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- PDB-3cb0: CobR -

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Basic information

Entry
Database: PDB / ID: 3cb0
TitleCobR
Components4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE
KeywordsOXIDOREDUCTASE / Corrin reductase / CobR / six-stranded anti-parallel beta-barrel
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 MONONUCLEOTIDE / 4-hydroxyphenylacetate 3-monooxygenase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsLawrence, A.D. / Warren, M.J. / Pickersgill, R.W.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Identification, characterization, and structure/function analysis of a corrin reductase involved in adenosylcobalamin biosynthesis
Authors: Lawrence, A.D. / Deery, E. / McLean, K.J. / Munro, A.W. / Pickersgill, R.W. / Rigby, S.E. / Warren, M.J.
History
DepositionFeb 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE
C: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE
D: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9026
Polymers74,9894
Non-polymers9132
Water21,6361201
1
A: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE
C: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9513
Polymers37,4942
Non-polymers4561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-51.3 kcal/mol
Surface area13110 Å2
MethodPISA
2
B: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE
D: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9513
Polymers37,4942
Non-polymers4561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-49.1 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.661, 105.084, 140.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE / CobR / Corrin Reductase


Mass: 18747.221 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: cobR / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YHT7, EC: 1.14.13.3
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1201 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5-1.0M Li2S04, 15-20% polyethylene glycol 800, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.6→42.8 Å / Num. obs: 97683 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 6.8 / Num. unique all: 14080 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→42.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.56 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23063 4880 5 %RANDOM
Rwork0.19482 ---
obs0.1966 92717 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.008 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2---0.38 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 62 1201 6231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0215126
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.9556971
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90523.509228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82715809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.221536
X-RAY DIFFRACTIONr_chiral_restr0.0690.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023858
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.22557
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23480
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.21038
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.291
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5381.53331
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91425151
X-RAY DIFFRACTIONr_scbond_it1.632085
X-RAY DIFFRACTIONr_scangle_it2.4924.51820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 352 -
Rwork0.227 6697 -
obs--98.75 %

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