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- PDB-5hu7: Crystal structure of the trans-AT PKS dehydratase domain of C0ZGQ... -

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Basic information

Entry
Database: PDB / ID: 5hu7
TitleCrystal structure of the trans-AT PKS dehydratase domain of C0ZGQ4 from Brevibacillus brevis
ComponentsPutative polyketide synthase
KeywordsLYASE / polyketide / trans-AT PKS / Polyketide Synthase / dehydratase
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site ...Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / 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 / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Putative polyketide synthase
Similarity search - Component
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJakob, R.P. / Hauswirth, P. / Dilmi, J. / Herbst, D.A. / Maier, T.
CitationJournal: To Be Published
Title: Crystal Structures of Dehydratase Domains from trans-AT Polyketide Biosynthetic Pathway
Authors: Jakob, R.P. / Herbst, D.A. / Muller, R. / Maier, T.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative polyketide synthase
B: Putative polyketide synthase


Theoretical massNumber of molelcules
Total (without water)71,1862
Polymers71,1862
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-8 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.610, 83.010, 48.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-3231-

HOH

21A-3242-

HOH

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Components

#1: Protein Putative polyketide synthase /


Mass: 35593.000 Da / Num. of mol.: 2 / Fragment: dehydratase domain, 2841-3160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (strain 47 / JCM 6285 / NBRC 100599) (bacteria)
Gene: BBR47_39860 / Plasmid: pNIC28a-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C0ZGQ4, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, Hepes pH 7.5, 25% PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→28.44 Å / Num. obs: 26210 / % possible obs: 99.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 72.83 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.3
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG9

3kg9


Resolution: 2.4→28.44 Å / Cor.coef. Fo:Fc: 0.9175 / Cor.coef. Fo:Fc free: 0.8945 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.35 / SU Rfree Blow DPI: 0.249
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1311 5 %RANDOM
Rwork0.2236 ---
obs0.2257 26210 99.57 %-
Displacement parametersBiso mean: 98.16 Å2
Baniso -1Baniso -2Baniso -3
1-9.1177 Å20 Å20 Å2
2--19.1525 Å20 Å2
3----28.2702 Å2
Refine analyzeLuzzati coordinate error obs: 0.376 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 0 0 65 4124
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018119HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1314661HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1786SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1192HARMONIC5
X-RAY DIFFRACTIONt_it8119HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion14.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion546SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8349SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.5 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.307 144 4.99 %
Rwork0.252 2741 -
all0.2548 2885 -
obs--99.62 %
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)
13.9848-0.31270.24524.01020.16470.23050.07610.1105-0.43-0.24040.0232-0.27350.0920.0385-0.0994-0.23050.0377-0.0807-0.3054-0.0746-0.2291-1.343219.868-2.0194
25.9124-1.88924.10821.4695-0.76953.0147-0.12920.01040.08570.11530.16050.1471-0.11680.0222-0.0313-0.2757-0.071-0.2689-0.40390.1304-0.0724-38.144538.0186-31.5466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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