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- PDB-3mgx: Crystal Structure of P450 OxyD that is involved in the Biosynthes... -

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Basic information

Entry
Database: PDB / ID: 3mgx
TitleCrystal Structure of P450 OxyD that is involved in the Biosynthesis of Vancomycin-type Antibiotics
ComponentsPutative P450 monooxygenase
KeywordsOXIDOREDUCTASE / Cytochrome P450 Oxidase / Haem Protein / Vancomycin Biosynthesis / Carrier Protein
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / hydrolase 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 / Putative P450 monooxygenase
Similarity search - Component
Biological speciesAmycolatopsis balhimycina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCryle, M.J. / Schlichting, I.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural characterization of oxyd, a cytochrome p450 involved in {beta}-hydroxytyrosine formation in vancomycin biosynthesis
Authors: Cryle, M.J. / Meinhart, A. / Schlichting, I.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative P450 monooxygenase
B: Putative P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,90814
Polymers90,7542
Non-polymers2,15412
Water3,675204
1
A: Putative P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4547
Polymers45,3771
Non-polymers1,0776
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4547
Polymers45,3771
Non-polymers1,0776
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.850, 61.050, 100.640
Angle α, β, γ (deg.)90.00, 102.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative P450 monooxygenase / Cytochrome P450 OxyD (CYP146)


Mass: 45377.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis balhimycina (bacteria) / Strain: DSM 5908 / Gene: oxyD / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q939Y1, unspecific monooxygenase
#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.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 18% PEG 2000 MME, 0.1M Bis-Tris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 45824 / Num. obs: 44661 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Redundancy: 7.9 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.5 / Num. unique all: 5487 / % possible all: 92.4

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EJB

3ejb


Resolution: 2.1→19.75 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.716 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23302 2286 5 %RANDOM
Rwork0.20786 ---
obs0.20913 43424 100 %-
all-45824 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.757 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.71 Å2
2--0.79 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5968 0 146 204 6318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216261
X-RAY DIFFRACTIONr_angle_refined_deg0.8842.0138552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1625781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66522.724279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37615966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.391568
X-RAY DIFFRACTIONr_chiral_restr0.0550.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214801
X-RAY DIFFRACTIONr_mcbond_it0.1521.53888
X-RAY DIFFRACTIONr_mcangle_it0.28726281
X-RAY DIFFRACTIONr_scbond_it0.40832373
X-RAY DIFFRACTIONr_scangle_it0.6914.52269
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 164 -
Rwork0.242 3123 -
obs-3123 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)
12.8278-0.33230.79951.8684-0.98273.3343-0.1301-0.23520.35780.06140.08850.144-0.0306-0.33230.04160.0186-0.011-0.00420.1708-0.03870.069337.42812.858341.2618
26.098-0.9560.75727.0938-1.6695.7556-0.079-0.5633-0.6866-0.211-0.06540.22830.9498-0.36080.14440.2828-0.09930.03850.22780.03550.094342.5656-5.786145.3629
38.37092.57781.41711.05852.45294.0958-0.157-0.79270.12931.10240.1236-0.65140.17350.20920.03340.18990.0702-0.07870.30090.00650.060151.51621.977360.1704
42.1208-0.3131-0.09112.1637-1.07393.5184-0.12910.20380.3413-0.20110.13380.07280.0478-0.2144-0.00460.0344-0.0442-0.03070.2007-0.00380.075341.84212.725733.3622
59.1821-2.4556-0.82414.18570.80483.59130.05310.7308-1.0873-0.8978-0.07210.3890.6844-0.20210.0190.5119-0.161-0.06950.2518-0.02670.152939.5025-3.815926.8996
62.44971.71180.18931.87140.44373.9173-0.27150.1932-0.0805-0.12780.0706-0.4435-0.06160.75990.20090.117-0.06290.00040.23110.07430.293529.945713.246711.3165
72.82041.0261.31472.22830.84122.4435-0.17280.36670.1697-0.10540.02420.1416-0.09230.1880.14860.0804-0.01050.03690.05620.0260.110311.14176.04983.1881
84.22940.21710.75622.86830.40763.3330.16850.3283-0.4027-0.1937-0.03820.07310.29660.2859-0.13030.12580.0436-0.00520.0479-0.05470.13979.165-9.2998-1.4069
92.09670.36811.07441.90590.7012.6426-0.099-0.09590.3070.1396-0.07670.0987-0.1489-0.00310.17560.0708-0.01610.01290.0167-0.00340.119212.577310.44813.7617
107.20331.871-0.20663.6568-0.93734.4220.4175-0.7724-0.51710.7764-0.3198-0.16410.4860.1813-0.09770.4157-0.0786-0.01450.09870.03530.110514.5222-4.571723.0907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 135
2X-RAY DIFFRACTION2A136 - 190
3X-RAY DIFFRACTION3A191 - 224
4X-RAY DIFFRACTION4A225 - 358
5X-RAY DIFFRACTION5A359 - 396
6X-RAY DIFFRACTION6B6 - 44
7X-RAY DIFFRACTION7B45 - 138
8X-RAY DIFFRACTION8B139 - 227
9X-RAY DIFFRACTION9B228 - 357
10X-RAY DIFFRACTION10B358 - 396

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