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- PDB-3kg6: Dehydratase domain from CurF module of Curacin polyketide synthase -

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Basic information

Entry
Database: PDB / ID: 3kg6
TitleDehydratase domain from CurF module of Curacin polyketide synthase
ComponentsCurF
KeywordsLYASE / polyketide synthase / double hotdog fold / dehydratase
Function / homology
Function and homology information


: / 3-hydroxyacyl-CoA dehydrogenase activity / organonitrogen compound biosynthetic process / : / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / nucleotide binding / identical protein binding / metal ion binding
Similarity search - Function
Polyketide synthase dehydratase / Zinc-binding dehydrogenase / : / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Polyketide synthase dehydratase N-terminal domain / Condensation domain ...Polyketide synthase dehydratase / Zinc-binding dehydrogenase / : / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / 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 / Thiol Ester Dehydrase; Chain A / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 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. / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Putative AMP-binding domain signature. / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / 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 / GroES-like superfamily / ClpP/crotonase-like domain 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: 2.7 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 / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: CurF
B: CurF
C: CurF
D: CurF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2489
Polymers128,0474
Non-polymers2005
Water93752
1
A: CurF
C: CurF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1445
Polymers64,0242
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CurF
D: CurF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1044
Polymers64,0242
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: CurF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1324
Polymers32,0121
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: CurF


Theoretical massNumber of molelcules
Total (without water)32,0121
Polymers32,0121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: CurF


Theoretical massNumber of molelcules
Total (without water)32,0121
Polymers32,0121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: CurF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0923
Polymers32,0121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.379, 198.385, 146.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1-

CA

21D-1-

CA

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Components

#1: Protein
CurF


Mass: 32011.855 Da / Num. of mol.: 4 / Fragment: Dehydratase domain, residues 1687-1968
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Gene: curF / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNE7, EC: 4.2.1.61
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / pH: 8
Details: 14% (w/v) PEG 4000, 200 mM CaCl2, 10% (v/v) glycerol, 2 mM DTT, 100 mM Tris pH 8.0, 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: 0.97942
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 35542 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 18.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.792 / % possible all: 100

