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- PDB-2f06: Crystal structure of protein BT0572 from Bacteroides thetaiotaomicron -

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Basic information

Entry
Database: PDB / ID: 2f06
TitleCrystal structure of protein BT0572 from Bacteroides thetaiotaomicron
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / structural genomics Hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


ACT domain pair / ACT domain pair / VC0802-like / VC0802-like / ACT domain profile. / ACT domain / ACT-like domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / Acetohydroxyacid synthase small subunit Related
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsChang, C. / Volkart, L. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of protein BT0572 from Bacteroides thetaiotaomicron
Authors: Chang, C. / Volkart, L. / Collart, F. / Joachimiak, A.
History
DepositionNov 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 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 / struct_site
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 / _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

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Assembly

Deposited unit
A: conserved hypothetical protein
B: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8724
Polymers31,5602
Non-polymers3122
Water1,53185
1
A: conserved hypothetical protein
B: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
B: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7448
Polymers63,1194
Non-polymers6254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Unit cell
Length a, b, c (Å)64.622, 64.622, 244.942
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Detailstetramer generated by symmetry operation (x,x-y+1,1/6-z) of dimer

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Components

#1: Protein conserved hypothetical protein


Mass: 15779.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q8AA93
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8% PEG 6000, 0.1M Mes pH 6.5, 20% glycerol, 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: 0.97940 0.97954, 0.97172
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2005
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979541
30.971721
ReflectionResolution: 2.1→50 Å / Num. all: 18814 / Num. obs: 18739 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 21.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 60.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1782 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.954 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24941 953 5.1 %RANDOM
Rwork0.20252 ---
all0.20481 18628 --
obs0.20481 18628 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 22 85 2298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222329
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2531.9783168
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.7485312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55726.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69615428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.578156
X-RAY DIFFRACTIONr_chiral_restr0.2670.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021732
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2560.21010
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21616
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2118
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.2130
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3410.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4151.51530
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98522399
X-RAY DIFFRACTIONr_scbond_it3.6513903
X-RAY DIFFRACTIONr_scangle_it5.0724.5756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 87 -
Rwork0.241 1249 -
obs--98.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6202-1.1378-0.25624.3265-0.76175.997-0.0469-0.5749-0.54470.57250.43560.28090.49250.2109-0.3886-0.0638-0.0266-0.0955-0.1690.1246-0.18271.78526.81429.334
24.42591.60030.2612.26791.34294.40240.15770.4566-0.0068-0.76890.13230.2121-0.04890.1877-0.29010.00210.0329-0.0928-0.0974-0.0673-0.26956.80733.4227.921
30.3347-0.5895-0.1333.3523-0.16052.225-0.17840.23530.2397-0.09140.09160.0015-0.2744-0.07150.0868-0.0698-0.0052-0.0174-0.13380.0301-0.207421.43163.26713.843
42.3258-0.2697-0.68663.7590.73963.8767-0.01780.0413-0.3104-0.301-0.0902-0.15320.4830.10650.108-0.05290.0460.0414-0.09650.0076-0.297626.13241.379.972
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 41 - 7
2X-RAY DIFFRACTION1AA69 - 13972 - 142
3X-RAY DIFFRACTION2AA5 - 688 - 71
4X-RAY DIFFRACTION3BB-2 - 41 - 7
5X-RAY DIFFRACTION3BB69 - 13972 - 142
6X-RAY DIFFRACTION4BB5 - 688 - 71

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