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- PDB-6c4v: 1.9 Angstrom Resolution Crystal Structure of Acyl Carrier Protein... -

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Basic information

Entry
Database: PDB / ID: 6c4v
Title1.9 Angstrom Resolution Crystal Structure of Acyl Carrier Protein Domain (residues 1350-1461) 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 / Pks13
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 / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase ...Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / 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: 1.9 Å
AuthorsMinasov, G. / Brunzelle, J.S. / 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: 1.9 Angstrom Resolution Crystal Structure of Acyl Carrier Protein Domain (residues 1350-1461) of Polyketide Synthase Pks13 from Mycobacterium tuberculosis.
Authors: Minasov, G. / Brunzelle, J.S. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics ...Authors: Minasov, G. / Brunzelle, J.S. / 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 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)12,2643
Polymers12,1331
Non-polymers1312
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.189, 58.189, 101.683
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Polyketide synthase Pks13


Mass: 12133.424 Da / Num. of mol.: 1 / Fragment: residues 1349-1461
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.1 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 9.0 mg/ml, 0.01M Tris pH 8.3; Screen: PEGs II (B2) 0.01M Zinc sulfate, 0.1M MES pH 6.5, 25% (w/v) PEG 550 MME

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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: 1.9→30 Å / Num. obs: 8588 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 17.7 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.015 / Rrim(I) all: 0.064 / Rsym value: 0.062 / Χ2: 1.056 / Net I/σ(I): 46.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 408 / CC1/2: 0.924 / Rpim(I) all: 0.172 / Rrim(I) all: 0.741 / Rsym value: 0.72 / Χ2: 1.003 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.09 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.219 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21731 435 5.1 %RANDOM
Rwork0.19346 ---
obs0.19478 8113 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.758 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å20 Å2
2---0.72 Å20 Å2
3---2.33 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms610 0 2 36 648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019631
X-RAY DIFFRACTIONr_bond_other_d0.0010.02600
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.973860
X-RAY DIFFRACTIONr_angle_other_deg0.84131386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.367582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.9123.79329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.91815102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.388157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.021718
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02125
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_it1.452.564328
X-RAY DIFFRACTIONr_mcbond_other1.442.556327
X-RAY DIFFRACTIONr_mcangle_it2.1563.82410
X-RAY DIFFRACTIONr_mcangle_other2.1533.83411
X-RAY DIFFRACTIONr_scbond_it2.3082.946303
X-RAY DIFFRACTIONr_scbond_other2.3042.953304
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7074.286451
X-RAY DIFFRACTIONr_long_range_B_refined5.67532.197725
X-RAY DIFFRACTIONr_long_range_B_other5.61131.481714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 37 -
Rwork0.223 570 -
obs--100 %
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)
14.0071-1.32160.64681.6533-1.82354.0988-0.08110.13240.34990.2906-0.1618-0.4163-0.18080.26890.24290.0817-0.0433-0.09620.12820.04540.13130.4634.14948.6682
23.0148-1.2875-0.2714.2421-0.80443.5224-0.18670.0275-0.01610.33140.1001-0.0477-0.0305-0.08480.08660.0795-0.0144-0.030.08420.00770.017519.962429.726748.8047
34.1416-1.11370.46265.2718-2.08123.2642-0.10480.28540.01630.029-0.0382-0.0882-0.16860.13410.1430.0882-0.018-0.03290.11180.02930.020819.993234.450543.1174
411.4598-2.179-2.12064.0372-2.65215.15-0.07330.14960.4505-0.173-0.0323-0.338-0.0538-0.07290.10570.103-0.0144-0.04320.13390.06730.096821.532243.352640.0061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1370 - 1398
2X-RAY DIFFRACTION2A1399 - 1419
3X-RAY DIFFRACTION3A1420 - 1441
4X-RAY DIFFRACTION4A1442 - 1450

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