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- PDB-3nnj: Halogenase domain from CurA module (apo Hal) -

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Basic information

Entry
Database: PDB / ID: 3nnj
TitleHalogenase domain from CurA module (apo Hal)
ComponentsCurA
KeywordsBIOSYNTHETIC PROTEIN / non-haem Fe(II)/alpha-ketoglutarate-dependent enzyme / catalyzes a cryptic chlorination
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding
Similarity search - Function
q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain ...q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Acetyltransferase (GNAT) family / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / 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 / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Acyl-CoA N-acyltransferase / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesLyngbya majuscula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.601 Å
AuthorsKhare, D. / Smith, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Conformational switch triggered by alpha-ketoglutarate in a halogenase of curacin A biosynthesis
Authors: Khare, D. / Wang, B. / Gu, L. / Razelun, J. / Sherman, D.H. / Gerwick, W.H. / Hakansson, K. / Smith, J.L.
History
DepositionJun 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: CurA
B: CurA


Theoretical massNumber of molelcules
Total (without water)80,4792
Polymers80,4792
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-13 kcal/mol
Surface area30440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.772, 182.772, 182.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-382-

HOH

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Components

#1: Protein CurA


Mass: 40239.375 Da / Num. of mol.: 2 / Fragment: Hal domain (UNP residues 1600 to 1919)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula (bacteria) / Gene: curA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q6DNF2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM Sodium citrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 31274 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 31.4
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 3078

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Processing

Software
NameVersionClassification
JBluIce-EPICS- EPICSdata collection
SOLVEphasing
RESOLVEmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.601→48.848 Å / SU ML: 0.3 / σ(F): 1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 1515 5.08 %RANDOM
Rwork0.1897 ---
obs0.1922 29815 95.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.148 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.601→48.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 0 152 5151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095119
X-RAY DIFFRACTIONf_angle_d1.1836910
X-RAY DIFFRACTIONf_dihedral_angle_d17.0531856
X-RAY DIFFRACTIONf_chiral_restr0.079735
X-RAY DIFFRACTIONf_plane_restr0.004882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6015-2.68550.29761280.24682334X-RAY DIFFRACTION87
2.6855-2.78140.30971450.24792411X-RAY DIFFRACTION90
2.7814-2.89280.29171430.24572482X-RAY DIFFRACTION94
2.8928-3.02440.30941560.232540X-RAY DIFFRACTION95
3.0244-3.18380.28021330.23062586X-RAY DIFFRACTION97
3.1838-3.38330.32121130.21032639X-RAY DIFFRACTION97
3.3833-3.64440.24961330.1972662X-RAY DIFFRACTION99
3.6444-4.0110.21561450.16772655X-RAY DIFFRACTION99
4.011-4.5910.18871570.15292663X-RAY DIFFRACTION98
4.591-5.78270.20061430.15692645X-RAY DIFFRACTION98
5.7827-48.85650.22191190.18192683X-RAY DIFFRACTION95

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