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- PDB-4yuf: Crystal Structure of CorB -

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Basic information

Entry
Database: PDB / ID: 4yuf
TitleCrystal Structure of CorB
ComponentsCorB
KeywordsHYDROLASE / Interconnecting Ketosynthase / thiolase superfamily
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-(Acyl-carrier-protein) synthase III
Similarity search - Component
Biological speciesCorallococcus coralloides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsZocher, G. / Vilstrup, J. / Stehle, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Centre for Infection Research Germany
DFG766 and 854 Germany
CitationJournal: Chem Sci / Year: 2015
Title: Structural basis of head to head polyketide fusion by CorB.
Authors: Zocher, G. / Vilstrup, J. / Heine, D. / Hallab, A. / Goralski, E. / Hertweck, C. / Stahl, M. / Schaberle, T.F. / Stehle, T.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CorB


Theoretical massNumber of molelcules
Total (without water)36,6771
Polymers36,6771
Non-polymers00
Water4,594255
1
A: CorB

A: CorB


Theoretical massNumber of molelcules
Total (without water)73,3542
Polymers73,3542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5760 Å2
ΔGint-25 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.920, 106.310, 104.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

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Components

#1: Protein CorB


Mass: 36676.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corallococcus coralloides (bacteria) / Gene: corB / Production host: Escherichia coli (E. coli) / References: UniProt: D7RK32
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate (pH 6.5), 8% (w/v) PEG8000 and 34% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 23, 2013
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 52020 / % possible obs: 99.7 % / Redundancy: 12.7 % / Net I/σ(I): 22.1
Reflection shellResolution: 1.54→1.58 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.05 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0027refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→37.63 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.645 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18238 1561 3 %RANDOM
Rwork0.17652 ---
obs0.1767 50458 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.658 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2--1.29 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.54→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 0 255 2780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222601
X-RAY DIFFRACTIONr_bond_other_d0.0010.022471
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9773537
X-RAY DIFFRACTIONr_angle_other_deg0.80435681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.9775335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17222.857112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8115415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4281523
X-RAY DIFFRACTIONr_chiral_restr0.0990.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02590
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 111 -
Rwork0.28 3576 -
obs--97.26 %
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)
11.8533-0.5312-0.29979.28563.96652.8976-0.04150.0623-0.2282-0.1841-0.24720.4452-0.0088-0.16370.28880.01430.01340.00940.0424-0.00350.060722.226241.574739.4327
211.7274-1.24613.81747.6269-1.08795.5569-0.24680.33341.2636-0.162-0.040.5643-0.699-0.2270.28670.17580.0968-0.05030.08770.02010.28926.062568.983241.3643
32.0186-0.88440.51412.09470.00390.951-0.1012-0.14960.2170.12610.05350.063-0.1322-0.02030.04770.04870.0170.00230.0582-0.00590.042323.333356.722545.3457
42.27820.8725-0.46762.2443-0.70152.2875-0.0361-0.0650.16010.07010.07930.0007-0.16560.0253-0.04320.02490.0175-0.00260.0506-0.0130.015235.161849.867338.019
52.17670.0303-0.26520.59470.49251.63-0.05450.11250.0719-0.05380.05620.0172-0.067-0.0427-0.00170.019-0.0038-0.00050.05160.01990.008826.60647.794335.2726
63.3335-0.06551.14560.008-0.1013.28570.03930.18640.537-0.00970.02350.0064-0.1931-0.0838-0.06280.0625-0.0157-0.00340.06230.03040.149920.166352.29319.9714
733.4548.24321.444514.49684.6633.8897-0.0157-0.2742.6496-0.58760.32370.273-0.71510.4137-0.3080.3620.00530.04810.2263-0.18150.79824.130669.806420.4469
83.8164-1.88481.413211.292-5.34584.2318-0.02060.16620.18740.08990.19530.4132-0.0089-0.2533-0.17470.0288-0.01560.00190.1061-0.00120.09698.957745.046619.1255
92.0634-0.05810.59341.70390.3431.5871-0.0609-0.0742-0.077-0.01160.00330.24950.0376-0.22010.05760.04380.0150.01320.08710.01260.04419.370746.637436.4805
101.2214-0.1371-0.33670.9502-0.71072.5544-0.0394-0.1049-0.1410.03590.09920.18650.126-0.1315-0.05990.0472-0.00210.0180.04370.02120.053214.317340.090834.6276
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 23
2X-RAY DIFFRACTION2A24 - 45
3X-RAY DIFFRACTION3A46 - 72
4X-RAY DIFFRACTION4A73 - 104
5X-RAY DIFFRACTION5A105 - 184
6X-RAY DIFFRACTION6A185 - 210
7X-RAY DIFFRACTION7A211 - 227
8X-RAY DIFFRACTION8A228 - 250
9X-RAY DIFFRACTION9A251 - 307
10X-RAY DIFFRACTION10A308 - 335

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