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- PDB-2gax: Structure of Protein of Unknown Function Atu0240 from Agrobacteri... -

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Basic information

Entry
Database: PDB / ID: 2gax
TitleStructure of Protein of Unknown Function Atu0240 from Agrobacteriium tumerfaciencs str. C58
Componentshypothetical protein Atu0240
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / agrobacterium tumfaciens / hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Protein of unknown function DUF2000 / Protein of unknown function (DUF2000) / Bit1 / Bit1 / Peptidyl-tRNA hydrolase II domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DUF2000 family protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsBinkowski, T.A. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Hypothetical protein Atu0240 from Agrobacteriium tumerfaciencs str. C58
Authors: Binkowski, T.A. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Joachimiak, A.
History
DepositionMar 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 16, 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein Atu0240
B: hypothetical protein Atu0240
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6654
Polymers30,4752
Non-polymers1902
Water4,053225
1
A: hypothetical protein Atu0240
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3332
Polymers15,2381
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein Atu0240
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3332
Polymers15,2381
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: hypothetical protein Atu0240
hetero molecules

B: hypothetical protein Atu0240
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6654
Polymers30,4752
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area5130 Å2
ΔGint-54 kcal/mol
Surface area11580 Å2
MethodPISA, PQS
4
A: hypothetical protein Atu0240
hetero molecules

A: hypothetical protein Atu0240
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6654
Polymers30,4752
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5000 Å2
ΔGint-53 kcal/mol
Surface area11620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.965, 68.998, 120.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein hypothetical protein Atu0240


Mass: 15237.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Species: Agrobacterium tumefaciens / Strain: c58 / Gene: atu0240 / Plasmid: PET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UIQ3, UniProt: A9CKI6*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Ammonium sulphate, 0.1M Tris, 25%P3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: SBC-2 / Detector: CCD / Date: Oct 12, 2005
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.801→60.412 Å / Num. all: 25734 / Num. obs: 24976 / % possible obs: 97.0542 %
Reflection shellResolution: 1.801→1.847 Å / % possible all: 86.24

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.801→60.41 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.888 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.177 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28416 1315 5 %RANDOM
Rwork0.24747 ---
all0.24931 25734 --
obs0.2475 24976 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.801→60.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 10 225 2339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222146
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9552902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88923.8394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41515384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1191516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021578
X-RAY DIFFRACTIONr_nbd_refined0.2190.2978
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21507
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.2160
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.227
X-RAY DIFFRACTIONr_mcbond_it1.0231.51391
X-RAY DIFFRACTIONr_mcangle_it1.21122164
X-RAY DIFFRACTIONr_scbond_it2.1623848
X-RAY DIFFRACTIONr_scangle_it3.254.5738
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 80 -
Rwork0.399 1638 -
obs--86.24 %

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