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- PDB-2nuh: Crystal structure of CutA from the phytopathgen bacterium Xylella... -

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Basic information

Entry
Database: PDB / ID: 2nuh
TitleCrystal structure of CutA from the phytopathgen bacterium Xylella fastidiosa
ComponentsPeriplasmic divalent cation tolerance protein
KeywordsUNKNOWN FUNCTION / CutA
Function / homology
Function and homology information


response to metal ion / copper ion binding
Similarity search - Function
Divalent ion tolerance protein, CutA / CutA1 divalent ion tolerance protein / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Periplasmic divalent cation tolerance protein
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsMedrano, F.J. / Benedetti, C.E.
CitationJournal: To be published
Title: Crystal structure of CutA from the phytopathgen bacterium Xylella fastidiosa
Authors: Medrano, F.J. / Benedetti, C.E.
History
DepositionNov 9, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Periplasmic divalent cation tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4463
Polymers13,3081
Non-polymers1382
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Periplasmic divalent cation tolerance protein
hetero molecules

A: Periplasmic divalent cation tolerance protein
hetero molecules

A: Periplasmic divalent cation tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3399
Polymers39,9253
Non-polymers4156
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7790 Å2
ΔGint-37 kcal/mol
Surface area12330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.590, 70.590, 35.502
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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Components

#1: Protein Periplasmic divalent cation tolerance protein


Mass: 13308.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Strain: 9a5c / Gene: cutA / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9PFN8
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Mes Buffer, 1.6M Ammonium sulfate, 10% Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 1.39→61.08 Å / Num. obs: 19947 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.2
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3.2 / % possible all: 82.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHF

1vhf


Resolution: 1.39→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.975 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1012 5.1 %RANDOM
Rwork0.196 ---
obs0.197 19713 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.443 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.13 Å20 Å2
2---0.25 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.39→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 10 103 925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022844
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9761154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.235103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43524.41234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59315139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.346155
X-RAY DIFFRACTIONr_chiral_restr0.1120.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02622
X-RAY DIFFRACTIONr_nbd_refined0.2210.2440
X-RAY DIFFRACTIONr_nbtor_refined0.3280.2611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.221
X-RAY DIFFRACTIONr_mcbond_it0.8331.5532
X-RAY DIFFRACTIONr_mcangle_it1.442862
X-RAY DIFFRACTIONr_scbond_it2.1623348
X-RAY DIFFRACTIONr_scangle_it3.1744.5292
LS refinement shellResolution: 1.394→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 62 -
Rwork0.42 1130 -
obs-1192 79.68 %

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