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- PDB-2qni: Crystal structure of uncharacterized protein Atu0299 -

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Basic information

Entry
Database: PDB / ID: 2qni
TitleCrystal structure of uncharacterized protein Atu0299
ComponentsUncharacterized protein Atu0299
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / Atu0299 / In situ proteolysis / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / Uncharacterized protein
Function / homologyPhosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsDong, A. / Xu, X. / Gu, J. / Zheng, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein Atu0299.
Authors: Dong, A. / Xu, X. / Gu, J. / Zheng, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A.
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. AUTHORS STATE THAT THE BIOLOGICAL UNIT INFORMATION OF THIS PROTEIN IS NOT AVAILABLE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Atu0299


Theoretical massNumber of molelcules
Total (without water)24,3891
Polymers24,3891
Non-polymers00
Water3,189177
1
A: Uncharacterized protein Atu0299

A: Uncharacterized protein Atu0299


Theoretical massNumber of molelcules
Total (without water)48,7772
Polymers48,7772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area2370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.347, 111.347, 136.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Uncharacterized protein Atu0299 / AGR_C_517p


Mass: 24388.555 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 / Gene: AGR_C_517, Atu0299 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q8UIJ6, UniProt: A9CKF0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.33 Å3/Da / Density % sol: 63.03 %
Description: Due to a number of circumstances, initial data processing was only accomplished in space group C2. Scaling statistics is provided for that space group. Using the program XPREP, the ...Description: Due to a number of circumstances, initial data processing was only accomplished in space group C2. Scaling statistics is provided for that space group. Using the program XPREP, the higher symmetry (H32) was detected and used in refinement. The structure factor file contains both data sets: for H32 and for C2 space group assignments
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na(OAC) pH 4.6, 3.5M Sodium formate. THE CRYSTAL WAS OBTAINED BY IN SITU PROTEOLYSIS, PROTEIN SAMPLE WAS MIXED WITH 1:100 WEIGHT TO WEIGHT RATIO WITH CHYMOTRYPSIN IMMEDIATELY PRIOR TO ...Details: 0.1M Na(OAC) pH 4.6, 3.5M Sodium formate. THE CRYSTAL WAS OBTAINED BY IN SITU PROTEOLYSIS, PROTEIN SAMPLE WAS MIXED WITH 1:100 WEIGHT TO WEIGHT RATIO WITH CHYMOTRYPSIN IMMEDIATELY PRIOR TO SETTING UP CRYSTALLIZATION, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Temp details: THE CRYSTAL WAS OBTAINED BY IN SITU PROTEOLYSIS, PROTEIN SAMPLE WAS MIXED WITH 1:100 WEIGHT TO WEIGHT RATIO WITH CHYMOTRYPSIN IMMEDIATELY PRIOR TO SETTING UP CRYSTALLIZATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 88206 / Num. obs: 88206 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 10.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.92 / Num. unique all: 8762 / Rsym value: 0.749 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.034 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARP/wARP 6.1.1 and COOT 0.1 programs were also used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.22067 967 3.2 %RANDOM
Rwork0.19931 ---
all0.19998 29193 --
obs0.19998 29193 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 0 177 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211527
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.9252067
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2865190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61622.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91715236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2841514
X-RAY DIFFRACTIONr_chiral_restr0.080.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021181
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2743
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21044
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9441.5991
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37921524
X-RAY DIFFRACTIONr_scbond_it2.3843622
X-RAY DIFFRACTIONr_scangle_it3.5014.5543
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 64 -
Rwork0.272 2140 -
obs--100 %

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