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- PDB-4ira: CobR in complex with FAD -

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Basic information

Entry
Database: PDB / ID: 4ira
TitleCobR in complex with FAD
Components4-hydroxyphenylacetate 3-monooxygenase
KeywordsOXIDOREDUCTASE / six-stranded anti-parallel beta-barrel / Corrin reductase
Function / homology
Function and homology information


4-hydroxyphenylacetate 3-monooxygenase activity / 4-hydroxyphenylacetate 3-monooxygenase / pyrimidine nucleobase catabolic process / riboflavin reductase (NADPH) activity / FMN binding
Similarity search - Function
: / 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 / 4-hydroxyphenylacetate 3-monooxygenase
Similarity search - Component
Biological speciesBrucella melitensis bv. 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLawrence, A.D. / Scott, A.F. / Warren, M.J. / Pickersgill, R.W.
CitationJournal: To be Published
Title: Biophysical characterisation and structure-function analysis of Brucella melitensis CobR: Protein-flavin interactions determine function and stability
Authors: Lawrence, A.D. / Taylor, S.L. / Scott, A.F. / Rowe, M.L. / Johnson, C.M. / Rigby, S.E.J. / Geeves, S.A. / Pickersgill, R.W. / Howard, M.J. / Warren, M.J.
History
DepositionJan 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 4-hydroxyphenylacetate 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,99110
Polymers18,7471
Non-polymers2,2449
Water1,928107
1
A: 4-hydroxyphenylacetate 3-monooxygenase
hetero molecules

A: 4-hydroxyphenylacetate 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,98220
Polymers37,4942
Non-polymers4,48718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area12030 Å2
ΔGint-215 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.193, 103.193, 133.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-350-

HOH

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Components

#1: Protein 4-hydroxyphenylacetate 3-monooxygenase / Flavin reductase domain-containing protein FMN-binding


Mass: 18747.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis bv. 1 (bacteria) / Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BAWG_2682, BMEI0709, CobR / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8YHT7, EC: 1.14.13.3
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 5.76 Å3/Da / Density % sol: 77.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M (NH4)2SO4, 0.02 M Na Acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.117 Å / Relative weight: 1
ReflectionResolution: 2.2→53.377 Å / Num. all: 21887 / Num. obs: 21883 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.2-2.321100
6.96-74.12199.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→53.377 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.985 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25032 1119 5.1 %RANDOM
Rwork0.22348 ---
obs0.22485 21883 99.98 %-
all-21887 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→53.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 141 107 1483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211411
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1732.061942
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1723.50957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65115203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.568159
X-RAY DIFFRACTIONr_chiral_restr0.1180.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021019
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5241.5807
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00421291
X-RAY DIFFRACTIONr_scbond_it1.6943604
X-RAY DIFFRACTIONr_scangle_it2.6894.5651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 88 -
Rwork0.275 1487 -
obs--100 %

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