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- PDB-3do9: Crystal structure of protein ba1542 from bacillus anthracis str.ames -

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Basic information

Entry
Database: PDB / ID: 3do9
TitleCrystal structure of protein ba1542 from bacillus anthracis str.ames
ComponentsUPF0302 protein BA_1542/GBAA1542/BAS1430
Keywordsstructural genomics / unknown function / UNCHARACTERIZED PROTEIN / PROTEIN STRUCTURE INITIATIVE / PSI / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / ** NYSGXRC / STRUCTUR GENOMICS / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Uncharacterised family UPF0302, N-terminal domain / Uncharacterised protein family UPF0302 / IDEAL domain / Uncharacterised domain UPF0302, N-terminal / UPF0302, N-terminal domain superfamily / IDEAL domain / UPF0302 domain / IDEAL / Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A ...Uncharacterised family UPF0302, N-terminal domain / Uncharacterised protein family UPF0302 / IDEAL domain / Uncharacterised domain UPF0302, N-terminal / UPF0302, N-terminal domain superfamily / IDEAL domain / UPF0302 domain / IDEAL / Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A / Virus scaffolding protein, C-terminal / hypothetical protein tt1805 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0302 protein BA_1542/GBAA_1542/BAS1430
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsPatskovsky, Y. / Ozyurt, S. / Freeman, J. / Iizuka, M. / Maletic, M. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Protein Ba1542 from Bacillus Anthracis Str.Ames.
Authors: Patskovsky, Y. / Ozyurt, S. / Freeman, J. / Iizuka, M. / Maletic, M. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0302 protein BA_1542/GBAA1542/BAS1430
B: UPF0302 protein BA_1542/GBAA1542/BAS1430
C: UPF0302 protein BA_1542/GBAA1542/BAS1430


Theoretical massNumber of molelcules
Total (without water)68,0433
Polymers68,0433
Non-polymers00
Water1629
1
A: UPF0302 protein BA_1542/GBAA1542/BAS1430


Theoretical massNumber of molelcules
Total (without water)22,6811
Polymers22,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UPF0302 protein BA_1542/GBAA1542/BAS1430


Theoretical massNumber of molelcules
Total (without water)22,6811
Polymers22,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UPF0302 protein BA_1542/GBAA1542/BAS1430


Theoretical massNumber of molelcules
Total (without water)22,6811
Polymers22,6811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.742, 127.742, 196.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 1 / Auth seq-ID: 4 - 123 / Label seq-ID: 6 - 125

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein UPF0302 protein BA_1542/GBAA1542/BAS1430


Mass: 22680.902 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BA_1542, GBAA1542, BAS1430 / References: UniProt: Q81SV3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.51 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100MM BIS-TRIS,PH 6.5, 3500MM SODIUM CHLORIDE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 6.50

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 17, 2007
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 26606 / % possible obs: 99.7 % / Observed criterion σ(I): -0.5 / Redundancy: 7.7 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 4.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SHELXDphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.894 / SU B: 19.428 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R: 0.608 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31204 797 3.2 %RANDOM
Rwork0.26378 ---
obs0.26532 24341 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.025 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20.9 Å20 Å2
2--1.81 Å20 Å2
3----2.71 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4454 0 0 9 4463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224566
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8951.9316148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.0335525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.45224.221263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.06815848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1371530
X-RAY DIFFRACTIONr_chiral_restr0.5230.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.023505
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.32332
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3390.53030
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.5298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.3145
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3590.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.76622657
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.86334256
X-RAY DIFFRACTIONr_scbond_it14.73942074
X-RAY DIFFRACTIONr_scangle_it20.97861889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 985 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.190.05
2Btight positional0.220.05
3Ctight positional0.170.05
1Atight thermal26.8425
2Btight thermal23.9525
3Ctight thermal13.7225
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 59 -
Rwork0.365 1731 -
obs--99.94 %

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