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- PDB-3nnm: Halogenase domain from CurA module (crystal form IV) -

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Basic information

Entry
Database: PDB / ID: 3nnm
TitleHalogenase domain from CurA module (crystal form IV)
ComponentsCurA
KeywordsBIOSYNTHETIC PROTEIN / non-haem Fe(II)/alpha-ketoglutarate-dependent enzyme / catalyzes a cryptic chlorination
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 / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
CurL-like, PKS C-terminal / q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / PKS_PP_betabranch / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...CurL-like, PKS C-terminal / q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / PKS_PP_betabranch / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Acetyltransferase (GNAT) family / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / 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 / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Thiolase-like / Acyl-CoA N-acyltransferase / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / 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 / MOLECULAR REPLACEMENT / Resolution: 2.69 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_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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CurA
B: CurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,42115
Polymers79,8222
Non-polymers59813
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-10 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.673, 87.950, 157.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CurA


Mass: 39911.113 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): BL21(DE3) / References: UniProt: Q6DNF2
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.81 Å3/Da / Density % sol: 67.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 4.0 M Sodium formate, 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: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 34181 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 66.18 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 34.878
Reflection shellResolution: 2.7→2.8 Å / Num. unique all: 3355

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Processing

Software
NameVersionClassification
JBluIce-EPICS- EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: crystal form II of curA Hal

Resolution: 2.69→39.308 Å / SU ML: 0.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1651 5.01 %RANDOM
Rwork0.185 ---
obs0.1872 32955 95.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.828 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3214 Å20 Å20 Å2
2--7.248 Å2-0 Å2
3----10.5694 Å2
Refinement stepCycle: LAST / Resolution: 2.69→39.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5228 0 39 108 5375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085374
X-RAY DIFFRACTIONf_angle_d1.127229
X-RAY DIFFRACTIONf_dihedral_angle_d17.8851960
X-RAY DIFFRACTIONf_chiral_restr0.074774
X-RAY DIFFRACTIONf_plane_restr0.004922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6903-2.76950.29111000.26652132X-RAY DIFFRACTION79
2.7695-2.85890.29091460.24382420X-RAY DIFFRACTION90
2.8589-2.9610.27921480.23822483X-RAY DIFFRACTION93
2.961-3.07950.26831500.23732533X-RAY DIFFRACTION95
3.0795-3.21960.26491190.23622641X-RAY DIFFRACTION97
3.2196-3.38930.29371260.21672684X-RAY DIFFRACTION98
3.3893-3.60150.26051360.20492662X-RAY DIFFRACTION98
3.6015-3.87930.2321400.16982713X-RAY DIFFRACTION99
3.8793-4.26930.22181720.15452700X-RAY DIFFRACTION99
4.2693-4.88610.19891310.14262752X-RAY DIFFRACTION99
4.8861-6.15210.1851490.16172747X-RAY DIFFRACTION99
6.1521-39.31170.20641340.1842837X-RAY DIFFRACTION97

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