[English] 日本語
Yorodumi
- PDB-3fif: Crystal structure of the ygdR protein from E.coli. Northeast Stru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fif
TitleCrystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target ER382A.
Components
  • Uncharacterized ligand
  • Uncharacterized lipoprotein ygdR
Keywordsstructural genomics / unknown function / ygdR YGDR_ECOLI NESG X-RAY STRUCTURE / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Cell membrane / Lipoprotein / Membrane / Palmitate
Function / homology
Function and homology information


: / Protein of unknown function DUF903 / Bacterial protein of unknown function (DUF903) / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Mainly Beta
Similarity search - Domain/homology
Uncharacterized lipoprotein YgdR
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Rossi, P. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J.C. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Rossi, P. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J.C. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target ER382A.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Rossi, P. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J.C. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / ...Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Rossi, P. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J.C. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized lipoprotein ygdR
B: Uncharacterized lipoprotein ygdR
C: Uncharacterized lipoprotein ygdR
D: Uncharacterized lipoprotein ygdR
E: Uncharacterized lipoprotein ygdR
F: Uncharacterized lipoprotein ygdR
G: Uncharacterized lipoprotein ygdR
H: Uncharacterized lipoprotein ygdR
Y: Uncharacterized ligand


Theoretical massNumber of molelcules
Total (without water)58,3329
Polymers58,3329
Non-polymers00
Water1,63991
1
A: Uncharacterized lipoprotein ygdR


Theoretical massNumber of molelcules
Total (without water)7,2391
Polymers7,2391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized lipoprotein ygdR


Theoretical massNumber of molelcules
Total (without water)7,2391
Polymers7,2391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized lipoprotein ygdR


Theoretical massNumber of molelcules
Total (without water)7,2391
Polymers7,2391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized lipoprotein ygdR


Theoretical massNumber of molelcules
Total (without water)7,2391
Polymers7,2391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Uncharacterized lipoprotein ygdR


Theoretical massNumber of molelcules
Total (without water)7,2391
Polymers7,2391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Uncharacterized lipoprotein ygdR


Theoretical massNumber of molelcules
Total (without water)7,2391
Polymers7,2391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Uncharacterized lipoprotein ygdR


Theoretical massNumber of molelcules
Total (without water)7,2391
Polymers7,2391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Uncharacterized lipoprotein ygdR


Theoretical massNumber of molelcules
Total (without water)7,2391
Polymers7,2391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
Y: Uncharacterized ligand


  • defined by author&software
  • 417 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)4171
Polymers4171
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.017, 41.056, 73.748
Angle α, β, γ (deg.)99.95, 102.33, 104.40
Int Tables number1
Space group name H-MP1
Detailsmonomer

-
Components

#1: Protein
Uncharacterized lipoprotein ygdR


Mass: 7239.302 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ygdR, b2833, JW2801 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: P65294
#2: Protein/peptide Uncharacterized ligand


Mass: 417.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT CHAIN Y IS UNKNOWN LIGAND MODELED AS POLY-GLY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 12% PEG400, 0.1M Na-Acetate, 0.1M KH2PO4, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 453287 / Num. obs: 22734 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 21.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.059 / Mean I/σ(I) obs: 13.5 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RB6

2rb6


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.875 / SU B: 30.04 / SU ML: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25253 555 4.8 %RANDOM
Rwork0.23802 ---
obs0.23871 11125 100 %-
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: 17.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.76 Å2-0.44 Å2
2--0 Å2-0.38 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 0 91 3649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213598
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.944836
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0275441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16825.604207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97515652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7441524
X-RAY DIFFRACTIONr_chiral_restr0.080.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022766
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.21403
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22298
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.2186
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3831.52272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4423565
X-RAY DIFFRACTIONr_scbond_it0.75431433
X-RAY DIFFRACTIONr_scangle_it1.154.51271
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.702→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 36 -
Rwork0.254 742 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -12.4824 Å / Origin y: -4.151 Å / Origin z: 6.7935 Å
111213212223313233
T0.0912 Å20.0044 Å20.0044 Å2-0.089 Å2-0.0022 Å2--0.0709 Å2
L0.1264 °20.0152 °20.0206 °2-0.0258 °20.0358 °2--0.0496 °2
S0.019 Å °0.004 Å °-0.023 Å °0.0201 Å °-0.0275 Å °-0.0045 Å °-0.0138 Å °0.0112 Å °0.0085 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H62 - 94
2X-RAY DIFFRACTION1F62 - 86
3X-RAY DIFFRACTION1G62 - 99
4X-RAY DIFFRACTION1D62 - 87
5X-RAY DIFFRACTION1E62 - 96
6X-RAY DIFFRACTION1B62 - 93
7X-RAY DIFFRACTION1C62 - 76
8X-RAY DIFFRACTION1A62 - 91
9X-RAY DIFFRACTION1Y1 - 7
10X-RAY DIFFRACTION1H2 - 57
11X-RAY DIFFRACTION1F2 - 57
12X-RAY DIFFRACTION1G2 - 58
13X-RAY DIFFRACTION1D2 - 58
14X-RAY DIFFRACTION1E2 - 57
15X-RAY DIFFRACTION1B2 - 57
16X-RAY DIFFRACTION1C2 - 58
17X-RAY DIFFRACTION1A3 - 57

+
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