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- PDB-1u5w: Crystal structure of hypothetical protein yjjX from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1u5w
TitleCrystal structure of hypothetical protein yjjX from Escherichia coli
ComponentsHypothetical UPF0244 protein yjjX
KeywordsUNKNOWN FUNCTION / 3 layers Alpha/Beta/Alpha protein / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


inosine/xanthosine triphosphatase / ITPase activity / thiamine metabolic process / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / response to antibiotic / nucleotide binding / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Inosine/xanthosine triphosphatase / Non-canonical purine NTP phosphatase/PRRC1 / : / Protein of unknown function DUF84 / Maf protein - #10 / Inosine triphosphate pyrophosphatase-like / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Inosine/xanthosine triphosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.3 Å
AuthorsZheng, J. / Singh, V.K. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Structure / Year: 2005
Title: Identification of an ITPase/XTPase in Escherichia coli by Structural and Biochemical Analysis
Authors: Zheng, J. / Singh, V.K. / Jia, Z.
History
DepositionJul 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical UPF0244 protein yjjX
B: Hypothetical UPF0244 protein yjjX
C: Hypothetical UPF0244 protein yjjX
D: Hypothetical UPF0244 protein yjjX
E: Hypothetical UPF0244 protein yjjX
F: Hypothetical UPF0244 protein yjjX
G: Hypothetical UPF0244 protein yjjX
H: Hypothetical UPF0244 protein yjjX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,02923
Polymers159,5898
Non-polymers1,44115
Water12,286682
1
A: Hypothetical UPF0244 protein yjjX
B: Hypothetical UPF0244 protein yjjX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2816
Polymers39,8972
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-67 kcal/mol
Surface area13760 Å2
MethodPISA
2
C: Hypothetical UPF0244 protein yjjX
D: Hypothetical UPF0244 protein yjjX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2816
Polymers39,8972
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-69 kcal/mol
Surface area14200 Å2
MethodPISA
3
E: Hypothetical UPF0244 protein yjjX
F: Hypothetical UPF0244 protein yjjX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2816
Polymers39,8972
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-73 kcal/mol
Surface area14250 Å2
MethodPISA
4
G: Hypothetical UPF0244 protein yjjX
H: Hypothetical UPF0244 protein yjjX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1855
Polymers39,8972
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-59 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.996, 129.336, 85.378
Angle α, β, γ (deg.)90.00, 90.227, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypothetical UPF0244 protein yjjX


Mass: 19948.566 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yjjX / Plasmid: pET21B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P39411
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.4 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Li sulfate, MPD, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 0.980312 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980312 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 69338 / Num. obs: 62056 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.075 / Rsym value: 0.058 / Net I/σ(I): 10.55
Reflection shellHighest resolution: 2.3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 10.5 / Rsym value: 0.058 / % possible all: 91.4

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 6226 -RANDOM
Rwork0.2 ---
all0.278 69338 --
obs0.278 62056 89.5 %-
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10260 0 75 682 11017
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection
Rfree0.255 6226
Rwork0.2 -
obs-62056

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