFFRACTION4D12 - 503
5X-RAY DIFFRACTION5E13 - 503
6X-RAY DIFFRACTION6F11 - 701

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