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- PDB-2fb6: Structure of Conserved Protein of Unknown Function BT1422 from Ba... -

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Basic information

Entry
Database: PDB / ID: 2fb6
TitleStructure of Conserved Protein of Unknown Function BT1422 from Bacteroides thetaiotaomicron
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyDsrEFH-like / DsrEFH-like / Hypothetical Protein Ychn; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta / : / DsrE family protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.46 Å
AuthorsOsipiuk, J. / Mulligan, R. / Abdullah, J. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of conserved hypothetical protein BT1422 from Bacteroides thetaiotaomicron
Authors: Osipiuk, J. / Mulligan, R. / Abdullah, J. / Collart, F. / Joachimiak, A.
History
DepositionDec 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT OF THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)13,3311
Polymers13,3311
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: conserved hypothetical protein

A: conserved hypothetical protein

A: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)39,9923
Polymers39,9923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4520 Å2
ΔGint-30 kcal/mol
Surface area14450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.880, 64.880, 70.457
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

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Components

#1: Protein conserved hypothetical protein


Mass: 13330.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT1422 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 29338729, UniProt: Q8A7V2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 35% tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.46→40 Å / Num. all: 19084 / Num. obs: 19084 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 30.8
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.99 / Num. unique all: 1024 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.46→40 Å / Cor.coef. Fo:Fc: 0.98 / SU B: 1.75 / SU ML: 0.031 / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.1613 983 -RANDOM
Rwork0.1318 ---
all0.1332 19083 --
obs0.1332 19083 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.221 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.46→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 0 133 1042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221048
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.9491448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8285149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.95626.52246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0515208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.042153
X-RAY DIFFRACTIONr_chiral_restr0.0780.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02779
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2482
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2724
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9771.5659
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43321058
X-RAY DIFFRACTIONr_scbond_it2.4613448
X-RAY DIFFRACTIONr_scangle_it3.1254.5374
X-RAY DIFFRACTIONr_rigid_bond_restr1.79231107
X-RAY DIFFRACTIONr_sphericity_free3.3523133
X-RAY DIFFRACTIONr_sphericity_bonded2.40731017
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 75 -
Rwork0.231 1318 -
obs-1318 92.04 %

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