[English] 日本語
Yorodumi
- PDB-3ld7: Crystal structure of the Lin0431 protein from Listeria innocua, N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ld7
TitleCrystal structure of the Lin0431 protein from Listeria innocua, Northeast Structural Genomics Consortium Target LkR112
ComponentsLin0431 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Lin0431 / DUF1312 / PF07009 / LkR112 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyN-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / Sandwich / Mainly Beta / Lin0431 protein
Function and homology information
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.547 Å
AuthorsVorobiev, S. / Chen, Y. / Lee, D. / Patel, D.J. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Vorobiev, S. / Chen, Y. / Lee, D. / Patel, D.J. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Lin0431 protein from Listeria innocua
Authors: Vorobiev, S. / Chen, Y. / Lee, D. / Patel, D.J. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.name
Revision 1.3Nov 20, 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lin0431 protein
B: Lin0431 protein
C: Lin0431 protein


Theoretical massNumber of molelcules
Total (without water)34,6133
Polymers34,6133
Non-polymers00
Water5,549308
1
A: Lin0431 protein


Theoretical massNumber of molelcules
Total (without water)11,5381
Polymers11,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lin0431 protein


Theoretical massNumber of molelcules
Total (without water)11,5381
Polymers11,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lin0431 protein


Theoretical massNumber of molelcules
Total (without water)11,5381
Polymers11,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.360, 54.782, 71.733
Angle α, β, γ (deg.)90.00, 111.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

Detailsmonomer according to gel filtration

-
Components

#1: Protein Lin0431 protein


Mass: 11537.740 Da / Num. of mol.: 3 / Fragment: sequence database residues 36-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: CLIP 11262/Serovar 6a / Gene: lin0431 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q92EM7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 8.2
Details: 0.072M sodium phosphate monobasic, 1.728M potassium phosphate dibasic, pH 8.2, microbatch under paraffin oil, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97814 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97814 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 84850 / Num. obs: 84087 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 19.53 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.3
Reflection shellHighest resolution: 1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.4 / Num. unique all: 8496 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.547→31.547 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.194 4234 5.04 %RANDOM
Rwork0.1654 ---
obs0.1669 84064 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.156 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2611 Å2-0 Å2-0.8854 Å2
2---0.2922 Å20 Å2
3---1.5533 Å2
Refinement stepCycle: LAST / Resolution: 1.547→31.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 0 308 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012055
X-RAY DIFFRACTIONf_angle_d1.2452767
X-RAY DIFFRACTIONf_dihedral_angle_d16.442791
X-RAY DIFFRACTIONf_chiral_restr0.078313
X-RAY DIFFRACTIONf_plane_restr0.005360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5467-1.56430.21871150.16892344X-RAY DIFFRACTION87
1.5643-1.58270.20021350.15572680X-RAY DIFFRACTION99
1.5827-1.6020.20281340.14662679X-RAY DIFFRACTION99
1.602-1.62230.1871430.13832598X-RAY DIFFRACTION99
1.6223-1.64360.20621660.13762733X-RAY DIFFRACTION99
1.6436-1.66620.20771400.14052666X-RAY DIFFRACTION99
1.6662-1.690.17491350.14012632X-RAY DIFFRACTION99
1.69-1.71520.22261090.13392759X-RAY DIFFRACTION99
1.7152-1.7420.19371220.13162655X-RAY DIFFRACTION99
1.742-1.77050.16231450.12952765X-RAY DIFFRACTION99
1.7705-1.80110.16851370.13792601X-RAY DIFFRACTION100
1.8011-1.83380.19951300.13812743X-RAY DIFFRACTION100
1.8338-1.86910.17731430.13782659X-RAY DIFFRACTION100
1.8691-1.90720.20291650.12732667X-RAY DIFFRACTION100
1.9072-1.94870.13871460.13822675X-RAY DIFFRACTION100
1.9487-1.9940.15681450.13232704X-RAY DIFFRACTION100
1.994-2.04390.19011600.14422689X-RAY DIFFRACTION100
2.0439-2.09910.19211310.14672703X-RAY DIFFRACTION100
2.0991-2.16090.19341480.14542685X-RAY DIFFRACTION100
2.1609-2.23060.16281460.14852668X-RAY DIFFRACTION100
2.2306-2.31030.17651300.15392687X-RAY DIFFRACTION100
2.3103-2.40280.17961480.15842678X-RAY DIFFRACTION100
2.4028-2.51210.19261280.17592724X-RAY DIFFRACTION100
2.5121-2.64450.23571440.18472676X-RAY DIFFRACTION100
2.6445-2.81010.24431570.18972701X-RAY DIFFRACTION100
2.8101-3.02690.18181440.19032670X-RAY DIFFRACTION100
3.0269-3.33120.19021430.1732729X-RAY DIFFRACTION100
3.3312-3.81250.15391600.15472642X-RAY DIFFRACTION99
3.8125-4.80060.17651320.15982595X-RAY DIFFRACTION97
4.8006-31.55390.24041530.19212423X-RAY DIFFRACTION90

+
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