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- PDB-5cho: Crystal Structure of BorF, the Flavin Reductase Component of a Ba... -

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Basic information

Entry
Database: PDB / ID: 5cho
TitleCrystal Structure of BorF, the Flavin Reductase Component of a Bacterial Two-Component Tryptophan Halogenase
ComponentsFlavin reductase
KeywordsHYDROLASE / flavin reductase / two-component halogenase
Function / homology
Function and homology information


Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavin reductase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsMa, Z. / Bellizzi, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1 R15 GM110679-01A1 United States
CitationJournal: To be published
Title: Crystal Structure of BorF, the Flavin Reductase Component of a Bacterial Two-Component Tryptophan Halogenase
Authors: Ma, Z. / Bellizzi, J.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

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Assembly

Deposited unit
A: Flavin reductase
B: Flavin reductase
C: Flavin reductase
D: Flavin reductase
E: Flavin reductase
F: Flavin reductase
G: Flavin reductase
H: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,51416
Polymers169,2298
Non-polymers6,2848
Water2,828157
1
A: Flavin reductase
B: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8784
Polymers42,3072
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-60 kcal/mol
Surface area13800 Å2
MethodPISA
2
C: Flavin reductase
D: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8784
Polymers42,3072
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-59 kcal/mol
Surface area14020 Å2
MethodPISA
3
E: Flavin reductase
F: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8784
Polymers42,3072
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-57 kcal/mol
Surface area13210 Å2
MethodPISA
4
G: Flavin reductase
H: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8784
Polymers42,3072
Non-polymers1,5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-60 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)278.010, 62.340, 101.880
Angle α, β, γ (deg.)90.000, 110.840, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Flavin reductase /


Mass: 21153.658 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: borF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: M9QXS1
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Drop containing 1 uL of 10 mg/mL (0.474 mM) BorF in 20 mM Tris pH 7.5, 100 mM NaCl, with 1 mM FAD mixed with 1 uL of reservoir solution containing 20% PEG 400, 0.1 M HEPES pH 7.6, 5% v/v ...Details: Drop containing 1 uL of 10 mg/mL (0.474 mM) BorF in 20 mM Tris pH 7.5, 100 mM NaCl, with 1 mM FAD mixed with 1 uL of reservoir solution containing 20% PEG 400, 0.1 M HEPES pH 7.6, 5% v/v glycerol against 200 micro liter reservoir
PH range: 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.988 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.37→50.937 Å / Num. obs: 64289 / % possible obs: 100 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4
Reflection shellResolution: 2.37→2.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HX6

4hx6


Resolution: 2.37→47.607 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1378 2.07 %Random selection
Rwork0.2151 65324 --
obs0.2158 66702 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.8 Å2 / Biso mean: 53.2596 Å2 / Biso min: 16.09 Å2
Refinement stepCycle: final / Resolution: 2.37→47.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9688 0 424 157 10269
Biso mean--52.6 39.07 -
Num. residues----1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410411
X-RAY DIFFRACTIONf_angle_d0.9914298
X-RAY DIFFRACTIONf_chiral_restr0.0361560
X-RAY DIFFRACTIONf_plane_restr0.0051804
X-RAY DIFFRACTIONf_dihedral_angle_d17.543494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.37-2.45470.35051290.296264616590100
2.4547-2.5530.30341420.282764986640100
2.553-2.66920.3121470.266664566603100
2.6692-2.80990.27231230.262465066629100
2.8099-2.98590.31161380.252565536691100
2.9859-3.21640.30411370.245264736610100
3.2164-3.540.25911450.232965206665100
3.54-4.0520.24531280.205365466674100
4.052-5.10410.18471360.171866206756100
5.1041-47.6170.21061530.18166691684499

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