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- PDB-2oal: RebH with bound FAD -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2oal
TitleRebH with bound FAD
ComponentsTryptophan halogenase
KeywordsBIOSYNTHETIC PROTEIN / FLAVOPROTEIN / tryptophan-7-halogenase / flavin-binding / rebeccamycin biosynthesis
Function / homology
Function and homology information


tryptophan 7-halogenase / monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / : / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Tryptophan 7-halogenase RebH
Similarity search - Component
Biological speciesLechevalieria aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsBlasiak, L.C. / Drennan, C.L.
CitationJournal: Biochemistry / Year: 2007
Title: Chlorination by a long-lived intermediate in the mechanism of flavin-dependent halogenases
Authors: Yeh, E. / Blasiak, L.C. / Koglin, A. / Drennan, C.L. / Walsh, C.T.
History
DepositionDec 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan halogenase
B: Tryptophan halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6875
Polymers125,0802
Non-polymers1,6073
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-33 kcal/mol
Surface area38720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.725, 114.725, 230.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-1242-

HOH

21A-1275-

HOH

31A-1276-

HOH

41B-852-

HOH

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Components

#1: Protein Tryptophan halogenase / Putative halogenase of tryptophan / Halogenase


Mass: 62540.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria)
Gene: rbmJ, rebH / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8KHZ8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 7
Details: 1.2 M Na/K phosphate, pH 7.0, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97496 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2006
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97496 Å / Relative weight: 1
ReflectionResolution: 2.1→35.9 Å / Num. all: 99732 / Num. obs: 99732 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.5 Å2 / Rsym value: 0.042 / Χ2: 1.112 / Net I/σ(I): 15.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 9741 / Rsym value: 0.176 / Χ2: 0.733 / % possible all: 97.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2E4G

2e4g


Resolution: 2.1→35.9 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4874 4.9 %random
Rwork0.197 ---
all0.215 99855 --
obs-97699 97.8 %-
Solvent computationBsol: 50.772 Å2
Displacement parametersBiso mean: 38.397 Å2
Baniso -1Baniso -2Baniso -3
1--3.276 Å2-3.712 Å20 Å2
2---3.276 Å20 Å2
3---6.552 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.281 Å0.248 Å
Luzzati d res low-5 Å
Luzzati sigma a0.248 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8458 0 106 572 9136
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3361.5
X-RAY DIFFRACTIONc_scbond_it2.0762
X-RAY DIFFRACTIONc_mcangle_it2.0542
X-RAY DIFFRACTIONc_scangle_it3.0882.5
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d22.78
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.1→2.18 Å
RfactorNum. reflection% reflection
Rfree0.27 459 -
Rwork0.25 --
obs-9323 93.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4fad.par

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