[English] 日本語
Yorodumi
- PDB-1yqh: Structure of domain of unknown function DUF77 from Bacillus cereus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yqh
TitleStructure of domain of unknown function DUF77 from Bacillus cereus
ComponentsIG hypothetical 16092
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Bacillus cereus / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyThiamine-binding protein / : / Thiamine-binding protein / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / IG hypothetical 16092
Function and homology information
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsMidwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of domain of unknown function DUF77 from Bacillus cereus
Authors: Cuff, M.E. / Quartey, P. / Zhou, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionFeb 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 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
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: IG hypothetical 16092
B: IG hypothetical 16092


Theoretical massNumber of molelcules
Total (without water)24,4432
Polymers24,4432
Non-polymers00
Water5,260292
1
A: IG hypothetical 16092
B: IG hypothetical 16092

A: IG hypothetical 16092
B: IG hypothetical 16092


Theoretical massNumber of molelcules
Total (without water)48,8854
Polymers48,8854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9860 Å2
ΔGint-39 kcal/mol
Surface area16750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.716, 55.175, 49.875
Angle α, β, γ (deg.)90.00, 120.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-257-

HOH

21B-191-

HOH

DetailsUNKNOWN: It is likely a homotetramer. The asymmetric unit contains a dimer,(x,y,z). To generate the tetramer, add the crystallographic dimer (1-x,y,1-z).

-
Components

#1: Protein IG hypothetical 16092 / DUF77


Mass: 12221.331 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: ATCC 14579 / DSM 31 / Gene: IG hypothetical 16092 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q81IG4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 1.9 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, Tris-HCL, MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97931,0.97947
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 22, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979471
ReflectionResolution: 1.7→43 Å / Num. all: 18421 / Num. obs: 18421 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.72→1.79 Å / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 5.1 / % possible all: 59.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.7→43.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.553 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.119
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20062 945 5.1 %RANDOM
Rwork0.16204 ---
all0.16402 18420 --
obs0.16402 17475 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.553 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20.16 Å2
2---0.14 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 0 292 1887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221692
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9522305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2655219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.82425.94979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14115307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.673158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021278
X-RAY DIFFRACTIONr_nbd_refined0.1890.2835
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.256
X-RAY DIFFRACTIONr_mcbond_it0.7691.51091
X-RAY DIFFRACTIONr_mcangle_it1.19421745
X-RAY DIFFRACTIONr_scbond_it2.2353674
X-RAY DIFFRACTIONr_scangle_it3.5094.5560
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 33 -
Rwork0.188 829 -
obs--59.45 %
Refinement TLS params.Method: refined / Origin x: 16.1599 Å / Origin y: 22.7136 Å / Origin z: 21.4395 Å
111213212223313233
T-0.0258 Å2-0.0003 Å2-0.0036 Å2--0.0174 Å20.0057 Å2---0.0211 Å2
L0.4458 °20.0024 °2-0.0483 °2-0.4286 °20.1571 °2--0.2066 °2
S0.0024 Å °0.0015 Å °-0.0017 Å °-0.0081 Å °-0.0118 Å °0.0508 Å °-0.0003 Å °-0.0018 Å °0.0093 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 1001 - 103
2X-RAY DIFFRACTION1BB2 - 1015 - 104

+
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