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- PDB-2q2x: Crystal Structure of the ECH2 decarboxylase domain of CurF from L... -

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Basic information

Entry
Database: PDB / ID: 2q2x
TitleCrystal Structure of the ECH2 decarboxylase domain of CurF from Lyngbya majuscula
ComponentsCurF
KeywordsLYASE / CROTONASE
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
Light-harvesting Protein - #20 / Light-harvesting Protein / 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 ...Light-harvesting Protein - #20 / Light-harvesting Protein / 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 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Other non-globular / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 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 / Special / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesLyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsGeders, T.W. / Mowers, J.C. / Smith, J.L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the ECH2 catalytic domain of CurF from Lyngbya majuscula. Insights into a decarboxylase involved in polyketide chain beta-branching.
Authors: Geders, T.W. / Gu, L. / Mowers, J.C. / Liu, H. / Gerwick, W.H. / Hakansson, K. / Sherman, D.H. / Smith, J.L.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CurF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2843
Polymers27,0991
Non-polymers1842
Water2,612145
1
A: CurF
hetero molecules

A: CurF
hetero molecules

A: CurF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8519
Polymers81,2983
Non-polymers5536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7890 Å2
ΔGint-40 kcal/mol
Surface area28670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.433, 105.433, 46.314
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-3310-

HOH

21A-3398-

HOH

31A-3430-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y+1, x-y, z and -x+y+1, -x+1, z.

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Components

#1: Protein CurF


Mass: 27099.365 Da / Num. of mol.: 1 / Fragment: ECH2 decarboxylase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Strain: 19L / Gene: curF / Plasmid: pMCSG7:CurFd17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNE7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.15
Details: 1.5M sodium malonate pH 7.0, 50 mM HEPES pH 6.8, 20 mM Tris pH 7.9, 500 mM NaCl, 10% glycerol, pH 7.15, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332,0.97942,0.97956,0.95373
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2006
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.979421
30.979561
40.953731
Reflection

D res low: 50 Å / % possible obs: 100 / Redundancy: 5.9 %

IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs
17.81501490.10112.325544
27.71325200.1021.012.422536
39.91495250.0881.022.325512
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955099.810.0421.0295.9
3.934.9510010.060.9955.9
3.443.9310010.0670.9695.9
3.123.4410010.0960.9775.9
2.93.1210010.1580.9945.9
2.732.910010.2221.0015.9
2.592.7310010.2940.9995.9
2.482.5910010.3660.9965.9
2.382.4810010.520.9895.8
2.32.3810010.6551.0035.8
5.175099.820.0381.0155.9
4.15.1710020.0541.0195.9
3.584.110020.0721.0225.9
3.263.5810020.0881.0135.9
3.023.2610020.1450.9945.9
2.853.0210020.2261.0135.9
2.72.8510020.3131.0075.9
2.592.710020.4171.0225.9
2.492.5910020.5140.9985.8
2.42.4910020.7061.0055.8
4.955099.830.0360.9945.9
3.934.9510030.0550.9975.9
3.443.9310030.0691.0025.9
3.123.4410030.0881.0015.9
2.93.1210030.1471.0065.9
2.732.910030.2151.0255.9
2.592.7310030.3031.0095.9
2.482.5910030.3771.0035.9
2.382.4810030.5361.0895.8
2.32.3810030.6721.0525.6
ReflectionResolution: 2→50 Å / Num. all: 20390 / Num. obs: 20390 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.063 / Χ2: 0.994 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2020 / Χ2: 0.937 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97946.98-8.99
13 wavelength20.97963.65-9.19
13 wavelength30.95373.32-2.11
Phasing dmFOM : 0.69 / FOM acentric: 0.69 / FOM centric: 0.69 / Reflection: 13133 / Reflection acentric: 11974 / Reflection centric: 1159
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-34.7830.950.950.93626479147
4.1-6.60.940.940.918161576240
3.3-4.10.910.920.8322402029211
2.9-3.30.790.80.6822482072176
2.5-2.90.570.580.4639183660258
2.3-2.50.320.320.322852158127

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.11phasing
RESOLVE2.11phasing
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2→41.31 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.655 / SU ML: 0.129 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1024 5 %RANDOM
Rwork0.202 ---
obs0.204 20378 99.91 %-
all-21970 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.711 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.18 Å20 Å2
2--0.37 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 12 145 2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221949
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9772628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3275245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89724.77388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58715348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5051510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021454
X-RAY DIFFRACTIONr_nbd_refined0.2020.2902
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21359
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.213
X-RAY DIFFRACTIONr_mcbond_it1.03721245
X-RAY DIFFRACTIONr_mcangle_it1.78231937
X-RAY DIFFRACTIONr_scbond_it4.0546788
X-RAY DIFFRACTIONr_scangle_it6.2929689
LS refinement shellResolution: 2→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 67 -
Rwork0.292 1434 -
obs-1501 99.67 %

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