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- PDB-6c4q: 1.16 Angstrom Resolution Crystal Structure of Acyl Carrier Protei... -

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Basic information

Entry
Database: PDB / ID: 6c4q
Title1.16 Angstrom Resolution Crystal Structure of Acyl Carrier Protein Domain (residues 1-100) of Polyketide Synthase Pks13 from Mycobacterium tuberculosis
ComponentsPolyketide synthase Pks13
KeywordsTRANSPORT PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Acyl Carrier Protein
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
Thioesterase / Thioesterase domain / : / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...Thioesterase / Thioesterase domain / : / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / 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 / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.16 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.16 Angstrom Resolution Crystal Structure of Acyl Carrier Protein Domain (residues 1-100) of Polyketide Synthase Pks13 from Mycobacterium tuberculosis.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3373
Polymers11,1571
Non-polymers1802
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Polyketide synthase Pks13
hetero molecules

A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6746
Polymers22,3142
Non-polymers3604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2560 Å2
ΔGint-39 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.889, 51.889, 74.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Polyketide synthase Pks13


Mass: 11156.786 Da / Num. of mol.: 1 / Fragment: residues 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: pks13, Rv3800c / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: I6X8D2
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 10.4 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: AmSO4 (H8) 3.0M Ammonium sulfate, 1% (w/v) MPD. Cryo: Screen + 25% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.16→30 Å / Num. obs: 35889 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.028 / Rrim(I) all: 0.096 / Rsym value: 0.092 / Χ2: 2.131 / Net I/σ(I): 37.4
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1749 / CC1/2: 0.798 / Rpim(I) all: 0.276 / Rrim(I) all: 0.855 / Rsym value: 0.808 / Χ2: 1.003 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.16→26.13 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.783 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14456 1793 5 %RANDOM
Rwork0.12952 ---
obs0.13029 34027 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.387 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.16→26.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms634 0 12 124 770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019733
X-RAY DIFFRACTIONr_bond_other_d0.0010.02708
X-RAY DIFFRACTIONr_angle_refined_deg1.3922.0111005
X-RAY DIFFRACTIONr_angle_other_deg0.84731642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2165100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.06924.48329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.87715109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.316156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.021844
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02138
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_it1.1312.649379
X-RAY DIFFRACTIONr_mcbond_other1.1312.675378
X-RAY DIFFRACTIONr_mcangle_it1.578486
X-RAY DIFFRACTIONr_mcangle_other1.577487
X-RAY DIFFRACTIONr_scbond_it1.835354
X-RAY DIFFRACTIONr_scbond_other1.834354
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.121520
X-RAY DIFFRACTIONr_long_range_B_refined2.892891
X-RAY DIFFRACTIONr_long_range_B_other2.605861
X-RAY DIFFRACTIONr_rigid_bond_restr11.5233654
X-RAY DIFFRACTIONr_sphericity_free13.793131
X-RAY DIFFRACTIONr_sphericity_bonded7.7461668
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 142 -
Rwork0.201 2423 -
obs--99.73 %
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)
110.7393-6.2589-3.313711.3472-3.624410.3031-0.3865-0.37420.66330.03910.1668-1.1632-0.50210.64030.21980.131-0.0430.00350.1036-0.0550.15316.36821.89269.5442
20.737-0.03230.27910.15540.13290.2822-0.01920.02610.0097-0.01560.00760.0012-0.02110.00270.01160.0175-0.0010.00060.0198-0.00050.0014-5.855126.05238.0316
30.00980.02770.01630.09670.07430.13310.0010.0042-0.00010.0053-0.0040-0.0061-0.00590.0030.016-0.0005-0.00010.01990.00010.0002-10.713919.986714.429
43.89930.227-0.90641.53531.24691.32220.0014-0.1387-0.07230.1103-0.0148-0.00990.09830.03250.01340.0260.0093-0.00010.02660.00880.00360.635219.346819.8928
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 16
2X-RAY DIFFRACTION2A17 - 40
3X-RAY DIFFRACTION3A41 - 88
4X-RAY DIFFRACTION4A89 - 95

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