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- PDB-4kc5: Crystal structure of the C-terminal part of RhiE from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 4kc5
TitleCrystal structure of the C-terminal part of RhiE from Burkholderia rhizoxinica
ComponentsRhiE protein
KeywordsTRANSFERASE / KS-Domain / DHF-domain / beta-branching unit of RhiE
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #3290 / Polyketide synthase dehydratase / : / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH ...Alpha-Beta Plaits - #3290 / Polyketide synthase dehydratase / : / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Thiol Ester Dehydrase; Chain A / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Roll / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia rhizoxinica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsZocher, G. / Heim, J.B. / Stehle, T.
CitationJournal: Nature / Year: 2013
Title: Vinylogous chain branching catalysed by a dedicated polyketide synthase module.
Authors: Bretschneider, T. / Heim, J.B. / Heine, D. / Winkler, R. / Busch, B. / Kusebauch, B. / Stehle, T. / Zocher, G. / Hertweck, C.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: RhiE protein
B: RhiE protein
C: RhiE protein
D: RhiE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,7585
Polymers409,6654
Non-polymers921
Water18,3031016
1
A: RhiE protein
B: RhiE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,9253
Polymers204,8332
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-42 kcal/mol
Surface area65860 Å2
MethodPISA
2
C: RhiE protein
D: RhiE protein


Theoretical massNumber of molelcules
Total (without water)204,8332
Polymers204,8332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-42 kcal/mol
Surface area64610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.510, 144.130, 131.300
Angle α, β, γ (deg.)90.00, 96.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RhiE protein


Mass: 102416.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia rhizoxinica (bacteria) / Gene: rhiE / Production host: Escherichia coli (E. coli) / References: UniProt: A1KQS1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1016 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% (w/v) PEG 2000 MME, 100 mM Tris/HCl pH 8.5, 100 mM Trismethylamine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Oct 22, 2012
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. all: 254914 / Num. obs: 252811 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.14→2.2 Å / Mean I/σ(I) obs: 2.02 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0027refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→48.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.783 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22716 7585 3 %RANDOM
Rwork0.18076 ---
obs0.18213 245224 99.18 %-
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: 45.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-3.02 Å2
2---1.69 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.14→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28171 0 6 1016 29193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02228828
X-RAY DIFFRACTIONr_bond_other_d0.0010.0226903
X-RAY DIFFRACTIONr_angle_refined_deg1.551.95639163
X-RAY DIFFRACTIONr_angle_other_deg0.807361789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4953628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0324.1291332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.463154648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.56715170
X-RAY DIFFRACTIONr_chiral_restr0.0930.24337
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02133206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026752
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 550 -
Rwork0.269 17786 -
obs--97.81 %
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)
10.6680.1891-0.26080.764-0.16180.5554-0.029-0.0582-0.0484-0.06340.04540.1114-0.01220.0644-0.01630.0113-0.0130.00380.1010.01050.058540.261124.706850.2961
20.4258-0.0612-0.18170.88210.25920.96240.0190.03490.0034-0.27660.00950.4415-0.094-0.1297-0.02850.0955-0.0178-0.1580.11810.0580.343513.793645.80234.3266
30.920.3126-0.07620.820.01660.36880.0387-0.0875-0.05570.4738-0.0106-0.15360.0554-0.0065-0.02810.4142-0.008-0.07910.14680.00750.057478.165723.7517112.1955
40.5255-0.1049-0.24570.81250.13330.75680.00460.06180.05730.14560.03350.0544-0.0372-0.0645-0.03810.0648-0.02640.03260.15210.04060.048965.636344.728784.33
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3052 - 3965
2X-RAY DIFFRACTION2B3053 - 3965
3X-RAY DIFFRACTION3C3053 - 3964
4X-RAY DIFFRACTION4D3052 - 3965

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