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- PDB-2oam: Apo RebH from Lechevalieria aerocolonigenes -

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Basic information

Entry
Database: PDB / ID: 2oam
TitleApo RebH from Lechevalieria aerocolonigenes
ComponentsTryptophan halogenase
KeywordsBIOSYNTHETIC PROTEIN/FLAVOPROTEIN / tryptophan-7-halogenase / flavin-binding / rebeccamycin biosynthesis / BIOSYNTHETIC PROTEIN-FLAVOPROTEIN COMPLEX
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
Tryptophan 7-halogenase RebH
Similarity search - Component
Biological speciesLechevalieria aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan halogenase
B: Tryptophan halogenase


Theoretical massNumber of molelcules
Total (without water)125,0802
Polymers125,0802
Non-polymers00
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-13 kcal/mol
Surface area40100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.819, 114.819, 230.626
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
11B-647-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 64.93 %
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: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2006 / Details: Inter-frame total dead time: 3s.
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→41.7 Å / Num. all: 75915 / Num. obs: 75915 / % possible obs: 99.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 49.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 18.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 7545 / Rsym value: 0.495 / % possible all: 99.6

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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: 2.3→41.7 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3794 5 %random
Rwork0.199 ---
all-75915 --
obs-75897 99.7 %-
Solvent computationBsol: 40.41 Å2
Displacement parametersBiso mean: 38.989 Å2
Baniso -1Baniso -2Baniso -3
1--3.247 Å2-5.848 Å20 Å2
2---3.247 Å20 Å2
3---6.494 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.274 Å
Luzzati d res low-5 Å
Luzzati sigma a0.316 Å0.315 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8399 0 0 574 8973
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3021.5
X-RAY DIFFRACTIONc_scbond_it2.1342
X-RAY DIFFRACTIONc_mcangle_it2.1032
X-RAY DIFFRACTIONc_scangle_it3.2352.5
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.301 369 -
Rwork0.264 --
obs-7536 99.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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