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- PDB-2zom: Crystal structure of CutA1 from Oryza sativa -

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Basic information

Entry
Database: PDB / ID: 2zom
TitleCrystal structure of CutA1 from Oryza sativa
ComponentsProtein CutA, chloroplast, putative, expressed
KeywordsUNKNOWN FUNCTION / Trimeric structure / Protein stability
Function / homology
Function and homology information


response to metal ion / protein homotrimerization / chloroplast / 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
Protein CutA 1, chloroplastic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsKezuka, Y. / Bagautdinov, B. / Katoh, S. / Ohtake, Y. / Yutani, K. / Nonaka, T. / Katoh, E.
Citation
Journal: To be Published
Title: Crystal structure of CutA1 from Oryza sativa
Authors: Kezuka, Y. / Bagautdinov, B. / Katoh, S. / Ohtake, Y. / Yutani, K. / Nonaka, T. / Katoh, E.
#1: Journal: Biochemistry / Year: 2008
Title: Thermodynamic basis for the stabilities of three CutA1s from Pyrococcus horikoshii,Thermus thermophilus, and Oryza sativa, with unusually high denaturation temperatures
Authors: Sawano, M. / Yamamoto, H. / Ogasahara, K. / Kidokoro, S. / Katoh, S. / Ohnuma, T. / Katoh, E. / Yokoyama, S. / Yutani, K.
History
DepositionMay 23, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein CutA, chloroplast, putative, expressed
B: Protein CutA, chloroplast, putative, expressed
C: Protein CutA, chloroplast, putative, expressed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1799
Polymers37,6153
Non-polymers5646
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-93 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.214, 127.214, 121.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Protein CutA, chloroplast, putative, expressed / CutA1


Mass: 12538.320 Da / Num. of mol.: 3 / Fragment: UNP residues 65-177
Source method: isolated from a genetically manipulated source
Details: Tsunoda et al. (2005). Protein Expression Purif. 42, 268-277.
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Plasmid: pDEST-his vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q109R6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.28 Å3/Da / Density % sol: 62.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.8M Ammonium sulfate, 0.09M tri-Sodium citrate dihydrate pH5.6, 0.18M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 4, 2006 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.02→63.628 Å / Num. all: 10138 / Num. obs: 10138 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 76.463 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 8
Reflection shellResolution: 3.02→3.1 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.1 / Num. unique all: 742 / Rsym value: 0.231 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZFH

2zfh


Resolution: 3.02→63.61 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.881 / SU B: 15.553 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26674 490 4.8 %RANDOM
Rwork0.17826 ---
all0.18237 ---
obs0.18237 9635 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.314 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 3.02→63.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 33 3 2570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192609
X-RAY DIFFRACTIONr_bond_other_d0.0010.022446
X-RAY DIFFRACTIONr_angle_refined_deg2.2041.9843552
X-RAY DIFFRACTIONr_angle_other_deg1.02335713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7285321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.69925.40898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.56615464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.239159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02447
X-RAY DIFFRACTIONr_nbd_refined0.230.2612
X-RAY DIFFRACTIONr_nbd_other0.1910.22605
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21300
X-RAY DIFFRACTIONr_nbtor_other0.0990.21660
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.25
X-RAY DIFFRACTIONr_mcbond_it1.0971.52031
X-RAY DIFFRACTIONr_mcbond_other0.1621.5657
X-RAY DIFFRACTIONr_mcangle_it1.3822638
X-RAY DIFFRACTIONr_scbond_it1.95631155
X-RAY DIFFRACTIONr_scangle_it2.8744.5914
LS refinement shellResolution: 3.02→3.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 35 -
Rwork0.253 703 -
obs--100 %

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