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- PDB-3lqn: Crystal Structure of CBS Domain-containing Protein of Unknown Fun... -

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Basic information

Entry
Database: PDB / ID: 3lqn
TitleCrystal Structure of CBS Domain-containing Protein of Unknown Function from Bacillus anthracis str. Ames Ancestor
ComponentsCBS domain protein
KeywordsStructural Genomics / Unknown function / CBS domain / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


CBS-domain / CBS-domain / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / CBS domain protein / CBS domain protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, Y. / Mulligan, R. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of CBS Domain-containing Protein of Unknown Function from Bacillus anthracis str. Ames Ancestor
Authors: Kim, Y. / Mulligan, R. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionFeb 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: CBS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,90712
Polymers17,0541
Non-polymers85311
Water1,856103
1
A: CBS domain protein
hetero molecules

A: CBS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,81324
Polymers34,1082
Non-polymers1,70522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5960 Å2
ΔGint-167 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.585, 120.770, 80.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

21A-235-

HOH

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Components

#1: Protein CBS domain protein /


Mass: 17054.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS3893, BA_4196, GBAA4196, GBAA_4196 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81MQ0, UniProt: A0A3P1U8K3*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.95 Å3/Da / Density % sol: 37.06 %
Crystal growTemperature: 277 K / pH: 10.5
Details: 0.2M litium sulphate, 0.1 M CAPS pH 10.5, 2.0 M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 21, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 12662 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 28.91 Å2 / Rsym value: 0.029 / Net I/σ(I): 23.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.325 / % possible all: 81.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EMQ

2emq


Resolution: 1.8→24.4 Å / SU ML: 0.23 / Isotropic thermal model: mixed / σ(F): 1.35 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 622 4.92 %
Rwork0.1839 --
obs0.1864 12640 98.2 %
all-9287 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.472 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.408 Å2-0 Å2-0 Å2
2---0.3039 Å20 Å2
3----5.1041 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 48 103 1376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161295
X-RAY DIFFRACTIONf_angle_d1.6361758
X-RAY DIFFRACTIONf_dihedral_angle_d20.051490
X-RAY DIFFRACTIONf_chiral_restr0.125195
X-RAY DIFFRACTIONf_plane_restr0.008223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8005-1.98160.26431360.19972837X-RAY DIFFRACTION94
1.9816-2.26820.24241770.17672970X-RAY DIFFRACTION100
2.2682-2.8570.27561580.17643051X-RAY DIFFRACTION100
2.857-24.40280.21141510.18283160X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 4.7088 Å / Origin y: 18.3059 Å / Origin z: 10.094 Å
111213212223313233
T0.1013 Å20.0082 Å2-0.0037 Å2-0.075 Å20.0077 Å2--0.0762 Å2
L1.0459 °20.4614 °2-0.5319 °2-1.6481 °20.7899 °2--1.9846 °2
S-0.1371 Å °0.0472 Å °-0.0329 Å °0.024 Å °0.0089 Å °-0.0629 Å °0.2603 Å °-0.0185 Å °0.1177 Å °
Refinement TLS groupSelection details: chain A

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