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- PDB-3kg7: Dehydratase domain from CurH module of Curacin polyketide synthase -

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Basic information

Entry
Database: PDB / ID: 3kg7
TitleDehydratase domain from CurH module of Curacin polyketide synthase
ComponentsCurH
KeywordsLYASE / polyketide synthase / double hotdog fold / dehydratase
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 / fatty acid biosynthetic process / oxidoreductase activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Beta-ketoacyl synthase-like, N-terminal / Polyketide synthase dehydratase / CurL-like, PKS C-terminal / Zinc-binding dehydrogenase / : / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH ...: / Beta-ketoacyl synthase-like, N-terminal / Polyketide synthase dehydratase / CurL-like, PKS C-terminal / Zinc-binding dehydrogenase / : / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Thiol Ester Dehydrase; Chain A / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / 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 / MAD / Resolution: 2.77 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 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CurH
B: CurH
C: CurH
D: CurH


Theoretical massNumber of molelcules
Total (without water)131,7934
Polymers131,7934
Non-polymers00
Water81145
1
A: CurH
C: CurH


Theoretical massNumber of molelcules
Total (without water)65,8962
Polymers65,8962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CurH
D: CurH


Theoretical massNumber of molelcules
Total (without water)65,8962
Polymers65,8962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: CurH


Theoretical massNumber of molelcules
Total (without water)32,9481
Polymers32,9481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: CurH


Theoretical massNumber of molelcules
Total (without water)32,9481
Polymers32,9481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: CurH


Theoretical massNumber of molelcules
Total (without water)32,9481
Polymers32,9481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: CurH


Theoretical massNumber of molelcules
Total (without water)32,9481
Polymers32,9481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.163, 74.447, 103.482
Angle α, β, γ (deg.)90.00, 108.84, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112B930 - 1038
2112A930 - 1038
1212B1045 - 1055
2212A1045 - 1055
1312B1080 - 1141
2312A1080 - 1141
1412B1153 - 1184
2412A1153 - 1184
1512B1191 - 1225
2512A1191 - 1225
1122C930 - 1038
2122A930 - 1038
1222C1045 - 1055
2222A1045 - 1055
1322C1080 - 1141
2322A1080 - 1141
1422C1153 - 1184
2422A1153 - 1184
1522C1191 - 1225
2522A1191 - 1225
1132D930 - 1038
2132A930 - 1038
1232D1045 - 1055
2232A1045 - 1055
1332D1080 - 1141
2332A1080 - 1141
1432D1153 - 1184
2432A1153 - 1184
1532D1191 - 1225
2532A1191 - 1225

