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- PDB-6p2v: RebH Variant 10S, Tryptamine 5-halogenase -

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Basic information

Entry
Database: PDB / ID: 6p2v
TitleRebH Variant 10S, Tryptamine 5-halogenase
ComponentsFlavin-dependent tryptophan halogenase RebH
KeywordsFLAVOPROTEIN / halogenase / oxidoreductase / flavin / directed evolution
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 / MOLECULAR REPLACEMENT / Resolution: 2.553 Å
AuthorsAndorfer, M.C. / Sukumar, N. / Lewis, J.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM115665 United States
National Science Foundation (NSF, United States)DGE-114408 United States
CitationJournal: To Be Published
Title: Structural and Computational Analysis of Laboratory-Evolved Halogenases Reveals Molecular Details of Site-Selectivity
Authors: Andorfer, M.A. / Yang, S. / He, C.Q. / Evans, D. / Girlich, A.M. / Vergara-Coll, J. / Sukumar, N. / Houk, K.N. / Lewis, J.C.
History
DepositionMay 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavin-dependent tryptophan halogenase RebH
B: Flavin-dependent tryptophan halogenase RebH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6274
Polymers125,0562
Non-polymers1,5712
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-31 kcal/mol
Surface area38820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.160, 115.160, 230.171
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-867-

HOH

21B-737-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 133 or (resid 134...
21chain B
12chain A and resid 601
22chain B and resid 601

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYGLYGLY(chain A and (resid 3 through 133 or (resid 134...AA3 - 13323 - 153
121LYSLYSLYSLYS(chain A and (resid 3 through 133 or (resid 134...AA134154
131METMETHISHIS(chain A and (resid 3 through 133 or (resid 134...AA1 - 52821 - 548
141METMETHISHIS(chain A and (resid 3 through 133 or (resid 134...AA1 - 52821 - 548
151METMETHISHIS(chain A and (resid 3 through 133 or (resid 134...AA1 - 52821 - 548
161METMETHISHIS(chain A and (resid 3 through 133 or (resid 134...AA1 - 52821 - 548
211GLYGLYHISHISchain BBB3 - 52823 - 548
112FADFADFADFADchain A and resid 601AC601
212FADFADFADFADchain B and resid 601B - AD - C601

NCS ensembles :
ID
1
2

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Components

#1: Protein Flavin-dependent tryptophan halogenase RebH


Mass: 62528.016 Da / Num. of mol.: 2 / Mutation: I52H, L380F, F465C, N470S, Q494R, R509Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria)
Gene: rebH, rbmJ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KHZ8, tryptophan 7-halogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.72 Å3/Da / Density % sol: 66.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.3M Na/K phosphate buffer, pH 6.8, Vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 55848 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.091 / Rrim(I) all: 0.25 / Χ2: 0.958 / Net I/σ(I): 4 / Num. measured all: 427490
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.55-2.647.61.39855250.6690.5481.5030.821
2.64-2.757.61.09355610.7660.4271.1740.845
2.75-2.877.70.77756350.8720.3010.8340.89
2.87-3.027.70.61755730.9090.240.6630.916
3.02-3.217.70.40455490.9560.1570.4340.981
3.21-3.467.70.27255700.9770.1050.2921.098
3.46-3.817.70.19755840.9840.0770.2111.081
3.81-4.367.60.15155800.9890.0590.1621.01
4.36-5.497.60.11355970.9920.0440.1221.004
5.49-507.70.07456740.9970.0280.0790.932

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OAL

2oal


Resolution: 2.553→48.735 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 2786 5 %
Rwork0.1709 52989 -
obs0.1729 55775 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.11 Å2 / Biso mean: 39.9714 Å2 / Biso min: 18.8 Å2
Refinement stepCycle: final / Resolution: 2.553→48.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8347 0 106 432 8885
Biso mean--66.41 40.95 -
Num. residues----1044
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3188X-RAY DIFFRACTION4.575TORSIONAL
12B3188X-RAY DIFFRACTION4.575TORSIONAL
21A32X-RAY DIFFRACTION4.575TORSIONAL
22B32X-RAY DIFFRACTION4.575TORSIONAL

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