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- PDB-3ahp: Crystal structure of stable protein, CutA1, from a psychrotrophic... -

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Basic information

Entry
Database: PDB / ID: 3ahp
TitleCrystal structure of stable protein, CutA1, from a psychrotrophic bacterium Shewanella sp. SIB1
ComponentsCutA1
KeywordsELECTRON TRANSPORT / CutA1 / thermostable protein
Function / homology
Function and homology information


response to metal ion / copper ion binding
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 speciesShewanella (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTanaka, S. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: J.SYNCHROTRON RADIAT. / Year: 2011
Title: Crystal structure of stable protein CutA1 from psychrotrophic bacterium Shewanella sp. SIB1
Authors: Sato, A. / Yokotani, S. / Tadokoro, T. / Tanaka, S.I. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionApr 26, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2011Provider: 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
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: CutA1
B: CutA1
C: CutA1
D: CutA1
E: CutA1
F: CutA1


Theoretical massNumber of molelcules
Total (without water)72,5946
Polymers72,5946
Non-polymers00
Water1,13563
1
A: CutA1
B: CutA1
C: CutA1


Theoretical massNumber of molelcules
Total (without water)36,2973
Polymers36,2973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-46 kcal/mol
Surface area13530 Å2
MethodPISA
2
D: CutA1
E: CutA1
F: CutA1


Theoretical massNumber of molelcules
Total (without water)36,2973
Polymers36,2973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-49 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.671, 134.671, 128.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
CutA1


Mass: 12098.943 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella (bacteria) / Strain: SIB1 / Plasmid: pET-25b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E7FH74*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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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: 4.01 Å3/Da / Density % sol: 69.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.0M Na/K-phosphate, 100mM acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2009 / Details: mirrors
RadiationMonochromator: Rh mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 33076 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Rmerge(I) obs: 0.175 / Rsym value: 0.143 / Net I/σ(I): 18.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 3.03 / Num. unique all: 1627 / Rsym value: 0.689 / % possible all: 100

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Processing

Software
NameVersionClassification
BL38B1BSS softwaredata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAQ

1naq


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.355 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.381 / ESU R Free: 0.288
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26059 1673 5.1 %RANDOM
Rwork0.20517 ---
obs0.20798 31314 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.397 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 0 63 5067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225128
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.967020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.3125634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.63526.168214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.41315826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.669156
X-RAY DIFFRACTIONr_chiral_restr0.140.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0223876
X-RAY DIFFRACTIONr_mcbond_it1.2861.53224
X-RAY DIFFRACTIONr_mcangle_it2.44625288
X-RAY DIFFRACTIONr_scbond_it3.72731904
X-RAY DIFFRACTIONr_scangle_it5.7484.51732
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 131 -
Rwork0.258 2236 -
obs--100 %

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