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- PDB-1osc: Crystal structure of rat CUTA1 at 2.15 A resolution -

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Basic information

Entry
Database: PDB / ID: 1osc
TitleCrystal structure of rat CUTA1 at 2.15 A resolution
Componentssimilar to divalent cation tolerant protein CUTA
KeywordsUNKNOWN FUNCTION / CUTA / copper resistance / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


response to metal ion / intracellular protein localization / copper ion binding / enzyme binding / mitochondrion / membrane
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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsArnesano, F. / Banci, L. / Benvenuti, M. / Bertini, I. / Calderone, V. / Mangani, S. / Viezzoli, M.S. / Structural Proteomics in Europe (SPINE)
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: The Evolutionarily Conserved Trimeric Structure of CutA1 Proteins Suggests a Role in Signal Transduction
Authors: Arnesano, F. / Banci, L. / Benvenuti, M. / Bertini, I. / Calderone, V. / Mangani, S. / Viezzoli, M.S.
#1: Journal: To be Published
Title: Structure of protein TM1056, CUTA
Authors: SAVCHENKO, A. / ZHANG, R. / JOACHIMIAK, A. / EDWARDS, A. / AKARINA, T.
#2: Journal: To be Published
Title: The trimeric structure of CutA1 proteins of bacteria and mammals is reminiscent of the architecture of signal transduction proteins.
Authors: Calderone, V. / Mangani, S. / Benvenuti, M. / Viezzoli, M.S. / Banci, L. / Bertini, I.
History
DepositionMar 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: similar to divalent cation tolerant protein CUTA
B: similar to divalent cation tolerant protein CUTA
C: similar to divalent cation tolerant protein CUTA
D: similar to divalent cation tolerant protein CUTA
E: similar to divalent cation tolerant protein CUTA
F: similar to divalent cation tolerant protein CUTA


Theoretical massNumber of molelcules
Total (without water)81,6036
Polymers81,6036
Non-polymers00
Water7,296405
1
A: similar to divalent cation tolerant protein CUTA
B: similar to divalent cation tolerant protein CUTA
C: similar to divalent cation tolerant protein CUTA


Theoretical massNumber of molelcules
Total (without water)40,8023
Polymers40,8023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-49 kcal/mol
Surface area13840 Å2
MethodPISA
2
D: similar to divalent cation tolerant protein CUTA
E: similar to divalent cation tolerant protein CUTA
F: similar to divalent cation tolerant protein CUTA


Theoretical massNumber of molelcules
Total (without water)40,8023
Polymers40,8023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-48 kcal/mol
Surface area13950 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15730 Å2
ΔGint-114 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.387, 88.287, 125.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12D
22E
32F

NCS domain segments:

Component-ID: 1 / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA6 - 11018 - 122
21TYRTYRBB6 - 11018 - 122
31TYRTYRCC6 - 11018 - 122
12SERSERDD4 - 11016 - 122
22GLYGLYEE3 - 11015 - 122
32GLYGLYFF3 - 11015 - 122

NCS ensembles :
ID
1
2
DetailsThe biological functional unit is a trimer; the asymetric unit is made of two trimers

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Components

#1: Protein
similar to divalent cation tolerant protein CUTA


Mass: 13600.518 Da / Num. of mol.: 6 / Fragment: residue 44-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CutA, CutA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MGD0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.53 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Na Acetate, CuSO4, CaCl2, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.1 Msodium acetate1reservoirpH4.6
330 %MPD1reservoir
45 mM1reservoirCuSO4
520 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9322 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2003 / Details: Diamond (111), Ge(220)
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9322 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 43312 / Num. obs: 43312 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 5.3
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.47 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 46060 / % possible obs: 100 % / Num. measured all: 300781
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 6646 / Num. measured obs: 32115 / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.1.80refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NAQ

1naq


Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.271 / SU ML: 0.161 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26001 3615 8.3 %RANDOM
Rwork0.18946 ---
obs0.1954 39701 100 %-
all-41116 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.19 Å20 Å20 Å2
2---1.98 Å20 Å2
3----4.2 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5090 0 0 405 5495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0225240
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6851.9547160
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0045652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.230.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023886
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2780.22629
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2421
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3590.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8321.53312
X-RAY DIFFRACTIONr_mcangle_it3.29425435
X-RAY DIFFRACTIONr_scbond_it4.86331928
X-RAY DIFFRACTIONr_scangle_it7.7744.51725
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A424medium positional0.240.5
12B424medium positional0.170.5
13C424medium positional0.240.5
21D424medium positional0.210.5
22E424medium positional0.280.5
23F424medium positional0.310.5
11A402loose positional0.715
12B402loose positional0.785
13C402loose positional0.85
21D402loose positional0.815
22E402loose positional0.915
23F402loose positional15
11A424medium thermal1.832
12B424medium thermal2.412
13C424medium thermal2.042
21D424medium thermal2.852
22E424medium thermal2.32
23F424medium thermal2.252
11A402loose thermal4.0910
12B402loose thermal3.6410
13C402loose thermal3.0910
21D402loose thermal4.3610
22E402loose thermal3.6110
23F402loose thermal4.0110
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 273
Rwork0.292 2871
Software
*PLUS
Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.03
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.6

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