[English] 日本語
Yorodumi
- PDB-2g3w: The Crystal Structure of YaeQ Protein from Xanthomonas axonopodis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g3w
TitleThe Crystal Structure of YaeQ Protein from Xanthomonas axonopodis pv. citri
Componentshypothetical protein XAC2396
KeywordsUNKNOWN FUNCTION / YaeQ protein / Xanthomonas axonopodis pv citri
Function / homology
Function and homology information


Restriction endonuclease-like alpha-beta roll fold / Restriction endonuclease-like alpha-beta roll domain / YaeQ / YaeQ superfamily / YaeQ protein / YaeQ / Restriction endonuclease type II-like / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsFarah, C.S. / Guzzo, C.R. / Barbosa, J.A.R.G. / Nagem, R.A.P.
Citation
Journal: Proteins / Year: 2007
Title: Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif
Authors: Guzzo, C.R. / Nagem, R.A.P. / Barbosa, J.A.R.G. / Farah, C.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Expression, purification, crystallization and preliminary X-ray analysis of YaeQ (XAC2396) from Xanthomonas axonopodis pv. citri
Authors: Guzzo, C.R. / Nagem, R.A.P. / Galvao-Botton, L.M.P. / Guimaraes, B.G. / Medrano, F.J. / Barbosa, J.A.R.G. / Farah, C.S.
History
DepositionFeb 21, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: hypothetical protein XAC2396
B: hypothetical protein XAC2396
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0974
Polymers41,9792
Non-polymers1182
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.766, 91.969, 48.031
Angle α, β, γ (deg.)90.00, 108.35, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein hypothetical protein XAC2396 / YaeQ protein


Mass: 20989.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: str. 306 / Gene: XAC2396 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8PJY1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris pH 9, 0.2M ammonium acetate, 32% PEG 4000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97952, 0.97962, 1.00000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 29, 2004
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979521
20.979621
311
ReflectionResolution: 1.9→40 Å / Num. all: 24538 / Num. obs: 24538 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.07 / Net I/σ(I): 33.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 2210 / Rsym value: 0.425 / % possible all: 86.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.694 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1244 5.1 %RANDOM
Rwork0.192 ---
all0.194 24508 --
obs0.194 24508 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.299 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20.33 Å2
2--2.46 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 8 218 3067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222927
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9493964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9235362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79123160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68215501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3621539
X-RAY DIFFRACTIONr_chiral_restr0.1060.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022299
X-RAY DIFFRACTIONr_nbd_refined0.2090.21237
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21902
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.222
X-RAY DIFFRACTIONr_mcbond_it0.911.51844
X-RAY DIFFRACTIONr_mcangle_it1.36422849
X-RAY DIFFRACTIONr_scbond_it2.32831244
X-RAY DIFFRACTIONr_scangle_it3.3894.51111
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 86 -
Rwork0.253 1530 -
obs-1616 85.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.628-1.15420.67293.0873-0.59121.832-0.16-0.02950.48720.11520.1657-0.1642-0.2361-0.0106-0.0057-0.08470.021-0.0205-0.1799-0.0393-0.06329.657929.301723.4734
21.45540.0437-0.07290.94330.91186.3436-0.0786-0.2741-0.16720.08740.0193-0.00840.16480.40430.0593-0.12640.037-0.0005-0.0526-0.0326-0.098143.378810.336946.3478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1824 - 182
2X-RAY DIFFRACTION2BB4 - 1804 - 180

+
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