[English] 日本語
Yorodumi
- PDB-3dc7: Crystal structure of the protein Q88SR8 from Lactobacillus planta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dc7
TitleCrystal structure of the protein Q88SR8 from Lactobacillus plantarum. Northeast Structural Genomics consortium target LpR109.
ComponentsPutative uncharacterized protein lp_3323
Keywordsstructural genomics / unknown function / NESG LpR109 X-RAY lp_3323 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologySGNH hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsKuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Seetharaman, J. / Zhao, L. / Mao, L. / Ciccosanti, C. / Xiao, R. / Nair, R. / Baran, M.C. ...Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Seetharaman, J. / Zhao, L. / Mao, L. / Ciccosanti, C. / Xiao, R. / Nair, R. / Baran, M.C. / 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 protein Q88SR8 from Lactobacillus plantarum. Northeast Structural Genomics consortium target LpR109. (CASP Target)
Authors: Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Seetharaman, J. / Zhao, L. / Mao, L. / Ciccosanti, C. / Xiao, R. / Nair, R. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein lp_3323
B: Putative uncharacterized protein lp_3323
C: Putative uncharacterized protein lp_3323
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4789
Polymers77,1193
Non-polymers3586
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-19 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.610, 101.440, 125.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Putative uncharacterized protein lp_3323


Mass: 25706.439 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lactobacillus plantarum (bacteria) / References: UniProt: Q88SR8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M MgSo4, 0.1M Bis-Tris, 16% PEG8K, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791, 0.9679, 0.9794
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 22, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.96791
30.97941
ReflectionResolution: 2.12→50 Å / Num. obs: 54518 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.4
Reflection shellResolution: 2.27→2.35 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 7.5 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.12→19.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.47 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22431 1572 5.1 %RANDOM
Rwork0.18388 ---
obs0.18598 29260 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: 29.192 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.12→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 18 155 5025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215087
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9276878
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9623.388245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24915727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1991530
X-RAY DIFFRACTIONr_chiral_restr0.0850.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023980
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.22407
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23444
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6671.53136
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31824999
X-RAY DIFFRACTIONr_scbond_it2.35231996
X-RAY DIFFRACTIONr_scangle_it3.5644.51876
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.123→2.177 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 73 -
Rwork0.218 1527 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 7.131 Å / Origin y: 45.639 Å / Origin z: 77.076 Å
111213212223313233
T-0.0865 Å2-0.0015 Å20.0112 Å2--0.034 Å2-0.0056 Å2---0.0362 Å2
L0.2344 °2-0.0329 °2-0.0426 °2-0.8311 °20.2843 °2--0.7256 °2
S0.0007 Å °-0.0288 Å °0.0543 Å °-0.025 Å °0.0238 Å °0.0296 Å °-0.0852 Å °-0.0393 Å °-0.0245 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B236 - 279
2X-RAY DIFFRACTION1C250 - 308
3X-RAY DIFFRACTION1A236 - 291
4X-RAY DIFFRACTION1B233 - 234
5X-RAY DIFFRACTION1C233 - 234
6X-RAY DIFFRACTION1A233 - 235
7X-RAY DIFFRACTION1B18 - 226
8X-RAY DIFFRACTION1C18 - 225
9X-RAY DIFFRACTION1A18 - 230

+
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