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- PDB-2q35: Crystal Structure of the Y82F variant of ECH2 decarboxylase domai... -

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Basic information

Entry
Database: PDB / ID: 2q35
TitleCrystal Structure of the Y82F variant of ECH2 decarboxylase domain of CurF from Lyngbya majuscula
ComponentsCurF
KeywordsLYASE / CROTONASE
Function / homology
Function and homology information


organic cyclic compound metabolic process / 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 / Polyketide synthase, C-terminal extension / Enoyl-CoA hydratase/isomerase / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / 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 / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 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
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CurF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0233
Polymers26,8961
Non-polymers1282
Water5,531307
1
A: CurF
hetero molecules

A: CurF
hetero molecules

A: CurF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0709
Polymers80,6873
Non-polymers3836
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7330 Å2
ΔGint-70 kcal/mol
Surface area29690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.138, 106.138, 119.497
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-3595-

HOH

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

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Components

#1: Protein CurF


Mass: 26895.785 Da / Num. of mol.: 1 / Fragment: ECH2 decarboxylase domain / Mutation: Y82F
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2006
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
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: 1.65→50 Å / Num. all: 31133 / Num. obs: 31133 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.9 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.061 / Χ2: 0.973 / Net I/σ(I): 12.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3069 / Χ2: 0.848 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q34

2q34


Resolution: 1.65→33.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.569 / SU ML: 0.062 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1571 5 %RANDOM
Rwork0.167 ---
obs0.169 31124 99.7 %-
all-31133 --
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: 21.465 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å2-0.82 Å20 Å2
2---1.64 Å20 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 7 307 2208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221932
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9722605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9415242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18824.71387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07615345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2371510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021445
X-RAY DIFFRACTIONr_nbd_refined0.2040.2950
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21366
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.231
X-RAY DIFFRACTIONr_mcbond_it1.20621238
X-RAY DIFFRACTIONr_mcangle_it1.76131933
X-RAY DIFFRACTIONr_scbond_it3.8786772
X-RAY DIFFRACTIONr_scangle_it5.9669672
LS refinement shellResolution: 1.65→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 117 -
Rwork0.233 2096 -
obs-2213 96.89 %

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