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- PDB-1vki: Crystal structure of a putative oligo-nucleotide binding protein ... -

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Basic information

Entry
Database: PDB / ID: 1vki
TitleCrystal structure of a putative oligo-nucleotide binding protein (atu3699, agr_l_2275) from agrobacterium tumefaciens str. c58 at 1.60 A resolution
ComponentsHYPOTHETICAL PROTEIN ATU3699
KeywordsTRANSLATION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


aminoacyl-tRNA deacylase activity
Similarity search - Function
Prolyl-tRNA editing protein ProX/PRXD1 / YbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
YbaK/aminoacyl-tRNA synthetase-associated domain-containing protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (ATU3699) from Agrobacterium tumefaciens at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _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

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN ATU3699
B: HYPOTHETICAL PROTEIN ATU3699
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6648
Polymers40,1032
Non-polymers5616
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-55 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.997, 64.848, 77.427
Angle α, β, γ (deg.)90.00, 100.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 5 - 169 / Label seq-ID: 17 - 181

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

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Components

#1: Protein HYPOTHETICAL PROTEIN ATU3699


Mass: 20051.648 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 / ATCC 33970 / Gene: ATU3699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U9M7, UniProt: A9CFJ8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.02 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 20.025% PEG 8000, 0.08M HEPES, 0.02M HEPES_Na , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Oct 1, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 44165 / % possible obs: 95.39 % / Redundancy: 2.56 % / Biso Wilson estimate: 20.66 Å2 / Rsym value: 0.051 / Net I/σ(I): 19.88
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.76 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3277 / Rsym value: 0.303 / % possible all: 71.07

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0001refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJF

1vjf


Resolution: 1.6→49.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.364 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. TWO SULFATE IONS COULD BE SOMETHING ELSE
RfactorNum. reflection% reflectionSelection details
Rfree0.18496 2209 5 %RANDOM
Rwork0.15201 ---
obs0.15366 41937 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å2-0.57 Å2
2---0.43 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 34 510 3094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222652
X-RAY DIFFRACTIONr_bond_other_d0.0020.022456
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9623595
X-RAY DIFFRACTIONr_angle_other_deg0.83535727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6755329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14324.867113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.97815463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5241512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
X-RAY DIFFRACTIONr_nbd_refined0.2170.2524
X-RAY DIFFRACTIONr_nbd_other0.1750.22609
X-RAY DIFFRACTIONr_nbtor_other0.0820.21600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2374
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.225
X-RAY DIFFRACTIONr_mcbond_it2.2231749
X-RAY DIFFRACTIONr_mcbond_other0.5813676
X-RAY DIFFRACTIONr_mcangle_it2.6352700
X-RAY DIFFRACTIONr_scbond_it4.5981049
X-RAY DIFFRACTIONr_scangle_it6.45111895
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2410 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.330.5
medium thermal0.722
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 121 5.23 %
Rwork0.213 2191 -

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