[English] 日本語
Yorodumi
- PDB-2qik: Crystal structure of YkqA from Bacillus subtilis. Northeast Struc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qik
TitleCrystal structure of YkqA from Bacillus subtilis. Northeast Structural Genomics Target SR631
ComponentsUPF0131 protein ykqA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YKQA / NESG / SR631 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


gamma-glutamylaminecyclotransferase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cytosol
Similarity search - Function
AIG2-like family / Gamma-glutamylaminecyclotransferase / Gamma-glutamylcyclotransferase, AIG2-like domain / Gamma-glutamyl cyclotransferase, AIG2-like / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / Gamma-glutamyl cyclotransferase-like / Gamma-glutamyl cyclotransferase-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Putative gamma-glutamylcyclotransferase YkqA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsBenach, J. / Chen, Y. / Forouhar, F. / Seetharaman, J. / Baran, M.C. / Cunningham, K. / Ma, L.-C. / Owens, L. / Chen, C.X. / Rong, X. ...Benach, J. / Chen, Y. / Forouhar, F. / Seetharaman, J. / Baran, M.C. / Cunningham, K. / Ma, L.-C. / Owens, L. / Chen, C.X. / Rong, X. / Janjua, H. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of YkqA from Bacillus subtilis.
Authors: Benach, J. / Chen, Y. / Forouhar, F. / Seetharaman, J. / Baran, M.C. / Cunningham, K. / Ma, L.-C. / Owens, L. / Chen, C.X. / Rong, X. / Janjua, H. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJul 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Oct 16, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: UPF0131 protein ykqA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2482
Polymers33,0551
Non-polymers1921
Water8,035446
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.577, 62.131, 55.527
Angle α, β, γ (deg.)90.000, 101.690, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe AU contains the biological assembly

-
Components

#1: Protein UPF0131 protein ykqA


Mass: 33055.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ykqA, ylxU, yzaB, BSU14500 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P39759
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 1.9125 Å3/Da / Density % sol: 35.68 %
Crystal growTemperature: 277 K / Method: microbatch under oil
Details: 0.1 M NaCl, 0.1 Na Citrate, 60% PEG 400, MICROBATCH UNDER OIL, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 31, 2007 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 18.8 / Number: 414093 / Rmerge(I) obs: 0.041 / Χ2: 1.13 / D res high: 1.35 Å / D res low: 50 Å / Num. obs: 109890 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.915090.110.0281.0383.6
2.312.9110010.0331.1383.9
2.022.3110010.0381.1483.9
1.832.0210010.0451.1263.8
1.71.8310010.0571.1083.8
1.61.710010.0731.1933.8
1.521.610010.0881.1423.8
1.451.5299.910.1141.1563.7
1.41.4599.810.1431.1043.7
1.351.499.710.1791.0953.6
ReflectionResolution: 1.35→50 Å / Num. obs: 55141 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.041 / Χ2: 1.126 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.35-1.43.60.179110831.09599.7
1.4-1.453.70.143110521.10499.8
1.45-1.523.70.114111261.15699.9
1.52-1.63.80.088111471.142100
1.6-1.73.80.073110701.193100
1.7-1.833.80.057111021.108100
1.83-2.023.80.045110861.126100
2.02-2.313.90.038111151.148100
2.31-2.913.90.033110901.138100
2.91-503.60.028100191.03890.1

-
Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.91 / FOM acentric: 0.91 / FOM centric: 0.83 / Reflection: 23209 / Reflection acentric: 22314 / Reflection centric: 895
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.1-24.9070.960.960.9486177883
3.2-5.10.980.980.9729262765161
2.6-3.20.950.950.8939873820167
2.3-2.60.930.930.8239873841146
1.9-2.30.890.90.7770856867218
1.8-1.90.820.830.5943634243120

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.35→19.35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.436 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2801 5.1 %RANDOM
Rwork0.131 ---
obs0.133 55139 97.83 %-
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: 12.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.17 Å2
2---0.22 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 13 446 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222301
X-RAY DIFFRACTIONr_bond_other_d0.0020.022044
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.953116
X-RAY DIFFRACTIONr_angle_other_deg0.97334776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3765286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39923.596114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15815406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3891514
X-RAY DIFFRACTIONr_chiral_restr0.1450.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_nbd_refined0.2290.2479
X-RAY DIFFRACTIONr_nbd_other0.210.22070
X-RAY DIFFRACTIONr_nbtor_refined0.1970.21126
X-RAY DIFFRACTIONr_nbtor_other0.090.21307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.229
X-RAY DIFFRACTIONr_mcbond_it3.041.51602
X-RAY DIFFRACTIONr_mcbond_other0.9681.5562
X-RAY DIFFRACTIONr_mcangle_it3.50622196
X-RAY DIFFRACTIONr_scbond_it5.17331062
X-RAY DIFFRACTIONr_scangle_it6.4054.5910
X-RAY DIFFRACTIONr_rigid_bond_restr2.51535071
X-RAY DIFFRACTIONr_sphericity_free16.7235446
X-RAY DIFFRACTIONr_sphericity_bonded5.75754284
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 223 -
Rwork0.099 3795 -
obs-4018 96.8 %

+
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