[English] 日本語
Yorodumi
- PDB-3rns: Cupin 2 conserved barrel domain protein from Leptotrichia buccalis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rns
TitleCupin 2 conserved barrel domain protein from Leptotrichia buccalis
ComponentsCupin 2 conserved barrel domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG / conserved barrel domain
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Cupin 2 conserved barrel domain protein
Similarity search - Component
Biological speciesLeptotrichia buccalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å
AuthorsOsipiuk, J. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Cupin 2 conserved barrel domain protein from Leptotrichia buccalis.
Authors: Osipiuk, J. / Tesar, C. / Bearden, J. / Joachimiak, A.
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 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: Cupin 2 conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7312
Polymers25,6721
Non-polymers591
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.684, 58.684, 143.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Cupin 2 conserved barrel domain protein


Mass: 25672.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia buccalis (bacteria) / Strain: C-1013-b / Gene: Lebu_0116 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7NCX6
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris-Propane:NaOH, 1.8 M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.07→35.9 Å / Num. all: 16116 / Num. obs: 16116 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.899 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.07-2.1110.90.8922.777921.338100
2.11-2.1411.80.7197541.289100
2.14-2.1912.40.758271.211100
2.19-2.2313.20.6747471.213100
2.23-2.2813.40.67921.121100
2.28-2.3313.70.487821.191100
2.33-2.3913.70.4917911.144100
2.39-2.4513.60.3517961.122100
2.45-2.5313.70.3317921.193100
2.53-2.6113.60.2937771.255100
2.61-2.713.70.2178051.3100
2.7-2.8113.60.1768081.449100
2.81-2.9413.60.1538051.664100
2.94-3.0913.60.1237991.999100
3.09-3.2913.50.0947992.251100
3.29-3.5413.30.0818072.809100
3.54-3.912.90.0758273.319100
3.9-4.4612.60.0688263.847100
4.46-5.6212.10.0578543.546100
5.62-5010.50.0619363.80798.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.07→35.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.18 / SU B: 8.636 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.151 / Phase error: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 785 4.9 %RANDOM
Rwork0.1717 ---
all0.1734 15938 --
obs0.1734 15938 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.06 Å2 / Biso mean: 43.4159 Å2 / Biso min: 24.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.07→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 4 61 1698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221771
X-RAY DIFFRACTIONr_bond_other_d0.0010.021200
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9742416
X-RAY DIFFRACTIONr_angle_other_deg0.88732987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.7426.3184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26215339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.425155
X-RAY DIFFRACTIONr_chiral_restr0.1070.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
X-RAY DIFFRACTIONr_mcbond_it0.9991.51088
X-RAY DIFFRACTIONr_mcbond_other0.2561.5436
X-RAY DIFFRACTIONr_mcangle_it1.82721776
X-RAY DIFFRACTIONr_scbond_it2.8193683
X-RAY DIFFRACTIONr_scangle_it4.5854.5623
LS refinement shellResolution: 2.067→2.121 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 58 -
Rwork0.235 1053 -
all-1111 -
obs-1111 96.36 %
Refinement TLS params.Method: refined / Origin x: 27.8457 Å / Origin y: 6.6124 Å / Origin z: 37.1244 Å
111213212223313233
T0.0765 Å20.016 Å20.0164 Å2-0.0735 Å20.0065 Å2--0.0848 Å2
L1.0669 °2-0.1582 °2-0.1074 °2-0.8729 °20.1371 °2--3.8103 °2
S0.1162 Å °0.0775 Å °-0.2132 Å °-0.04 Å °-0.077 Å °0.0115 Å °0.2372 Å °-0.1069 Å °-0.0392 Å °

+
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