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- PDB-5ub7: XAC2383 from Xanthomonas citri bound to ATP -

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Basic information

Entry
Database: PDB / ID: 5ub7
TitleXAC2383 from Xanthomonas citri bound to ATP
ComponentsPhosphate-binding protein
KeywordsMETAL BINDING PROTEIN / Periplasmic binding protein Periplasmic sensor ATP Phosphonate-bd
Function / homologyABC transporter, phosphonate, periplasmic substrate-binding protein / ADENOSINE-5'-TRIPHOSPHATE / Phosphate-binding protein
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsTeixeira, R.D. / Guzzo, C.R. / Farah, C.S.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A bipartite periplasmic receptor-diguanylate cyclase pair (XAC2383-XAC2382) in the bacteriumXanthomonas citri.
Authors: Teixeira, R.D. / Guzzo, C.R. / Arevalo, S.J. / Andrade, M.O. / Abrahao, J. / de Souza, R.F. / Farah, C.S.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Phosphate-binding protein
B: Phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7494
Polymers62,7342
Non-polymers1,0142
Water2,180121
1
A: Phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8742
Polymers31,3671
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8742
Polymers31,3671
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.366, 67.115, 113.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphate-binding protein


Mass: 31367.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: XAC2383 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PJZ4
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 39.06 %
Crystal growTemperature: 298 K / Method: batch mode / Details: 20 mM Tris pH 8.0, 300 mM NaCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.48→43.38 Å / Num. obs: 29224 / % possible obs: 99.89 % / Redundancy: 6.8 % / Net I/σ(I): 5.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→43.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.345 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.214 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25497 1567 5.1 %RANDOM
Rwork0.19161 ---
obs0.19478 29224 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0 Å2
2---0.17 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.48→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4345 0 44 121 4510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194525
X-RAY DIFFRACTIONr_bond_other_d0.0020.024414
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.9936140
X-RAY DIFFRACTIONr_angle_other_deg1.007310090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3545556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04121.078204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09815776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9411565
X-RAY DIFFRACTIONr_chiral_restr0.0860.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215037
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021078
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4423.8732221
X-RAY DIFFRACTIONr_mcbond_other2.4333.8712220
X-RAY DIFFRACTIONr_mcangle_it3.6085.8022775
X-RAY DIFFRACTIONr_mcangle_other3.6095.8042776
X-RAY DIFFRACTIONr_scbond_it3.274.4182304
X-RAY DIFFRACTIONr_scbond_other3.2694.4192305
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2216.4843365
X-RAY DIFFRACTIONr_long_range_B_refined7.13431.9235030
X-RAY DIFFRACTIONr_long_range_B_other7.1331.9065011
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded

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