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- PDB-3ah6: Remarkable improvement of the heat stability of CutA1 from E.coli... -

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Basic information

Entry
Database: PDB / ID: 3ah6
TitleRemarkable improvement of the heat stability of CutA1 from E.coli by rational protein designing
ComponentsDivalent-cation tolerance protein cutA
KeywordsUNKNOWN FUNCTION / CutA1 / copper tolerance / stability / point mutation
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMatsuura, Y. / Tanaka, T. / Bagautdinov, B. / Kunishima, N. / Yutani, K.
CitationJournal: J.Biochem. / Year: 2010
Title: Remarkable improvement in the heat stability of CutA1 from Escherichia coli by rational protein design
Authors: Matsuura, Y. / Ota, M. / Tanaka, T. / Takehira, M. / Ogasahara, K. / Bagautdinov, B. / Kunishima, N. / Yutani, K.
History
DepositionApr 15, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)74,1246
Polymers74,1246
Non-polymers00
Water3,927218
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)37,0623
Polymers37,0623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-45 kcal/mol
Surface area12360 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)37,0623
Polymers37,0623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-45 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.239, 96.872, 106.352
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: 12354.078 Da / Num. of mol.: 6 / Mutation: S11V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cutA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P69488
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M HEPS (pH 7.5) including 1.4 M tri-sodium citrate dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 20K, temperature 293K

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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: Dec 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 25891 / Num. obs: 25891 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.52 / Num. unique all: 2540 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AA8

3aa8


Resolution: 2.4→38.23 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2611040.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1287 5 %RANDOM
Rwork0.202 ---
obs0.202 25793 100 %-
all-25891 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0562 Å2 / ksol: 0.433616 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.4→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 0 218 5004
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it2.712
X-RAY DIFFRACTIONc_scangle_it3.782.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 201 4.8 %
Rwork0.229 4007 -
obs-2540 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3dna-rna_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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