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- PDB-1v6h: The Trimeric Structure Of Divalent Cation Tolerance Protein CutA1... -

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Basic information

Entry
Database: PDB / ID: 1v6h
TitleThe Trimeric Structure Of Divalent Cation Tolerance Protein CutA1 From Thermus Thermophilus HB8
ComponentsDivalent Cation Tolerance Protein CutA1
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / CutA / Copper Tolerance / Trimer / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


response to metal ion / copper ion binding / cytoplasm
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
Divalent-cation tolerance protein CutA
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBagautdinov, B. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: The structures of the CutA1 proteins from Thermus thermophilus and Pyrococcus horikoshii: characterization of metal-binding sites and metal-induced assembly.
Authors: Bagautdinov, B.
History
DepositionNov 29, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 7, 2014Group: Database references
Revision 1.4May 14, 2014Group: Derived calculations
Revision 1.5Oct 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Divalent Cation Tolerance Protein CutA1
B: Divalent Cation Tolerance Protein CutA1
C: Divalent Cation Tolerance Protein CutA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0024
Polymers34,9063
Non-polymers961
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-48 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.753, 71.753, 100.399
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a trimer. The biological unit is identical to the asymmetric unit.

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Components

#1: Protein Divalent Cation Tolerance Protein CutA1


Mass: 11635.439 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: CutA / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIA8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.16 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: PEG 20K 16.5% w/w, HEPES 0.1M, 10% w/w of glycerol was added for cryoprotection, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 9, 2003 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 24112 / Num. obs: 23582 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.5
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 6.7 / Num. unique all: 2680 / % possible all: 90.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NZA

1nza


Resolution: 1.9→29.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1116 -RANDOM
Rwork0.188 ---
all-24102 --
obs-23009 95.4 %-
Displacement parametersBiso mean: 28.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å21.08 Å20 Å2
2--1.5 Å20 Å2
3----2.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 5 386 2848
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.293 103 -
Rwork0.238 --
obs-2680 90.4 %

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