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- PDB-1kr4: Structure Genomics, Protein TM1056, cutA -

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Basic information

Entry
Database: PDB / ID: 1kr4
TitleStructure Genomics, Protein TM1056, cutA
ComponentsProtein TM1056, cutA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / cutA / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsSavchenko, A. / Zhang, R. / Joachimiak, A. / Edwards, A. / Akarina, T. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2004
Title: X-ray crystal structure of CutA from Thermotoga maritima at 1.4 A resolution.
Authors: Savchenko, A. / Skarina, T. / Evdokimova, E. / Watson, J.D. / Laskowski, R. / Arrowsmith, C.H. / Edwards, A.M. / Joachimiak, A. / Zhang, R.G.
History
DepositionJan 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
Remark 999SEQUENCE The assignement of Ile94 was based on high resolution electron density maps

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein TM1056, cutA


Theoretical massNumber of molelcules
Total (without water)15,0221
Polymers15,0221
Non-polymers00
Water2,252125
1
A: Protein TM1056, cutA

A: Protein TM1056, cutA

A: Protein TM1056, cutA


Theoretical massNumber of molelcules
Total (without water)45,0653
Polymers45,0653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.237, 52.237, 33.846
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Protein TM1056, cutA


Mass: 15021.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria)
Plasmid details: Protein was expressed as fusion with N-terminal tag MGSSHHHHHHSSGRENLYFQGHM and C-terminal fusion of GS
Plasmid: modified peT15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X0E6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.77 Å3/Da / Density % sol: 30.7 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Details: Zhang, R.G., (2001) Structure, 9, 1095.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.5 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
31.75 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793,0.9791,0.95200
DetectorType: SBC-2 / Detector: CCD / Date: Nov 20, 2001 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97911
30.9521
ReflectionResolution: 1.4→50 Å / Num. all: 20453 / Num. obs: 19451 / % possible obs: 95.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 5.49 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.25
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.875 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.66 / Num. unique all: 1829 / % possible all: 87.7
Reflection
*PLUS
Lowest resolution: 50 Å

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Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→20.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 485887.96 / Data cutoff high rms absF: 485887.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1571 5.2 %RANDOM
Rwork0.218 ---
obs0.218 19451 74.1 %-
all-20453 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9317 Å2 / ksol: 0.389531 e/Å3
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.1 Å
Refinement stepCycle: LAST / Resolution: 1.4→20.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 0 125 1055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.66
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.232 145 5.5 %
Rwork0.22 2482 -
obs--38.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 40 Å / Num. reflection obs: 19651 / σ(F): 0 / Rfactor Rfree: 0.2408 / Rfactor Rwork: 0.2094
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

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