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- PDB-1j2v: Crystal Structure of CutA1 from Pyrococcus Horikoshii -

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Basic information

Entry
Database: PDB / ID: 1j2v
TitleCrystal Structure of CutA1 from Pyrococcus Horikoshii
Components102AA long hypothetical periplasmic divalent cation tolerance protein CUTA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA + BETA
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 speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsTanaka, Y. / Sakai, N. / Yasutake, Y. / Yao, M. / Tsumoto, K. / Kumagai, I. / Tanaka, I.
CitationJournal: Febs Lett. / Year: 2004
Title: Structural implications for heavy metal-induced reversible assembly and aggregation of a protein: the case of Pyrococcus horikoshii CutA.
Authors: Tanaka, Y. / Tsumoto, K. / Nakanishi, T. / Yasutake, Y. / Sakai, N. / Yao, M. / Tanaka, I. / Kumagai, I.
History
DepositionJan 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 102AA long hypothetical periplasmic divalent cation tolerance protein CUTA


Theoretical massNumber of molelcules
Total (without water)12,4791
Polymers12,4791
Non-polymers00
Water64936
1
A: 102AA long hypothetical periplasmic divalent cation tolerance protein CUTA

A: 102AA long hypothetical periplasmic divalent cation tolerance protein CUTA

A: 102AA long hypothetical periplasmic divalent cation tolerance protein CUTA


Theoretical massNumber of molelcules
Total (without water)37,4373
Polymers37,4373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6380 Å2
ΔGint-44 kcal/mol
Surface area13070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.569, 52.569, 58.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: (1-y, 1+x-y, z) and (y-x, 1-x, z).

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Components

#1: Protein 102AA long hypothetical periplasmic divalent cation tolerance protein CUTA / CutA1 / CutA1 homology protein PH0992


Mass: 12479.017 Da / Num. of mol.: 1 / Mutation: L26(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0992 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O58720
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.87 Å3/Da / Density % sol: 33.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Ammonium Sulfate , Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9000, 0.9792, 0.9794
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 11, 2002
RadiationMonochromator: MONOCHROMATOR + MIRROR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97921
30.97941
ReflectionResolution: 2→20 Å / Num. all: 6186 / Num. obs: 6154 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 11.2 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.058 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 6.9 / Num. unique all: 901 / Rsym value: 0.112 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
DMmodel building
CNS1refinement
HKL-2000data reduction
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2→10 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Model refinement was performed with a twinning operator of (h -h-k -l), and a twinning fraction of 0.16.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 589 9.5 %RANDOM
Rwork0.239 ---
all-6122 --
obs-6114 98.9 %-
Displacement parametersBiso mean: 23.657 Å2
Baniso -1Baniso -2Baniso -3
1--0.846 Å2-1.067 Å20 Å2
2---0.846 Å20 Å2
3---1.692 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 0 36 909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013115
X-RAY DIFFRACTIONc_angle_deg1.90039
X-RAY DIFFRACTIONc_dihedral_angle_d23.7386
X-RAY DIFFRACTIONc_improper_angle_d1.76773
X-RAY DIFFRACTIONc_mcbond_it1.26
X-RAY DIFFRACTIONc_mcangle_it1.73
X-RAY DIFFRACTIONc_scbond_it2.05
X-RAY DIFFRACTIONc_scangle_it2.63
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.379 64 -
Rwork0.292 607 -
obs-607 99 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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