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- PDB-4y6i: Crystal structure of E.coli CutA1 E61V/C16A/C39A/C79A mutation -

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Basic information

Entry
Database: PDB / ID: 4y6i
TitleCrystal structure of E.coli CutA1 E61V/C16A/C39A/C79A mutation
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 / molecular replacement / Resolution: 1.7 Å
Model detailscysteine free mutant
AuthorsTanaka, T. / Matsuura, Y. / Yutani, K.
CitationJournal: To Be Published
Title: Crystal structure of E.coli CutA1 E61V/C16A/C39A/C79A mutation
Authors: Tanaka, T. / Matsuura, Y. / Yutani, K.
History
DepositionFeb 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 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

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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)70,3646
Polymers70,3646
Non-polymers00
Water10,124562
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)35,1823
Polymers35,1823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-43 kcal/mol
Surface area12710 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)35,1823
Polymers35,1823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-43 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.720, 127.720, 38.201
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 11727.292 Da / Num. of mol.: 6 / Fragment: UNP residues 5-112 / Mutation: C16A,C39A,E61V,C79A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: cutA, cutA1, cycY, b4137, 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.: 562 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES-Na pH7.5 , 1.4M tri-Sodium Citrate dihydrate

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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 / Date: May 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→35.18 Å / Num. obs: 64900 / % possible obs: 99.64 % / Redundancy: 7.5 % / Net I/σ(I): 10.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.73 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 3464 5.1 %RANDOM
Rwork0.1706 ---
obs0.172 64900 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 102.59 Å2 / Biso mean: 15.427 Å2 / Biso min: 4.75 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.7→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4820 0 0 562 5382
Biso mean---29.59 -
Num. residues----629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225176
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9797179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5065713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.76425.806186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77815855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.525156
X-RAY DIFFRACTIONr_chiral_restr0.0730.2907
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213830
X-RAY DIFFRACTIONr_mcbond_it0.6621.53313
X-RAY DIFFRACTIONr_mcangle_it1.30625404
X-RAY DIFFRACTIONr_scbond_it2.07631863
X-RAY DIFFRACTIONr_scangle_it3.6284.51737
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 252 -
Rwork0.189 4733 -
all-4985 -
obs--99.13 %

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