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- PDB-5c5z: Crystal structure analysis of c4763, a uropathogenic E. coli-spec... -

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Basic information

Entry
Database: PDB / ID: 5c5z
TitleCrystal structure analysis of c4763, a uropathogenic E. coli-specific protein
ComponentsGlutamyl-tRNA amidotransferase
KeywordsHYDROLASE / GGCT-like domain / urea / uropathogenic E. coli
Function / homologyallophanate hydrolase activity / : / Allophanate hydrolase C-terminal domain / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / transferase activity / Roll / Alpha Beta / Glutamyl-tRNA amidotransferase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsKim, H. / Choi, J. / Kim, D. / Kim, K.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Crystal structure analysis of c4763, a uropathogenic Escherichia coli-specific protein.
Authors: Kim, H. / Choi, J. / Kim, D. / Kim, K.K.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamyl-tRNA amidotransferase
B: Glutamyl-tRNA amidotransferase


Theoretical massNumber of molelcules
Total (without water)31,2662
Polymers31,2662
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-13 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.628, 66.364, 69.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamyl-tRNA amidotransferase / Glutamyl-tRNA(Gln) amidotransferase subunit A / Strain ECONIH1 / complete genome


Mass: 15632.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECONIH1_22510, ERS451419_04892, SY51_21815 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B384(DE3) / References: UniProt: E2QI13
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.34 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.2 / Details: PEG 400, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.97883, 0.97923, 0.96000
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 11, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978831
20.979231
30.961
ReflectionRedundancy: 28.9 % / Number: 1394843 / Rmerge(I) obs: 0.088 / Χ2: 4.51 / D res high: 1.45 Å / D res low: 30 Å / Num. obs: 48282 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
3.123010.06110.29627.3
2.483.1210.0788.30429
2.172.4810.0926.46729.1
1.972.1710.1035.18829.2
1.831.9710.1283.97429.2
1.721.8310.1633.01829.2
1.631.7210.2072.40129.1
1.561.6310.2612.00329.1
1.51.5610.3171.71928.9
1.451.510.3891.53128.8
ReflectionResolution: 1.45→30 Å / Num. obs: 48241 / % possible obs: 99.9 % / Redundancy: 14.5 % / Biso Wilson estimate: 13.36 Å2 / Rmerge(I) obs: 0.078 / Χ2: 2.764 / Net I/av σ(I): 64.6 / Net I/σ(I): 14.3 / Num. measured all: 697928
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.45-1.514.10.44647661.152100
1.5-1.5614.50.36247661.297100
1.56-1.6314.60.28847611.457100
1.63-1.7214.60.22347601.685100
1.72-1.8314.60.16747602.035100
1.83-1.9714.60.12448222.523100
1.97-2.1714.60.09547963.187100
2.17-2.4814.60.08248433.794100
2.48-3.1214.60.06748964.631100
3.12-3013.80.0550715.74999.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.1refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIX1.8.1phasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→24.721 Å / FOM work R set: 0.8916 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.55 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 1982 4.12 %Random
Rwork0.188 46140 --
obs0.1887 48122 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.44 Å2 / Biso mean: 16.42 Å2 / Biso min: 6.97 Å2
Refinement stepCycle: final / Resolution: 1.45→24.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 0 228 2211
Biso mean---22.47 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062025
X-RAY DIFFRACTIONf_angle_d1.0842744
X-RAY DIFFRACTIONf_chiral_restr0.077305
X-RAY DIFFRACTIONf_plane_restr0.005352
X-RAY DIFFRACTIONf_dihedral_angle_d14.688732
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4491-1.48530.21071340.17563220335498
1.4853-1.52550.21761390.17193232337199
1.5255-1.57040.1831380.171332423380100
1.5704-1.6210.1841410.1723261340299
1.621-1.6790.1631440.169732443388100
1.679-1.74620.20621430.176232963439100
1.7462-1.82560.21091380.177932373375100
1.8256-1.92180.19971460.175932963442100
1.9218-2.04220.19261400.171632993439100
2.0422-2.19980.19271420.17833113453100
2.1998-2.4210.20111390.187733133452100
2.421-2.77090.19291410.198133393480100
2.7709-3.48950.25281460.200433743520100
3.4895-24.72440.19751510.20233476362799

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