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- PDB-7abb: The truncated structure of the Bottromycin biosynthetic protein SalCYP -

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Basic information

Entry
Database: PDB / ID: 7abb
TitleThe truncated structure of the Bottromycin biosynthetic protein SalCYP
ComponentsSalCYP truncation
KeywordsBIOSYNTHETIC PROTEIN / Cytochrome / P450 / Bottromycin
Function / homologyHEME C
Function and homology information
Biological speciesSalinispora tropica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.50004339457 Å
AuthorsAdam, S. / Koehnke, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO 4116/3-2 Germany
Citation
Journal: J.Am.Chem.Soc. / Year: 2020
Title: Characterization of the Stereoselective P450 Enzyme BotCYP Enables the In Vitro Biosynthesis of the Bottromycin Core Scaffold.
Authors: Adam, S. / Franz, L. / Milhim, M. / Bernhardt, R. / Kalinina, O.V. / Koehnke, J.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionSep 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SalCYP truncation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3992
Polymers43,7811
Non-polymers6191
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-24 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.538, 96.538, 49.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein SalCYP truncation


Mass: 43780.660 Da / Num. of mol.: 1 / Mutation: A199T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinispora tropica (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PEG8000, Glycerol, Magnesium acetate, Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.5→68.26 Å / Num. obs: 73906 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 18.3884898734 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.1
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.889 / Num. unique obs: 10737

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.11.1_2575refinement
Cootmodel building
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ABA

7aba


Resolution: 1.50004339457→48.269 Å / SU ML: 0.149346541196 / Cross valid method: FREE R-VALUE / σ(F): 1.34368568842 / Phase error: 21.7436909169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.181174718663 3691 4.99918734424 %
Rwork0.163416007036 70141 -
obs0.164302924969 73832 99.8904117002 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.1858038443 Å2
Refinement stepCycle: LAST / Resolution: 1.50004339457→48.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 0 306 3245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008086670109493028
X-RAY DIFFRACTIONf_angle_d0.965950927414141
X-RAY DIFFRACTIONf_chiral_restr0.0525586885495429
X-RAY DIFFRACTIONf_plane_restr0.00662916568899549
X-RAY DIFFRACTIONf_dihedral_angle_d17.84189663891763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.50005-1.51980.2847409203531340.3083223264712673X-RAY DIFFRACTION99.8577018855
1.5198-1.54060.3336146081861580.2727999685182675X-RAY DIFFRACTION99.9294532628
1.5406-1.56260.2676191315281150.2588262036032734X-RAY DIFFRACTION99.9298491757
1.5626-1.58590.2755432766741400.2337628689112641X-RAY DIFFRACTION99.8563734291
1.5859-1.61070.260638349481190.2299548602882738X-RAY DIFFRACTION99.7904296193
1.6107-1.63710.2131240885091590.2152027609842635X-RAY DIFFRACTION99.8570407434
1.6371-1.66540.2279453984631530.199254664362704X-RAY DIFFRACTION99.8601887452
1.6654-1.69560.2278173191661540.1919895662632636X-RAY DIFFRACTION99.8568360773
1.6956-1.72830.2341357807461490.1815267987692690X-RAY DIFFRACTION99.9647887324
1.7283-1.76350.2049951564741220.1786616711092689X-RAY DIFFRACTION100
1.7635-1.80190.1662820373051580.1678622488662691X-RAY DIFFRACTION99.8597967052
1.8019-1.84380.1899010656491460.1664073267332669X-RAY DIFFRACTION99.8581057112
1.8438-1.88990.1776969788551350.1607590178752661X-RAY DIFFRACTION99.9285203717
1.8899-1.9410.1850610813731600.1546034793822710X-RAY DIFFRACTION99.8955795336
1.941-1.99810.1904501277251340.1446285775862689X-RAY DIFFRACTION99.9645892351
1.9981-2.06260.1770629406481380.1442305452322694X-RAY DIFFRACTION100
2.0626-2.13630.1637948184121280.1430823337812727X-RAY DIFFRACTION99.9649859944
2.1363-2.22190.1703633297471490.1427317212472670X-RAY DIFFRACTION100
2.2219-2.3230.1618160466241500.1411450688892699X-RAY DIFFRACTION100
2.323-2.44550.1693052834271400.1370409817252684X-RAY DIFFRACTION99.3316918748
2.4455-2.59870.1642270015631480.1425896919472709X-RAY DIFFRACTION99.8252969951
2.5987-2.79930.1750261556381120.1403639705012738X-RAY DIFFRACTION99.9649245879
2.7993-3.0810.1502794462081620.1501385654532706X-RAY DIFFRACTION99.9651446497
3.081-3.52670.1780697178941430.150853255442705X-RAY DIFFRACTION100
3.5267-4.44280.1654067864971380.1493732032132758X-RAY DIFFRACTION100
4.4428-48.2680.188698264451470.196528842632816X-RAY DIFFRACTION99.7307303938
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)
13.878800605910.621469438331-1.78563020231.22130265829-0.3841044306931.384292989130.05019827561820.3022787215230.298699695691-0.1678421644510.02588933603050.00754457585613-0.0225462675975-0.0921222058216-0.05003893120550.214849107842-0.00289564251934-0.02326531002760.1681263401680.02160194171790.15335146726128.492105389737.4802191143-8.27854662575
21.80557302221-0.00540145033899-0.3489562448842.29865646704-0.03337661475620.5507982512060.03403515358170.1604615258740.0963423330765-0.25612005097-0.01665691009520.188714993965-0.0459472357518-0.0623137689418-0.0004545954982840.1624047209350.00147223072329-0.02421033039820.1549808231470.01409490547470.1190497788339.7744665969224.3553776366-3.10549471296
32.293049118521.59890593962-0.712486715975.7086229593-3.57854873363.897053164740.0206633192936-0.105372864824-0.04759943759810.07817173239-0.123585098697-0.242149422469-0.06371422734490.1427425154520.09119667828680.1179002671250.02136945797940.008414808561630.144220569533-0.02668130634840.15325960196633.699994159231.8935756394-1.9229676489
41.550707112260.17834418268-0.2973345928234.453129873830.2191479000910.902081780498-0.0238296942775-0.00121291578595-0.0292162896961-0.1320310784810.0436890891867-0.09740968937940.02150568174620.0269011508631-0.03753150569280.1286557180080.000975387081314-0.03113068694850.1689501987080.004977407557070.11580614391920.155645233816.1921112368-0.0550612742315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 290 )
3X-RAY DIFFRACTION3chain 'A' and (resid 291 through 344 )
4X-RAY DIFFRACTION4chain 'A' and (resid 345 through 400 )

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