[English] 日本語
Yorodumi
- PDB-3oms: Putative 3-demethylubiquinone-9 3-methyltransferase, PhnB protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oms
TitlePutative 3-demethylubiquinone-9 3-methyltransferase, PhnB protein, from Bacillus cereus.
ComponentsPhnB protein
KeywordsTRANSFERASE / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / methyltransferase / glyoxalase family
Function / homology
Function and homology information


Signal recognition particle alu RNA binding heterodimer, srp9/1 - #100 / Predicted 3-demethylubiquinone-9 3-methyltransferase, bacterial / Predicted 3-demethylubiquinone-9 3-methyltransferase / 3-demethylubiquinone-9 3-methyltransferase / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #110 / PhnB-like / Signal recognition particle alu RNA binding heterodimer, srp9/1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsOsipiuk, J. / Li, H. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative 3-demethylubiquinone-9 3-methyltransferase, PhnB protein, from Bacillus cereus.
Authors: Osipiuk, J. / Li, H. / Abdullah, J. / Joachimiak, A.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 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_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_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: PhnB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0023
Polymers15,8781
Non-polymers1242
Water1,856103
1
A: PhnB protein
hetero molecules

A: PhnB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0046
Polymers31,7562
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3520 Å2
ΔGint-14 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.302, 62.302, 90.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein PhnB protein


Mass: 15877.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC_2431 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81DD6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 40% PEG-300, 0.1 M phoshate citrate buffer, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 11, 2004
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: 1.9→36.7 Å / Num. all: 14643 / Num. obs: 14643 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.138 / Χ2: 3.39 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.9-1.9317.40.8563.097150.762100
1.93-1.9717.30.717080.771100
1.97-2.0117.30.5087240.759100
2.01-2.0517.40.4047000.847100
2.05-2.0917.20.3497130.996100
2.09-2.1417.30.3117280.923100
2.14-2.1917.20.2957021.085100
2.19-2.2517.10.2737351.286100
2.25-2.3217.10.2457161.435100
2.32-2.39170.2217261.538100
2.39-2.48170.2227231.911100
2.48-2.5816.70.1957182.368100
2.58-2.716.50.187303.114100
2.7-2.8416.20.1697373.919100
2.84-3.0215.80.1537304.903100
3.02-3.2514.90.1287466.084100
3.25-3.5814.10.1167347.403100
3.58-4.0912.70.1057618.85399.9
4.09-5.1610.20.09976911.15599.6
5.16-5011.60.11582816.18797.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→36.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.132 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 727 5 %RANDOM
Rwork0.1798 ---
all0.1814 14535 --
obs0.1814 14535 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.23 Å2 / Biso mean: 37.193 Å2 / Biso min: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 8 103 1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221117
X-RAY DIFFRACTIONr_bond_other_d0.0030.02736
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9331522
X-RAY DIFFRACTIONr_angle_other_deg0.931810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20425.35756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16315186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.823151
X-RAY DIFFRACTIONr_chiral_restr0.0890.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_mcbond_it0.9611.5663
X-RAY DIFFRACTIONr_mcbond_other0.2761.5270
X-RAY DIFFRACTIONr_mcangle_it1.70621080
X-RAY DIFFRACTIONr_scbond_it2.5193454
X-RAY DIFFRACTIONr_scangle_it4.0814.5434
LS refinement shellResolution: 1.902→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 60 -
Rwork0.254 990 -
all-1050 -
obs-1054 99.34 %
Refinement TLS params.Method: refined / Origin x: 5.6391 Å / Origin y: 11.5424 Å / Origin z: 36.6645 Å
111213212223313233
T0.0585 Å2-0.051 Å2-0.044 Å2-0.062 Å20.0319 Å2--0.0553 Å2
L3.1842 °2-0.3238 °2-0.3797 °2-1.5083 °2-0.213 °2--2.3468 °2
S-0.0614 Å °0.1872 Å °0.0293 Å °-0.0728 Å °0.0171 Å °-0.0668 Å °-0.0096 Å °-0.1116 Å °0.0443 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