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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: 2.7→41.89 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 32.369 / SU ML: 0.309 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 1980 5.6 %RANDOM
Rwork0.21254 ---
obs0.21549 33290 99.16 %-
all-35270 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.591 Å2
Baniso -1Baniso -2Baniso -3
1--3.06 Å2-0 Å20 Å2
2---1.42 Å20 Å2
3---4.49 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8802 0 5 52 8859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228991
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9181.9512195
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02551098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27925.404433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.946151537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9811528
X-RAY DIFFRACTIONr_chiral_restr0.0610.21365
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026810
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1720.23417
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25951
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0560.23
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8093.55690
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38958896
X-RAY DIFFRACTIONr_scbond_it0.583.53774
X-RAY DIFFRACTIONr_scangle_it0.88553299
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 140 -
Rwork0.298 2358 -
obs--96.6 %
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)
16.62871.6365-1.79898.9753-0.54633.9042-0.0743-0.3119-0.3170.11850.1414-0.36310.12940.1866-0.067-0.39790.1-0.0019-0.40630.0909-0.368447.89692.00712.272
25.0589-1.6908-0.79076.73952.0393.40040.0144-0.19120.33710.35420.18490.905-0.2406-0.5192-0.1993-0.32420.08540.144-0.14290.1470.050626.1699.58218.774
324.2904-8.55914.152411.7678-1.70054.98370.60280.36042.08450.2411-0.4271-1.5964-0.64640.814-0.17570.02010.07430.1366-0.467-0.1454-0.092643.698122.42818.376
43.6576-0.14-3.16644.29590.40093.8225-0.0633-0.20130.45490.40060.19930.3482-0.2863-0.1846-0.136-0.26350.1270.0622-0.33540.0406-0.203838.279111.13416.515
55.7599-1.77820.00458.98320.76295.12450.29060.60820.0596-0.7884-0.39390.0867-0.0793-0.00270.1033-0.10130.1658-0.0716-0.1316-0.1865-0.20771.176128.3816.831
66.5716-4.7217-1.773912.10196.74968.3983-0.1024-0.4194-0.11920.82-0.29241.03520.3353-0.52540.3948-0.14390.00030.0403-0.1042-0.2321-0.120263.041138.1536.823
77.0965-1.6932-10.59044.43126.578619.88090.39491.29061.6093-0.95740.1206-0.6639-2.0169-0.0449-0.51550.61390.25120.06110.08250.10590.757465.371159.72417.993
82.7519-1.70670.71796.45041.63697.64030.22730.27250.8437-0.4307-0.26240.3151-0.7647-0.35030.03510.04660.123-0.0508-0.2196-0.11880.204963.936147.94623.626
97.1322-1.6355-0.48838.67970.74923.18050.23460.44150.0981-0.2423-0.26890.0920.1131-0.23150.0344-0.26380.11680.0769-0.42530.1646-0.266352.09565.4398.006
109.1041-3.31863.59249.2395-2.78633.2352-0.2188-0.7043-0.24860.79620.2278-0.58620.04610.1675-0.009-0.00690.07480.0012-0.41350.1762-0.275762.09952.13524.908
1114.3751-2.00997.599514.4869-0.30368.89240.74051.7315-1.4014-1.0333-0.19010.92861.2004-0.5303-0.55040.26020.15640.1115-0.0443-0.08550.286756.24534.4432.826
123.0404-1.5354-0.21527.52840.05728.39320.39050.5667-0.746-0.1789-0.2506-0.09130.88160.244-0.1399-0.00530.12840.0192-0.40550.0727-0.052759.00344.62210.367
134.51181.5360.34469.612.44284.58140.0139-0.13170.15490.12290.00460.5465-0.1822-0.0716-0.0185-0.38250.06820.0257-0.3278-0.0521-0.256977.405103.16414.048
146.0881-5.6247-0.047511.89830.78913.1604-0.0994-0.22930.04520.26880.2929-1.11380.30420.6072-0.1936-0.39920.0912-0.0993-0.0466-0.14030.043498.76693.48917.638
1526.5178-10.2609-4.28358.2593-0.02483.4240.78710.8826-1.73650.0511-0.59510.76050.3245-0.6324-0.1920.0694-0.0161-0.0295-0.32140.01250.196280.96571.82610.724
166.0928-1.17013.93218.76771.01362.9039-0.153-0.0873-0.62160.06760.1674-0.1950.35150.3982-0.0144-0.16360.0835-0.0166-0.30390.0281-0.178786.52982.89512.237
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1685 - 1710
2X-RAY DIFFRACTION1A1729 - 1760
3X-RAY DIFFRACTION1A1770 - 1814
4X-RAY DIFFRACTION2A1711 - 1728
5X-RAY DIFFRACTION2A1761 - 1769
6X-RAY DIFFRACTION2A1837 - 1853
7X-RAY DIFFRACTION3A1815 - 1836
8X-RAY DIFFRACTION4A1854 - 1967
9X-RAY DIFFRACTION5B1684 - 1710
10X-RAY DIFFRACTION5B1729 - 1760
11X-RAY DIFFRACTION5B1770 - 1814
12X-RAY DIFFRACTION6B1711 - 1728
13X-RAY DIFFRACTION6B1761 - 1769
14X-RAY DIFFRACTION6B1837 - 1853
15X-RAY DIFFRACTION7B1815 - 1836
16X-RAY DIFFRACTION8B1854 - 1967
17X-RAY DIFFRACTION9C1685 - 1710
18X-RAY DIFFRACTION9C1729 - 1760
19X-RAY DIFFRACTION9C1770 - 1814
20X-RAY DIFFRACTION10C1711 - 1728
21X-RAY DIFFRACTION10C1761 - 1769
22X-RAY DIFFRACTION10C1837 - 1853
23X-RAY DIFFRACTION11C1815 - 1836
24X-RAY DIFFRACTION12C1854 - 1967
25X-RAY DIFFRACTION13D1685 - 1710
26X-RAY DIFFRACTION13D1729 - 1760
27X-RAY DIFFRACTION13D1770 - 1814
28X-RAY DIFFRACTION14D1711 - 1728
29X-RAY DIFFRACTION14D1761 - 1769
30X-RAY DIFFRACTION14D1837 - 1853
31X-RAY DIFFRACTION15D1815 - 1836
32X-RAY DIFFRACTION16D1854 - 1966

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