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- PDB-2b1y: Crystal Structure of Protein of Unknown Function ATU1913 from Agr... -

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Basic information

Entry
Database: PDB / ID: 2b1y
TitleCrystal Structure of Protein of Unknown Function ATU1913 from Agrobacterium tumefaciens str. C58
Componentshypothetical protein Atu1913
KeywordsUNKNOWN FUNCTION / hypothetical protein / new fold / structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyAtu1913-like / Atu1913-like / Domain of unknown function DUF1883 / DUF1883-like superfamily / Domain of unknown function (DUF1883) / Few Secondary Structures / Irregular / DUF1883 domain-containing protein / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsNocek, B. / Skarina, T. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Hypothetical Protein from Agrobacterium tumefaciens reveals a new fold.
Authors: Nocek, B. / Skarina, T. / SAVCHENKO, A. / EDWARDS, A. / Joachimiak, A.
History
DepositionSep 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: 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 1.3Oct 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein Atu1913
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1354
Polymers11,8471
Non-polymers2883
Water1,27971
1
A: hypothetical protein Atu1913
hetero molecules

A: hypothetical protein Atu1913
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2708
Polymers23,6942
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10250 Å2
ΔGint-105 kcal/mol
Surface area13160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.428, 99.646, 55.827
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 Atu1913


Mass: 11847.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UE48, UniProt: A9CIG4*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.37 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2M NH4Sulphate,5% iso-Propanol, 2Mm K/Na Tartrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 20120 / Num. obs: 10811 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.9
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→49.81 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.739 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HKL-3000, SHELXD, SHELXE, MLPHARE, DM, SOLVE/RESOLVE, O, COOT, and CCP4 WERE ALSO USED FOR STRUCTURE SOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 479 4.7 %RANDOM
Rwork0.2125 ---
all0.2129 10167 --
obs0.2129 9688 94.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.442 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2---1.05 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms795 0 15 71 881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9781177
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5945108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01122.22236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09415152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.144158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02642
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2236
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2591
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1791.5543
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7812857
X-RAY DIFFRACTIONr_scbond_it3.0823357
X-RAY DIFFRACTIONr_scangle_it4.5624.5320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 45 -
Rwork0.257 748 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 6.9132 Å / Origin y: -2.841 Å / Origin z: -4.5273 Å
111213212223313233
T-0.0964 Å2-0.003 Å20.0102 Å2--0.1013 Å20.0117 Å2---0.1243 Å2
L0.1547 °2-0.0968 °20.0332 °2-0.9087 °20.3564 °2--0.1749 °2
S-0.0317 Å °-0.0025 Å °-0.0257 Å °-0.003 Å °0.0078 Å °-0.068 Å °0.0079 Å °0.0157 Å °0.0239 Å °

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