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- PDB-7ju0: RebH Variant 0S, Tryptamine 7-halogenase with bound tryptamine -

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Basic information

Entry
Database: PDB / ID: 7ju0
TitleRebH Variant 0S, Tryptamine 7-halogenase with bound tryptamine
ComponentsFlavin-dependent tryptophan halogenase RebH
KeywordsFLAVOPROTEIN / oxidoreductase / halogenase / 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 superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 2-(1H-INDOL-3-YL)ETHANAMINE / Tryptophan 7-halogenase RebH
Similarity search - Component
Biological speciesLentzea aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsAndorfer, M.C. / Sukumar, N. / Lewis, J.C.
Funding support United States, 4items
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 RR029205 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
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)126,9186
Polymers125,0262
Non-polymers1,8924
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-39 kcal/mol
Surface area38230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.837, 114.837, 230.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Flavin-dependent tryptophan halogenase RebH


Mass: 62513.047 Da / Num. of mol.: 2 / Mutation: N470S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentzea 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: Chemical ChemComp-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE


Mass: 160.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.65 Å3/Da / Density % sol: 66.31 %
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-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 52474 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 52.97 Å2 / Rmerge(I) obs: 0.284 / Rpim(I) all: 0.116 / Rrim(I) all: 0.308 / Χ2: 1.107 / Net I/σ(I): 5.4 / Num. measured all: 335697
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.695.11.23852190.6240.5991.381.044100
2.69-2.86.31.02153000.7540.4371.1131.094100
2.8-2.936.60.78752290.8320.3280.8551.19199.9
2.93-3.086.60.60451890.8920.2490.6551.14899.9
3.08-3.286.50.43952740.9140.1840.4771.12599.8
3.28-3.5360.33252460.9350.1430.3631.15899.8
3.53-3.886.90.26652460.9530.1060.2871.11899.8
3.88-4.456.80.22852490.9660.0920.2471.03699.7
4.45-5.66.30.21852490.9590.0910.2371.10899.5
5.6-506.80.25952730.9320.1030.2791.03998.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OA1

2oa1


Resolution: 2.602→48.605 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 2004 3.82 %
Rwork0.1768 50459 -
obs0.1784 52463 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.4 Å2 / Biso mean: 55.2093 Å2 / Biso min: 32.68 Å2
Refinement stepCycle: final / Resolution: 2.602→48.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8457 0 130 82 8669
Biso mean--82.55 53.21 -
Num. residues----1055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018835
X-RAY DIFFRACTIONf_angle_d1.06512009
X-RAY DIFFRACTIONf_chiral_restr0.0581242
X-RAY DIFFRACTIONf_plane_restr0.0071565
X-RAY DIFFRACTIONf_dihedral_angle_d14.5065117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.602-2.66670.31431460.27433601100
2.6667-2.73880.29191450.24433606100
2.7388-2.81940.27021420.23133584100
2.8194-2.91030.29691350.22733589100
2.9103-3.01440.29141430.22443631100
3.0144-3.1350.32721400.21113600100
3.135-3.27770.26921440.20243603100
3.2777-3.45040.22841420.19353587100
3.4504-3.66650.22231480.16733607100
3.6665-3.94950.18091460.15663618100
3.9495-4.34680.18731440.14193585100
4.3468-4.97520.16271410.13643618100
4.9752-6.26610.2061440.17133613100
6.2661-48.6050.20181440.1697361799

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