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- PDB-5ex6: Structure of P450 StaH from glycopeptide antibiotic A47934 biosyn... -

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Basic information

Entry
Database: PDB / ID: 5ex6
TitleStructure of P450 StaH from glycopeptide antibiotic A47934 biosynthesis
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: 2.4 Å
AuthorsCryle, M.J. / Ulrich, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCR 392/1-1 Germany
CitationJournal: Mol Biosyst / Year: 2016
Title: More than just recruitment: the X-domain influences catalysis of the first phenolic coupling reaction in A47934 biosynthesis by Cytochrome P450 StaH.
Authors: Ulrich, V. / Peschke, M. / Brieke, C. / Cryle, M.J.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / 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 / _pdbx_audit_support.funding_organization / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cytochrome P450
A: Cytochrome P450
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,20812
Polymers143,8963
Non-polymers2,3129
Water4,197233
1
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6443
Polymers47,9651
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7985
Polymers47,9651
Non-polymers8334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7664
Polymers47,9651
Non-polymers8013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.520, 109.520, 187.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cytochrome P450 / StaH


Mass: 47965.402 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Gene: BU52_01285 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KLL9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / StaH / HEME


Mass: 616.487 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Gene: BU52_01285 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M (NH4)3 citrate pH 7.0, 16.0% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0039 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0039 Å / Relative weight: 1
ReflectionResolution: 2.4→47.4 Å / Num. obs: 47412 / % possible obs: 95.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.099 / Rsym value: 0.089 / Net I/σ(I): 14.7
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4 / % possible all: 88.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
PHASERphasing
XDSdata reduction
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LFK

1lfk


Resolution: 2.4→47.4 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 19.072 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.544 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24728 4681 9.5 %RANDOM
Rwork0.19587 ---
obs0.20072 44636 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: 42.591 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20.92 Å20 Å2
2--1.85 Å20 Å2
3----2.77 Å2
Refinement stepCycle: 1 / Resolution: 2.4→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9038 0 30 233 9301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0219257
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.082.02212596
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.73951136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88421.601431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.385151487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.05215131
X-RAY DIFFRACTIONr_chiral_restr0.0710.21389
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217148
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_it0.2581.55702
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.51429159
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.93433555
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5994.53437
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: 2.4→2.49 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.302 477 -
Rwork0.247 4672 -
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)
11.6104-1.0523-1.95630.79930.807111.4486-0.0456-0.3826-0.0289-0.06340.1947-0.14250.75171.2067-0.14910.16590.09490.08770.15830.02230.3407-24.92-59.8554-45.6491
210.17955.54990.15876.04863.24773.4381-0.1967-0.5537-0.78950.24910.0615-0.46340.25030.62060.13520.2742-0.1353-0.15520.64040.26030.4891-22.2989-41.9007-33.6596
30.36960.01620.08371.1535-1.16655.8973-0.0506-0.08640.0938-0.09910.1150.1185-0.2652-0.1957-0.06440.1650.0690.0020.0656-0.00310.129-37.112-34.3869-53.8376
45.13780.9487-3.99083.1685-0.42579.07110.0438-0.46480.12340.0718-0.09950.1041-0.79430.79410.05570.32120.0078-0.14120.2175-0.03850.1447-28.5379-27.3436-43.0669
51.9801-0.09241.53851.3206-0.44215.6859-0.0066-0.1202-0.0611-0.137-0.00660.1170.2729-0.0950.01320.10610.02910.06380.01730.02690.0772-36.2162-52.556-54.1102
60.602-0.57380.39161.8252-1.01593.9525-0.07470.0186-0.0699-0.23520.03220.0140.1620.08330.04260.11330.00320.03140.01440.00840.0744-36.2397-51.4102-58.7033
79.27266.5216-7.86015.1321-4.50898.6697-0.3650.0697-0.40170.36890.0053-0.18871.6752-0.17530.35961.0944-0.0572-0.0840.2415-0.02520.371-65.1884-75.5494-20.9205
82.85945.15920.62429.32010.95167.28010.16880.0334-0.83540.22580.051-1.48191.3690.7818-0.21980.45250.1955-0.02550.3271-0.00940.3559-57.8826-66.97-5.9869
91.86740.4909-0.3041.3643-0.7872.86660.0999-0.11570.1752-0.0882-0.0877-0.0528-0.26770.1938-0.01220.12380.09070.02420.20440.00890.124-48.448-48.0328-23.6661
103.311-2.6529-3.29748.44414.17186.95930.2669-0.78250.02990.6909-0.0759-0.25460.38940.4223-0.1910.3202-0.0329-0.07790.59970.11860.1757-37.0548-52.3017-12.5583
111.65370.03580.86432.5294-0.71634.3540.0577-0.051-0.1947-0.1099-0.05030.25630.5567-0.3766-0.00740.21690.0650.02720.1925-0.04910.1018-64.866-60.287-20.9389
120.48720.7437-0.92742.04770.22127.1395-0.10570.0956-0.0458-0.36280.04670.03990.4568-0.03580.0590.20490.1097-0.05510.1907-0.04290.0736-59.1919-55.8228-30.3855
131.79080.73090.52061.16020.63456.1251-0.05630.1304-0.28320.01280.15760.15780.723-0.4435-0.10130.1232-0.07310.03240.1504-0.00370.1938-17.6635-38.7247-7.1123
1418.639312.631-9.671418.5416-10.783421.4453-0.2474-0.9563-2.21940.8832-0.8933-0.40031.53360.40751.14080.41880.06710.18430.29860.1490.50280.2452-36.8276.5864
151.2430.9489-0.43872.6426-2.699710.6212-0.1990.11150.2739-0.0630.1166-0.0446-0.55290.19330.08240.0727-0.0402-0.02660.089-0.0070.2182-1.359-17.3484-12.0388
162.51940.15070.5891.2761-0.07123.6249-0.0397-0.04730.14870.02470.0998-0.0065-0.03470.101-0.06010.0078-0.01140.01690.12090.020.16358.4391-22.4134-12.943
171.5346-0.07410.40362.0039-0.54674.6998-0.13420.00150.1446-0.10180.11170.3654-0.1385-0.52780.02240.0327-0.0218-0.02290.1436-0.01690.1749-16.6958-26.5039-15.841
180.58540.5748-0.38681.5646-0.89554.3102-0.13850.2210.0343-0.2970.08480.1490.1097-0.32030.05370.0662-0.0423-0.04550.1645-0.00580.1675-14.4453-25.4789-21.538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 65
2X-RAY DIFFRACTION2A66 - 89
3X-RAY DIFFRACTION3A90 - 172
4X-RAY DIFFRACTION4A173 - 232
5X-RAY DIFFRACTION5A233 - 302
6X-RAY DIFFRACTION6A303 - 398
7X-RAY DIFFRACTION7B6 - 33
8X-RAY DIFFRACTION8B40 - 93
9X-RAY DIFFRACTION9B94 - 172
10X-RAY DIFFRACTION10B173 - 226
11X-RAY DIFFRACTION11B227 - 334
12X-RAY DIFFRACTION12B335 - 398
13X-RAY DIFFRACTION13C6 - 64
14X-RAY DIFFRACTION14C65 - 82
15X-RAY DIFFRACTION15C83 - 133
16X-RAY DIFFRACTION16C134 - 239
17X-RAY DIFFRACTION17C240 - 305
18X-RAY DIFFRACTION18C306 - 398

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