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- PDB-3kg8: Dehydratase domain from CurJ module of Curacin polyketide synthase -

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Basic information

Entry
Database: PDB / ID: 3kg8
TitleDehydratase domain from CurJ module of Curacin polyketide synthase
ComponentsCurJ
KeywordsLYASE / polyketide synthase / double hotdog fold / dehydratase
Function / homology
Function and homology information


phosphopantetheine binding / transferase activity / identical protein binding
Similarity search - Function
Thiol Ester Dehydrase; Chain A - #120 / : / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, ketoreductase domain / KR domain / Hotdog Thioesterase ...Thiol Ester Dehydrase; Chain A - #120 / : / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, ketoreductase domain / KR domain / Hotdog Thioesterase / 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. / Acyl transferase/acyl hydrolase/lysophospholipase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesLyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 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: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CurJ
B: CurJ


Theoretical massNumber of molelcules
Total (without water)69,1502
Polymers69,1502
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-14 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.416, 70.345, 174.812
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 CurJ


Mass: 34574.961 Da / Num. of mol.: 2 / Fragment: Dehydratase domain, residues 941-1245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Gene: curJ / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNE3, EC: 4.2.1.61
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 3350, 2-10% 1,4 butanediol, 250 mM NaCl, 100 mM bis-Tris propane pH 6.5, 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: 0.97945 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 21789 / Num. obs: 21789 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 15.6
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 2 / Rsym value: 0.799 / % possible all: 95

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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
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG8

Resolution: 2.45→43.69 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 19.247 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.692 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25849 1115 5.1 %RANDOM
Rwork0.19543 ---
obs0.19865 20616 97.71 %-
all-21731 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.288 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20 Å2
2--2.7 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.45→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 0 74 4577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.946250
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6515557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12725.591220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55215786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8651510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023466
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21843
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23077
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2177
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.35152893
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.58574563
X-RAY DIFFRACTIONr_scbond_it2.50551941
X-RAY DIFFRACTIONr_scangle_it3.4171687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.516 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 67 -
Rwork0.263 1267 -
obs--81.04 %
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)
14.0263-0.3849-1.1542.0881-0.62312.87-0.06590.4271-0.229-0.3452-0.0209-0.11280.00640.04990.0867-0.0668-0.03630.0442-0.0581-0.0661-0.067242.77238.42775.291
23.175-0.1817-0.15572.1004-0.0811.6383-0.1159-0.2008-0.19910.11670.04690.02030.1096-0.06910.0689-0.1069-0.01580.0306-0.09120.0071-0.061528.09533.91991.783
33.59420.8463-0.31732.1094-0.51441.6551-0.01410.46240.1062-0.10350.07820.2336-0.0267-0.279-0.0641-0.124-0.0076-0.04060.0133-0.0156-0.059720.80240.94979.374
41.33111.5735-3.54573.7526-2.723110.5843-0.3626-1.4753-1.0130.3114-0.0976-0.49850.99420.79640.46030.1987-0-0.0282-0.12440.08130.143128.89324.382101.052
54.6314-1.6222-3.31052.62290.15148.96960.1982-0.02710.3171-0.11660.01160.1253-0.06880.0774-0.2098-0.0904-0.0410.0941-0.0369-0.0608-0.15754.29841.45854.752
63.5630.6483-2.72623.6690.65747.6939-0.06150.39780.0099-0.19610.1147-0.0780.34280.1078-0.0532-0.0198-0.02780.05230.0209-0.0053-0.178562.39438.39734.834
74.79280.74580.21182.16921.22634.9110.0197-0.0288-0.60270.0044-0.26020.07441.50310.30070.24050.25380.12630.1612-0.0938-0.0422-0.088862.66924.50642.496
87.87690.81912.94480.4497-1.23497.6167-0.6430.63430.6736-0.17030.34050.2677-0.755-0.09550.30250.2443-0.17180.0230.2144-0.0295-0.123760.93345.17322.251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A941 - 968
2X-RAY DIFFRACTION1A987 - 1016
3X-RAY DIFFRACTION1A1027 - 1078
4X-RAY DIFFRACTION2A1118 - 1242
5X-RAY DIFFRACTION3A969 - 986
6X-RAY DIFFRACTION3A1017 - 1026
7X-RAY DIFFRACTION3A1101 - 1117
8X-RAY DIFFRACTION4A1079 - 1100
9X-RAY DIFFRACTION5B941 - 968
10X-RAY DIFFRACTION5B987 - 1016
11X-RAY DIFFRACTION5B1027 - 1078
12X-RAY DIFFRACTION6B1118 - 1242
13X-RAY DIFFRACTION7B969 - 986
14X-RAY DIFFRACTION7B1017 - 1026
15X-RAY DIFFRACTION7B1101 - 1117
16X-RAY DIFFRACTION8B1079 - 1100

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