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
CurH


Mass: 32948.219 Da / Num. of mol.: 4 / Fragment: Dehydratase domain, residues 934-1233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Gene: curH / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNE5, EC: 4.2.1.61
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 15% PEG 4000, 10% PEG 400, 2 mM DTT, 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, 0.97962
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2008 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979621
ReflectionRedundancy: 3.9 % / Av σ(I) over netI: 19.67 / Number: 228164 / Rmerge(I) obs: 0.091 / Χ2: 1.1 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 58230 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.035099.610.0560.9443.9
4.796.0310010.071.0534
4.184.7999.910.0741.0763.9
3.84.1810010.0840.9913.9
3.533.899.810.1191.0273.8
3.323.5310010.1621.0493.9
3.153.3210010.2331.0773.9
3.023.1510010.3561.1633.9
2.93.0210010.5681.313.9
2.82.910010.7841.3163.9
ReflectionResolution: 2.77→50 Å / Num. obs: 29940 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 80.8 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 19.7
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.813 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.77→48.97 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 39.651 / SU ML: 0.366 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1996 6.7 %RANDOM
Rwork0.203 ---
obs0.208 29844 98.8 %-
all-29844 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å20 Å20.41 Å2
2--5.39 Å20 Å2
3----3.44 Å2
Refinement stepCycle: LAST / Resolution: 2.77→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9031 0 0 45 9076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229267
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.95812668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48251139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86824.6437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.537151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1871552
X-RAY DIFFRACTIONr_chiral_restr0.0770.21429
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027164
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.23807
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.26243
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2301
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.67855890
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5279362
X-RAY DIFFRACTIONr_scbond_it1.83853818
X-RAY DIFFRACTIONr_scangle_it2.53273306
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B952tight positional0.030.05
2C956tight positional0.040.05
3D952tight positional0.040.05
1B938medium positional0.410.5
2C941medium positional0.550.5
3D938medium positional0.460.5
1B952tight thermal0.080.5
2C956tight thermal0.070.5
3D952tight thermal0.070.5
1B938medium thermal0.522
2C941medium thermal0.552
3D938medium thermal0.622
LS refinement shellResolution: 2.77→2.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 116 -
Rwork0.274 1801 -
obs--87.37 %
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)
14.1741-1.0019-3.24275.1833-0.3258.07650.21190.05350.019-0.0728-0.0258-0.2942-0.26520.3177-0.1861-0.2552-0.0302-0.0841-0.45850.0351-0.23937.47634.24148.569
24.3016-1.0071-1.84813.0694-0.76155.62060.0571-0.76130.02540.63690.1334-0.1214-0.30510.3288-0.19060.01620.0780.0046-0.20650.0962-0.292629.3932.49968.289
32.5640.49570.66634.1243-1.36677.50340.5516-0.08460.7830.40360.07170.2516-1.4494-0.4758-0.62330.14680.1380.2252-0.34790.0223-0.133124.85844.92161.31
48.6854-2.0817-3.25918.2552-2.52085.2506-0.6355-1.3028-0.68681.12550.51320.50730.80560.65110.1223-0.0067-0.0406-0.1831-0.17260.2229-0.236626.30419.66273.129
53.2303-0.1969-1.03073.3986-0.88689.51270.0211-0.57290.13060.2841-0.1488-0.0626-0.33110.98050.1276-0.4157-0.03480.0609-0.07820.0778-0.231370.55-0.2256.96
64.28690.2143-1.24393.3223-0.77175.91330.097-0.188-0.0007-0.4124-0.1381-0.2447-0.10621.07550.041-0.22730.040.0418-0.1150.1445-0.248175.2180.708-13.944
73.33331.0318-0.14432.0897-3.195211.8168-0.2249-0.1296-0.4282-0.2534-0.1738-0.35071.29241.9570.3987-0.28740.34640.18120.1460.1306-0.115681.209-11.247-7.209
86.4955-0.91622.30584.48690.482911.05330.00230.5687-0.3243-0.7424-0.5567-0.0983-0.6745-0.470.5543-0.0395-0.0646-0.0096-0.52880.2462-0.093566.1436.127-22.709
94.91914.02010.1936.18790.78446.39150.04310.284-0.69280.29610.1163-0.45250.3435-0.2394-0.1594-0.38820.04110.0537-0.3233-0.099-0.150844.84635.70826.91
104.0871.1917-0.23335.57820.50034.764-0.60651.0675-0.5819-1.3790.7619-0.91080.11680.4593-0.15540.0353-0.30820.34340.3381-0.2907-0.097650.79538.7426.367
1110.82292.1958-2.82975.38050.34032.9141-0.61731.5469-1.2352-1.35611.1147-0.39580.583-0.5275-0.49740.2069-0.35210.16390.2117-0.5002-0.202439.66328.6977.864
123.14822.4359-2.301610.9725-9.42188.1072-0.90520.48530.5456-1.0075-0.4237-0.5667-2.02321.28081.3288-0.0119-0.23460.29490.4490.08810.117955.20751.3892.374
137.30651.003-0.94892.6613-1.67655.24930.67370.17910.88970.1562-0.4513-0.0642-0.29570.4963-0.2224-0.1888-0.15870.155-0.1567-0.1167-0.218764.003-2.22628.808
146.30260.59580.77251.81270.17434.06060.7759-1.68880.51650.6854-0.442-0.0964-0.08990.2641-0.3340.1856-0.50770.08320.3621-0.1851-0.251258.644-6.2449.127
156.46041.0882-2.84941.6806-0.73147.77920.7409-0.6573-0.18580.363-0.50440.48020.4666-0.1062-0.2366-0.1309-0.30880.0893-0.1169-0.123-0.321648.144-10.68339.483
1613.24044.3404-4.71528.3411-4.98548.56480.058-1.7739-0.080.17940.0177-0.55890.75430.2895-0.07570.3066-0.3303-0.21150.4825-0.3281-0.400268.456-8.99458.436
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A938 - 962
2X-RAY DIFFRACTION1A981 - 1005
3X-RAY DIFFRACTION1A1016 - 1055
4X-RAY DIFFRACTION2A1096 - 1223
5X-RAY DIFFRACTION3A963 - 980
6X-RAY DIFFRACTION3A1006 - 1015
7X-RAY DIFFRACTION3A1080 - 1095
8X-RAY DIFFRACTION4A1056 - 1079
9X-RAY DIFFRACTION5B939 - 962
10X-RAY DIFFRACTION5B981 - 1005
11X-RAY DIFFRACTION5B1016 - 1055
12X-RAY DIFFRACTION6B1096 - 1223
13X-RAY DIFFRACTION7B963 - 980
14X-RAY DIFFRACTION7B1006 - 1015
15X-RAY DIFFRACTION7B1080 - 1095
16X-RAY DIFFRACTION8B1056 - 1079
17X-RAY DIFFRACTION9C937 - 962
18X-RAY DIFFRACTION9C981 - 1005
19X-RAY DIFFRACTION9C1016 - 1055
20X-RAY DIFFRACTION10C1096 - 1223
21X-RAY DIFFRACTION11C963 - 980
22X-RAY DIFFRACTION11C1006 - 1015
23X-RAY DIFFRACTION11C1080 - 1095
24X-RAY DIFFRACTION12C1056 - 1079
25X-RAY DIFFRACTION13D939 - 962
26X-RAY DIFFRACTION13D981 - 1005
27X-RAY DIFFRACTION13D1016 - 1055
28X-RAY DIFFRACTION14D1096 - 1223
29X-RAY DIFFRACTION15D963 - 980
30X-RAY DIFFRACTION15D1006 - 1015
31X-RAY DIFFRACTION15D1080 - 1095
32X-RAY DIFFRACTION16D1056 - 1079

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