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- PDB-4z37: Structure of the ketosynthase of module 2 of C0ZGQ5 (trans-AT PKS... -

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Basic information

Entry
Database: PDB / ID: 4z37
TitleStructure of the ketosynthase of module 2 of C0ZGQ5 (trans-AT PKS) from Brevibacillus brevis
ComponentsPutative mixed polyketide synthase/non-ribosomal peptide synthetase
KeywordsTRANSFERASE / polyketide / ketosynthase / trans-AT / AT-less / pks
Function / homology
Function and homology information


phosphopantetheine binding / ligase activity / antibiotic biosynthetic process / transferase activity
Similarity search - Function
Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain ...Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation 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 / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / 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 / NAD(P)-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative mixed polyketide synthase/non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsMartin, S.F. / Jakob, R.P. / Herbst, D.A. / Maier, T.
CitationJournal: To Be Published
Title: The structural organization of trans-AT polyketide synthases: ketoacyl synthase and trans-acting enoyl reductase
Authors: Martin, S.F. / Jakob, R.P. / Herbst, D.A. / Maier, T.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Putative mixed polyketide synthase/non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)72,2551
Polymers72,2551
Non-polymers00
Water7,927440
1
A: Putative mixed polyketide synthase/non-ribosomal peptide synthetase

A: Putative mixed polyketide synthase/non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)144,5102
Polymers144,5102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4750 Å2
ΔGint-27 kcal/mol
Surface area44380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.292, 85.800, 89.254
Angle α, β, γ (deg.)90.00, 121.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-3435-

HOH

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Components

#1: Protein Putative mixed polyketide synthase/non-ribosomal peptide synthetase


Mass: 72254.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (strain 47 / JCM 6285 / NBRC 100599) (bacteria)
Strain: 47 / JCM 6285 / NBRC 100599 / Gene: BBR47_39870 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: C0ZGQ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.56 Å3/Da / Density % sol: 51.96 % / Description: rod like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium malonate, pH 7, and 15% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.998→42.9 Å / Num. obs: 49103 / % possible obs: 99.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.9
Reflection shellResolution: 1.998→2.05 Å / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.5 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HG4

2hg4


Resolution: 1.998→42.9 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 2476 5.04 %
Rwork0.1732 --
obs0.1749 49103 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4751 0 0 440 5191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044944
X-RAY DIFFRACTIONf_angle_d0.7966704
X-RAY DIFFRACTIONf_dihedral_angle_d13.381840
X-RAY DIFFRACTIONf_chiral_restr0.037713
X-RAY DIFFRACTIONf_plane_restr0.003879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9979-2.03630.25051360.2662471X-RAY DIFFRACTION95
2.0363-2.07790.31631200.25882559X-RAY DIFFRACTION99
2.0779-2.1230.30061460.25062538X-RAY DIFFRACTION100
2.123-2.17240.26831270.24182631X-RAY DIFFRACTION99
2.1724-2.22680.23931290.22042602X-RAY DIFFRACTION100
2.2268-2.2870.26371370.20852599X-RAY DIFFRACTION100
2.287-2.35430.21571420.19572573X-RAY DIFFRACTION100
2.3543-2.43020.23911480.18972585X-RAY DIFFRACTION100
2.4302-2.51710.26221620.18172586X-RAY DIFFRACTION100
2.5171-2.61790.22741490.1862558X-RAY DIFFRACTION100
2.6179-2.7370.2361430.16912627X-RAY DIFFRACTION100
2.737-2.88120.21421330.17312601X-RAY DIFFRACTION100
2.8812-3.06170.22351460.17312591X-RAY DIFFRACTION100
3.0617-3.2980.19051220.16492593X-RAY DIFFRACTION100
3.298-3.62980.21091260.15722616X-RAY DIFFRACTION100
3.6298-4.15460.17081310.14532630X-RAY DIFFRACTION100
4.1546-5.23290.15641470.13462609X-RAY DIFFRACTION99
5.2329-42.90990.18511320.17112658X-RAY DIFFRACTION99
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)
13.19591.5981.19342.18110.98771.7789-0.06410.18060.4427-0.3111-0.09780.2131-0.19320.04160.14920.22170.0306-0.03670.2180.0620.26235.269148.2142-16.754
22.36530.0220.59863.06950.20462.03940.08990.02230.0165-0.0372-0.04220.12370.0235-0.1812-0.05760.12970.016-0.00720.22450.03050.1797-7.387440.0422-11.1119
32.51030.04840.42481.4482-0.10471.44460.05860.00490.108-0.0456-0.04510.0419-0.0247-0.0624-0.020.1680.0244-0.02530.1660.00940.18263.90140.9751-8.8378
42.2077-0.30330.68711.85660.26612.30830.1298-0.006-0.27610.0798-0.0265-0.17530.28980.1399-0.12990.18860.0304-0.02140.2130.0150.293114.446828.7619-3.7394
53.2602-0.18331.50681.0483-0.13721.9050.16570.5862-0.2954-0.2804-0.0532-0.18240.28870.4143-0.07130.26410.08180.03330.2957-0.05170.243114.815530.5915-20.6877
65.0991.28970.59962.6866-0.09722.3457-0.05790.7910.0188-0.7650.20660.41670.0696-0.1637-0.15990.56330.05-0.18820.5484-0.03210.3501-19.016833.8094-39.6544
75.00591.27331.93683.50141.07284.1727-0.09330.6585-0.2663-0.3269-0.0470.37750.1312-0.02610.12050.29720.0574-0.01760.3706-0.02770.2391-12.60934.0466-31.8673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2318 through 2426 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2427 through 2461 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2462 through 2577 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2578 through 2618 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2619 through 2819 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2820 through 2885 )
7X-RAY DIFFRACTION7chain 'A' and (resid 2886 through 2933 )

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