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- PDB-5b7w: Crystal structure of the YajQ-family protein XC_3703 from Xanthom... -

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Basic information

Entry
Database: PDB / ID: 5b7w
TitleCrystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv.campestris
ComponentsUPF0234 protein XC_3703
KeywordsUNKNOWN FUNCTION / Receptor
Function / homology
Function and homology information


nucleotide binding / cytosol
Similarity search - Function
YajQ-like, domain 2 / Protein of unknown function DUF520 / UPF0234, N-terminal / YajQ-like superfamily / Nucleotide-binding protein YajQ-like / Alpha-Beta Plaits - #860 / UPF0234-like, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0234 protein XC_3703
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.08 Å
AuthorsZhao, Z. / Wu, Z.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris
Authors: Zhao, Z. / Wu, Z. / Zhang, J.
History
DepositionJun 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0234 protein XC_3703
B: UPF0234 protein XC_3703


Theoretical massNumber of molelcules
Total (without water)38,6042
Polymers38,6042
Non-polymers00
Water2,090116
1
A: UPF0234 protein XC_3703


Theoretical massNumber of molelcules
Total (without water)19,3021
Polymers19,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UPF0234 protein XC_3703


Theoretical massNumber of molelcules
Total (without water)19,3021
Polymers19,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.510, 65.470, 52.284
Angle α, β, γ (deg.)90.00, 92.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UPF0234 protein XC_3703


Mass: 19301.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain 8004) (bacteria)
Strain: 8004 / Gene: XC_3703 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4UQD0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris pH5.5, 25% w/v Polyethylene glycol 3500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.08→40.83 Å / Num. obs: 20472 / % possible obs: 97.4 % / Redundancy: 3.6 % / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2411: ???)refinement
HKL-2000data processing
RefinementResolution: 2.08→35.821 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.02
RfactorNum. reflection% reflection
Rfree0.284 1973 9.65 %
Rwork0.2438 --
obs0.2476 20447 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.08→35.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 0 116 2674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032582
X-RAY DIFFRACTIONf_angle_d0.5823458
X-RAY DIFFRACTIONf_dihedral_angle_d21.6611012
X-RAY DIFFRACTIONf_chiral_restr0.04392
X-RAY DIFFRACTIONf_plane_restr0.003460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.079-2.1310.33491040.30251000X-RAY DIFFRACTION74
2.131-2.18860.35511520.30521334X-RAY DIFFRACTION99
2.1886-2.2530.31611250.30521364X-RAY DIFFRACTION99
2.253-2.32570.33641430.29351312X-RAY DIFFRACTION99
2.3257-2.40880.34221460.27931324X-RAY DIFFRACTION99
2.4088-2.50530.30541450.27591357X-RAY DIFFRACTION99
2.5053-2.61930.31821430.2721358X-RAY DIFFRACTION99
2.6193-2.75730.34861350.26271339X-RAY DIFFRACTION99
2.7573-2.930.30731520.26361330X-RAY DIFFRACTION99
2.93-3.15610.29881350.27621344X-RAY DIFFRACTION99
3.1561-3.47340.2691530.24711369X-RAY DIFFRACTION100
3.4734-3.97550.27051460.21461350X-RAY DIFFRACTION99
3.9755-5.00650.24661530.19371312X-RAY DIFFRACTION98
5.0065-35.82630.25981410.23791381X-RAY DIFFRACTION98

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