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- PDB-3x3u: Crystal structure of wild-type of E. coli CutA1 -

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Basic information

Entry
Database: PDB / ID: 3x3u
TitleCrystal structure of wild-type of E. coli CutA1
ComponentsDivalent-cation tolerance protein CutA
KeywordsMETAL BINDING PROTEIN / CutA1
Function / homology
Function and homology information


response to copper ion / copper ion binding / protein-containing complex / metal ion binding / cytoplasm
Similarity search - Function
Divalent cation tolerance protein CutA, Enterobacteria / 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 speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsTanaka, T. / Matsuura, Y. / Yutani, K.
CitationJournal: To be Published
Title: Crystal structure of wild-type of E. coli CutA1
Authors: Tanaka, T. / Matsuura, Y. / Yutani, K.
History
DepositionFeb 12, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Divalent-cation tolerance protein CutA
B: Divalent-cation tolerance protein CutA
C: Divalent-cation tolerance protein CutA
D: Divalent-cation tolerance protein CutA
E: Divalent-cation tolerance protein CutA
F: Divalent-cation tolerance protein CutA


Theoretical massNumber of molelcules
Total (without water)74,0526
Polymers74,0526
Non-polymers00
Water5,350297
1
A: Divalent-cation tolerance protein CutA
B: Divalent-cation tolerance protein CutA
C: Divalent-cation tolerance protein CutA


Theoretical massNumber of molelcules
Total (without water)37,0263
Polymers37,0263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-48 kcal/mol
Surface area12410 Å2
MethodPISA
2
D: Divalent-cation tolerance protein CutA
E: Divalent-cation tolerance protein CutA
F: Divalent-cation tolerance protein CutA


Theoretical massNumber of molelcules
Total (without water)37,0263
Polymers37,0263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-46 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.419, 96.868, 106.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Divalent-cation tolerance protein CutA / C-type cytochrome biogenesis protein CycY


Mass: 12342.025 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: b4137, cutA, cutA1, cycY, JW4097 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: P69488
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1M HEPES-Na pH7.5, 1.4M tri-Sodium Citrate dihydrate, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→38.27 Å / Num. all: 36800 / Num. obs: 36800 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→38.27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1948 5 %RANDOM
Rwork0.20832 ---
obs0.20845 36800 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.723 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.11 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.09→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 0 297 5097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194906
X-RAY DIFFRACTIONr_bond_other_d00.024680
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9776729
X-RAY DIFFRACTIONr_angle_other_deg3.474310821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.7525618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.99426.216185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89215802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.567152
X-RAY DIFFRACTIONr_chiral_restr0.0860.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215452
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02974
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.089→2.143 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 124 -
Rwork0.249 2480 -
obs--92.77 %

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