[English] 日本語
Yorodumi
- PDB-2pig: Crystal structure of ydcK from Salmonella cholerae at 2.38 A reso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pig
TitleCrystal structure of ydcK from Salmonella cholerae at 2.38 A resolution. Northeast Structural Genomics target SCR6
ComponentsPutative transferase
KeywordsTRANSFERASE / scr6 / nesg / ydcK / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


acyltransferase activity / nucleotidyltransferase activity / transferase activity / metal ion binding
Similarity search - Function
YdcK Beta solenoid repeat / : / YdcK Beta solenoid repeat / : / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
Transferase / Putative transferase
Similarity search - Component
Biological speciesSalmonella paratyphi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsBenach, J. / Chen, Y. / Vorobiev, S.M. / Seetharaman, J. / Ho, C.K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. ...Benach, J. / Chen, Y. / Vorobiev, S.M. / Seetharaman, J. / Ho, C.K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of ydcK from Salmonella cholerae at 2.38 A resolution.
Authors: Benach, J. / Chen, Y. / Vorobiev, S.M. / Seetharaman, J. / Ho, C.K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 30, 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative transferase
B: Putative transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4555
Polymers74,2582
Non-polymers1963
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-105 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.603, 103.603, 160.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThe AU contains the biological assembly

-
Components

#1: Protein Putative transferase


Mass: 37129.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella paratyphi (bacteria) / Strain: SARB42 / Gene: ydcK, SPA1259 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5PHU6, UniProt: A0A0H2WQ05*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mM MAGNESIUM SULFATE, 50 mM SODIUM CACODYLATE, 1.8 M LITHIUM SULFATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97877 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97877 Å / Relative weight: 1
ReflectionRedundancy: 7.8 % / Av σ(I) over netI: 8.8 / Number: 306807 / Rmerge(I) obs: 0.104 / Χ2: 1.09 / D res high: 2.3 Å / D res low: 20 Å / Num. obs: 39556 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.932010010.061.0577.4
3.934.9310010.0530.977.8
3.433.9310010.071.0947.9
3.123.4310010.0911.0658
2.93.1210010.1331.1958
2.732.910010.181.0317.9
2.592.7310010.2521.1057.8
2.482.5910010.3191.0997.7
2.382.4810010.3811.1767.5
2.32.3810010.4221.0897.5
ReflectionResolution: 2.3→20 Å / Num. obs: 39556 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.104 / Χ2: 1.087 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.387.50.42238471.089100
2.38-2.487.50.38139181.176100
2.48-2.597.70.31938761.099100
2.59-2.737.80.25239101.105100
2.73-2.97.90.1838991.031100
2.9-3.1280.13339271.195100
3.12-3.4380.09139371.065100
3.43-3.937.90.0739871.094100
3.93-4.937.80.05340300.97100
4.93-207.40.0642251.057100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F9C

2f9c


Resolution: 2.38→20 Å / FOM work R set: 0.826 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3190 8.9 %random
Rwork0.2195 ---
obs0.2195 32066 89.8 %-
Solvent computationBsol: 28.689 Å2
Displacement parametersBiso mean: 24.065 Å2
Baniso -1Baniso -2Baniso -3
1--0.304 Å20 Å20 Å2
2---0.304 Å20 Å2
3---0.608 Å2
Refinement stepCycle: LAST / Resolution: 2.38→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4886 0 3 135 5024
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005203
X-RAY DIFFRACTIONc_angle_deg1.2986
X-RAY DIFFRACTIONc_mcbond_it1.2471.5
X-RAY DIFFRACTIONc_scbond_it2.2022
X-RAY DIFFRACTIONc_mcangle_it2.0142
X-RAY DIFFRACTIONc_scangle_it3.2632.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.38-2.40.281580.222504562
2.4-2.410.29610.22490551
2.41-2.430.343660.244494560
2.43-2.450.303620.212471533
2.45-2.460.318470.234511558
2.46-2.480.282460.235492538
2.48-2.50.294630.218495558
2.5-2.520.307560.253506562
2.52-2.540.274520.211495547
2.54-2.560.302480.225529577
2.56-2.590.287630.239529592
2.59-2.610.312580.231528586
2.61-2.630.313480.234531579
2.63-2.650.236440.216548592
2.65-2.680.262640.241520584
2.68-2.710.333520.239533585
2.71-2.730.284720.262569641
2.73-2.760.331760.254531607
2.76-2.790.297590.252546605
2.79-2.820.297670.254574641
2.82-2.850.313620.255544606
2.85-2.890.306600.254576636
2.89-2.920.345710.256551622
2.92-2.960.286640.254580644
2.96-30.339620.27584646
3-3.040.335720.267612684
3.04-3.080.341600.274579639
3.08-3.130.264620.255611673
3.13-3.180.297640.262589653
3.18-3.230.261640.216596660
3.23-3.280.246770.231594671
3.28-3.340.298760.216607683
3.34-3.410.243770.213603680
3.41-3.480.254760.192603679
3.48-3.550.212580.191611669
3.55-3.630.224700.195620690
3.63-3.720.246660.197627693
3.72-3.820.215760.186615691
3.82-3.930.247710.187614685
3.93-4.060.22640.167637701
4.06-4.20.221610.191629690
4.2-4.370.173540.15659713
4.37-4.570.164680.149645713
4.57-4.810.202740.162628702
4.81-5.10.358710.204636707
5.1-5.490.257740.246653727
5.49-6.030.341670.268641708
6.03-6.870.336730.303649722
6.87-8.540.302670.27666733
8.54-200.28670.23721788
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
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