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- PDB-1qu9: 1.2 A CRYSTAL STRUCTURE OF YJGF GENE PRODUCT FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1qu9
Title1.2 A CRYSTAL STRUCTURE OF YJGF GENE PRODUCT FROM E. COLI
ComponentsYJGF PROTEIN
KeywordsSTRUCTURAL GENOMICS
Function / homology
Function and homology information


2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / deaminase activity / isoleucine biosynthetic process / protein homotrimerization / response to toxic substance / unfolded protein binding / protein-containing complex ...2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / deaminase activity / isoleucine biosynthetic process / protein homotrimerization / response to toxic substance / unfolded protein binding / protein-containing complex / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate/2-iminopropanoate deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsVolz, K.
CitationJournal: Protein Sci. / Year: 1999
Title: A test case for structure-based functional assignment: the 1.2 A crystal structure of the yjgF gene product from Escherichia coli
Authors: Volz, K.
History
DepositionJul 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 20, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YJGF PROTEIN
B: YJGF PROTEIN
C: YJGF PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,1173
Polymers41,1173
Non-polymers00
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-44 kcal/mol
Surface area14610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.22, 72.22, 72.22
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number16
Space group name H-MP222
Components on special symmetry positions
IDModelComponents
11A-256-

HOH

21A-284-

HOH

31A-345-

HOH

41B-456-

HOH

51B-484-

HOH

61B-545-

HOH

71C-656-

HOH

81C-684-

HOH

91C-745-

HOH

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Components

#1: Protein YJGF PROTEIN


Mass: 13705.514 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P39330, UniProt: P0AF93*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 8.1
Details: 50 mM tris HCL, 2.35 M ammonium sulphate, pH 8.1, microdialysis, temperature 4K
Crystal grow
*PLUS
Method: unknown / PH range low: 8.5 / PH range high: 7.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMTris-HCl11
22.35 Mammonium sulfate11

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Data collection

DiffractionMean temperature: 75 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.961
DetectorType: BRUKER / Detector: CCD / Date: May 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.961 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 118474 / Num. obs: 112350 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1
Reflection shellResolution: 1.2→1.27 Å / Num. unique all: 18335 / % possible all: 90.6
Reflection shell
*PLUS
% possible obs: 90.6 %

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Processing

Software
NameClassification
MLPHAREphasing
PROFFTrefinement
SMARTdata reduction
SAINTdata reduction
SMARTdata scaling
SAINTdata scaling
RefinementResolution: 1.2→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.164 --
all-112350 -
obs-103863 87.7 %
Displacement parametersBiso mean: 9.61 Å2
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 0 0 474 3321
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_planar_d0.0480.05
X-RAY DIFFRACTIONp_mcbond_it0.7271
X-RAY DIFFRACTIONp_mcangle_it1.1241.5
X-RAY DIFFRACTIONp_scbond_it1.1451
X-RAY DIFFRACTIONp_scangle_it1.7941.5
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.1310.15
X-RAY DIFFRACTIONp_singtor_nbd0.1640.5
X-RAY DIFFRACTIONp_multtor_nbd0.1420.5
X-RAY DIFFRACTIONp_xyhbond_nbd0.1320.5
X-RAY DIFFRACTIONp_planar_tor3.63
X-RAY DIFFRACTIONp_staggered_tor11.815
X-RAY DIFFRACTIONp_transverse_tor15.620
Software
*PLUS
Name: PROFFT / Classification: refinement
LS refinement shell
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 1.27 Å / Rfactor Rwork: 0.141 / Num. reflection obs: 18335

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