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- PDB-3kg9: Dehydratase domain from CurK module of Curacin polyketide synthase -

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Basic information

Entry
Database: PDB / ID: 3kg9
TitleDehydratase domain from CurK module of Curacin polyketide synthase
ComponentsCurK
KeywordsLYASE / polyketide synthase / double hotdog fold / dehydratase
Function / homology
Function and homology information


phosphopantetheine binding / transferase activity / oxidoreductase activity / identical protein binding
Similarity search - Function
Polyketide synthase dehydratase / : / 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 / Malonyl-CoA ACP transacylase, ACP-binding ...Polyketide synthase dehydratase / : / 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 / 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. / Alcohol dehydrogenase-like, C-terminal / Acyl transferase/acyl hydrolase/lysophospholipase / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / 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 / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesLyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsAkey, D.L. / Smith, J.L.
CitationJournal: Structure / Year: 2010
Title: Crystal Structures of Dehydratase Domains from the Curacin Polyketide Biosynthetic Pathway.
Authors: Akey, D.L. / Razelun, J.R. / Tehranisa, J. / Sherman, D.H. / Gerwick, W.H. / Smith, J.L.
History
DepositionOct 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Jan 31, 2024Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CurK
B: CurK


Theoretical massNumber of molelcules
Total (without water)65,4302
Polymers65,4302
Non-polymers00
Water9,044502
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CurK


Theoretical massNumber of molelcules
Total (without water)32,7151
Polymers32,7151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: CurK


Theoretical massNumber of molelcules
Total (without water)32,7151
Polymers32,7151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.122, 94.301, 150.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CurK


Mass: 32714.832 Da / Num. of mol.: 2 / Fragment: Dehydratase domain, residues 958-1250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Gene: curK / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNE2, EC: 4.2.1.61
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 1.3 M tri-sodium citrate, 30 mM (D)+sucrose, 100 mM tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 59477 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 20.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.3 / % possible all: 85.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG7

3kg7


Resolution: 1.7→30.77 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.186 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3003 5.1 %RANDOM
Rwork0.182 ---
obs0.184 59373 98 %-
all-59373 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å2-0 Å2
2---0.65 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4381 0 0 502 4883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224519
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9576145
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4635571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68826.117206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08115800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1321512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023374
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.21927
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23079
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2452
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.2107
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.261
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6613.52910
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44954560
X-RAY DIFFRACTIONr_scbond_it1.8673.51817
X-RAY DIFFRACTIONr_scangle_it2.84651585
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 167 -
Rwork0.24 3451 -
obs--82.06 %
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)
11.4483-0.46440.30611.0570.18210.743-0.01520.11420.1198-0.09580.0016-0.091-0.08330.06750.0136-0.0226-0.00440.0034-0.0320.0118-0.020440.11627.36796.684
20.94560.0518-0.0480.9031-0.11351.055-0.0113-0.1413-0.10150.13860.03780.01080.0278-0.0131-0.0265-0.03230.01880.003-0.02260.0113-0.021232.38113.391112.562
31.88210.4627-1.0881.7072-0.55422.2928-0.0184-0.15240.13730.2006-0.00470.2456-0.1821-0.08390.0231-0.01440.04380.0166-0.0296-0.0245-0.011522.16925.878111.692
40.43461.2533-0.88294.2079-4.41857.7009-0.0858-0.5702-0.63480.0316-0.3929-0.47210.99041.16770.4787-0.03450.1605-0.0320.04270.09870.079937.0460.84114.811
50.85750.2374-0.37731.8086-0.94922.20940.0797-0.074-0.02530.4136-0.2156-0.1865-0.14270.13590.13590.0624-0.0463-0.0717-0.03280.0399-0.049242.48448.16181.006
60.68170.3908-0.04511.4156-0.20131.43660.01010.09150.01270.1239-0.0373-0.0991-0.11460.03160.0273-0.01530.0199-0.0289-0.04470.0072-0.049643.43461.6563.002
70.48080.2766-0.21791.9279-0.68881.51210.01340.1092-0.0487-0.0598-0.0622-0.08920.0522-0.10180.0488-0.02240.01-0.0241-0.026-0.0158-0.034538.82447.0358.135
81.8590.83150.49255.73982.836410.46160.04960.01540.28760.19960.0063-0.2167-0.68520.4364-0.05580.0181-0.0223-0.0368-0.07480.0645-0.036244.30675.52558.478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A961 - 986
2X-RAY DIFFRACTION1A1006 - 1037
3X-RAY DIFFRACTION1A1046 - 1089
4X-RAY DIFFRACTION2A1129 - 1247
5X-RAY DIFFRACTION3A987 - 1005
6X-RAY DIFFRACTION3A1038 - 1045
7X-RAY DIFFRACTION3A1113 - 1128
8X-RAY DIFFRACTION4A1090 - 1112
9X-RAY DIFFRACTION5B961 - 986
10X-RAY DIFFRACTION5B1006 - 1037
11X-RAY DIFFRACTION5B1046 - 1089
12X-RAY DIFFRACTION6B1129 - 1250
13X-RAY DIFFRACTION7B987 - 1005
14X-RAY DIFFRACTION7B1038 - 1045
15X-RAY DIFFRACTION7B1113 - 1128
16X-RAY DIFFRACTION8B1095 - 1112

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