[English] 日本語
Yorodumi
- PDB-2zom: Crystal structure of CutA1 from Oryza sativa -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more