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- PDB-2obb: Structure of the conserved protein coded by locus BT_0820 from Ba... -

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Basic information

Entry
Database: PDB / ID: 2obb
TitleStructure of the conserved protein coded by locus BT_0820 from Bacteroides thetaiotaomicron
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Bacteroides thetaiotaomicron / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyBacteriophage SP01, Orf1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Hydrolase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsCuff, M.E. / Bigelow, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of the conserved protein coded by locus BT_0820 from Bacteroides thetaiotaomicron
Authors: Cuff, M.E. / Bigelow, L. / Abdullah, J. / Joachimiak, A.
History
DepositionDec 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. THE DIMERIC ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9782
Polymers16,9541
Non-polymers241
Water1,49583
1
A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9564
Polymers33,9082
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3220 Å2
ΔGint-30 kcal/mol
Surface area12410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.898, 50.898, 129.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-220-

HOH

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Components

#1: Protein Hypothetical protein


Mass: 16953.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_0820 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8A9J5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M MgCl2, 0.1M Bis-Tris pH 6.5, 25% PEG 3350, 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: 0.97906, 0.97923
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979061
20.979231
ReflectionResolution: 2.2→32.34 Å / Num. all: 8658 / Num. obs: 8658 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 42.3 Å2 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.26 Å / % possible all: 65.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
autoSHARPphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.2→32.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.95 / SU B: 12.946 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.266 / ESU R Free: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24475 407 4.7 %RANDOM
Rwork0.21227 ---
all0.21382 8250 --
obs0.21382 8250 94.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.062 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å20 Å2
2--2.28 Å20 Å2
3----4.55 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 1 83 1084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221066
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9521444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43724.23759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54915191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.725158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02838
X-RAY DIFFRACTIONr_nbd_refined0.2170.2501
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.275
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.216
X-RAY DIFFRACTIONr_mcbond_it0.8441.5642
X-RAY DIFFRACTIONr_mcangle_it1.32621007
X-RAY DIFFRACTIONr_scbond_it1.9473488
X-RAY DIFFRACTIONr_scangle_it3.0784.5437
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 21 -
Rwork0.293 404 -
obs--65.38 %
Refinement TLS params.Method: refined / Origin x: 13.6343 Å / Origin y: -7.7183 Å / Origin z: 22.8788 Å
111213212223313233
T-0.1493 Å2-0.0322 Å20.0205 Å2--0.2333 Å20.0036 Å2---0.297 Å2
L2.9109 °20.9536 °2-0.4306 °2-4.2476 °2-0.1924 °2--3.2623 °2
S-0.0639 Å °0.0969 Å °-0.0077 Å °-0.275 Å °0.0457 Å °-0.0719 Å °-0.1685 Å °-0.0214 Å °0.0182 Å °

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