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- PDB-5dp2: CurF ER cyclopropanase from curacin A biosynthetic pathway -

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Basic information

Entry
Database: PDB / ID: 5dp2
TitleCurF ER cyclopropanase from curacin A biosynthetic pathway
ComponentsCurF
KeywordsOXIDOREDUCTASE / Polyketide synthase / curacin A / cyclopropane
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
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 ...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 / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / CurF
Similarity search - Component
Biological speciesLyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsKhare, D. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2015
Title: Structural Basis for Cyclopropanation by a Unique Enoyl-Acyl Carrier Protein Reductase.
Authors: Khare, D. / Hale, W.A. / Tripathi, A. / Gu, L. / Sherman, D.H. / Gerwick, W.H. / Hakansson, K. / Smith, J.L.
History
DepositionSep 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,9642
Polymers38,2211
Non-polymers7431
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.906, 47.294, 76.902
Angle α, β, γ (deg.)90.00, 123.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-953-

HOH

21A-1032-

HOH

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Components

#1: Protein CurF


Mass: 38220.641 Da / Num. of mol.: 1 / Fragment: UNP residues 273-611
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Gene: curF / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DNE7
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.72932 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72932 Å / Relative weight: 1
ReflectionResolution: 0.96→30 Å / Num. obs: 197326 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DOZ

5doz


Resolution: 0.96→30 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.467 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13058 9948 5 %RANDOM
Rwork0.11652 ---
obs0.11724 187338 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.994 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.14 Å2
2--0.09 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 0.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 48 558 3253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192992
X-RAY DIFFRACTIONr_bond_other_d0.0010.022914
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9784114
X-RAY DIFFRACTIONr_angle_other_deg0.81436756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46523.63135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42415536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7311521
X-RAY DIFFRACTIONr_chiral_restr0.0990.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213405
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02713
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9390.8321414
X-RAY DIFFRACTIONr_mcbond_other0.9370.8311413
X-RAY DIFFRACTIONr_mcangle_it1.2651.2631785
X-RAY DIFFRACTIONr_mcangle_other1.2651.2641786
X-RAY DIFFRACTIONr_scbond_it1.9021.0971578
X-RAY DIFFRACTIONr_scbond_other1.9021.0971579
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3011.5512295
X-RAY DIFFRACTIONr_long_range_B_refined5.63710.0593919
X-RAY DIFFRACTIONr_long_range_B_other5.63610.0593920
X-RAY DIFFRACTIONr_rigid_bond_restr2.42535906
X-RAY DIFFRACTIONr_sphericity_free54.4725101
X-RAY DIFFRACTIONr_sphericity_bonded12.12356257
LS refinement shellResolution: 0.96→0.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 628 -
Rwork0.291 12870 -
obs--92.31 %

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