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- PDB-3fbq: The crystal structure of the conserved domain protein from Bacill... -

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Basic information

Entry
Database: PDB / ID: 3fbq
TitleThe crystal structure of the conserved domain protein from Bacillus anthracis
ComponentsConserved domain proteinProtein domain
Keywordsstructural genomics / unknown function / conserved domain protein / Bacillus anthracis / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


bacillus anthracis domain / Conserved domain protein. / Domain of unknown function DUF4179 / Domain of unknown function DUF5643 / Domain of unknown function (DUF4179) / Family of unknown function (DUF5643) / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Conserved domain protein / Conserved domain protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.71 Å
AuthorsZhang, R. / Joachimiak, G. / Kim, Y. / Gornicki, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the conserved domain protein from Bacillus anthracis
Authors: Zhang, R. / Joachimiak, G. / Kim, Y. / Gornicki, P. / Joachimiak, A.
History
DepositionNov 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved domain protein


Theoretical massNumber of molelcules
Total (without water)32,5921
Polymers32,5921
Non-polymers00
Water48627
1
A: Conserved domain protein

A: Conserved domain protein

A: Conserved domain protein


Theoretical massNumber of molelcules
Total (without water)97,7753
Polymers97,7753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)101.406, 101.406, 101.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThis protein existed as trimer. The second and third part of the biological are genarated by the three fold axis: z,x,y and y,z,x

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Components

#1: Protein Conserved domain protein / Protein domain


Mass: 32591.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: str. Sterne / Gene: BAS1627, BA_1754, GBAA1754, GI:49178568 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81SB1, UniProt: A0A6L8PDV7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2M (NH4)2SO4, 0.1M Tris and 0.2M Li2SO4, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 2.7→71.8 Å / Num. all: 9267 / Num. obs: 9226 / % possible obs: 99.56 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 21.45
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.72 / Num. unique all: 696 / % possible all: 97.41

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.71→71.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.866 / SU B: 29.511 / SU ML: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.79 / ESU R Free: 0.385
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28285 465 4.8 %RANDOM
Rwork0.20584 ---
obs0.20952 9226 99.56 %-
all-9267 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.118 Å2
Refinement stepCycle: LAST / Resolution: 2.71→71.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 0 27 2249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222257
X-RAY DIFFRACTIONr_angle_refined_deg2.5561.9553035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.8775281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.78825.429105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.84415428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4041511
X-RAY DIFFRACTIONr_chiral_restr0.2110.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021672
X-RAY DIFFRACTIONr_mcbond_it0.9531.51393
X-RAY DIFFRACTIONr_mcangle_it1.81822250
X-RAY DIFFRACTIONr_scbond_it2.9063864
X-RAY DIFFRACTIONr_scangle_it4.8224.5785
LS refinement shellResolution: 2.707→2.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 36 -
Rwork0.257 642 -
obs-678 97.41 %
Refinement TLS params.Method: refined / Origin x: 24.579 Å / Origin y: -0.317 Å / Origin z: 26.542 Å
111213212223313233
T0.209 Å20.0539 Å2-0.0015 Å2-0.1039 Å20.0291 Å2--0.0707 Å2
L0.8247 °2-0.375 °2-0.1159 °2-1.2852 °2-0.7066 °2--1.3958 °2
S-0.0006 Å °-0.0783 Å °0.056 Å °-0.1088 Å °-0.0617 Å °-0.0536 Å °0.313 Å °0.1214 Å °0.0623 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 150
4X-RAY DIFFRACTION1A151 - 200
5X-RAY DIFFRACTION1A201 - 250
6X-RAY DIFFRACTION1A256 - 279
7X-RAY DIFFRACTION1A280 - 291

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