[English] 日本語
Yorodumi
- PDB-3eo4: The crystal structure of a domain from Methanocaldococcus jannasc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eo4
TitleThe crystal structure of a domain from Methanocaldococcus jannaschii DSM 2661
ComponentsUncharacterized protein MJ1062
Keywordsstructural genomics / unknown function / APC60792.2 / MJ_1062 / Methanocaldococcus jannaschii DSM 2661 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


hexosyltransferase activity / N-acetyltransferase activity
Similarity search - Function
UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase / Glycosyl transferase, family 28, C-terminal / Glycosyltransferase family 28 C-terminal domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase ...UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase / Glycosyl transferase, family 28, C-terminal / Glycosyltransferase family 28 C-terminal domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PG6 / Uncharacterized protein MJ1062
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsTan, K. / Hatzos, C. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a domain from Methanocaldococcus jannaschii DSM 2661
Authors: Tan, K. / Hatzos, C. / Freeman, L. / Joachimiak, A.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein MJ1062
B: Uncharacterized protein MJ1062
C: Uncharacterized protein MJ1062
D: Uncharacterized protein MJ1062
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,75216
Polymers78,7384
Non-polymers2,01412
Water4,216234
1
A: Uncharacterized protein MJ1062
B: Uncharacterized protein MJ1062
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4788
Polymers39,3692
Non-polymers1,1096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint20 kcal/mol
Surface area15670 Å2
MethodPISA
2
C: Uncharacterized protein MJ1062
D: Uncharacterized protein MJ1062
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2748
Polymers39,3692
Non-polymers9056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint20 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.374, 96.871, 83.212
Angle α, β, γ (deg.)90.00, 126.63, 90.00
Int Tables number5
Space group name H-MC121
Detailsauthors state that the biological unit is experimentaly unknown. The chains A and B, C and D are predicted to form dimers respectively.

-
Components

#1: Protein
Uncharacterized protein MJ1062


Mass: 19684.471 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: Methanocaldococcus jannaschii, MJ1062 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q58462
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M NaAcetate, 0.1M MES, 30%(w/v)PEG2000MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2008 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.19→49 Å / Num. all: 41356 / Num. obs: 41356 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 16.8
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.75 / Num. unique all: 2629 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→48.45 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.749 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.26 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23958 2072 5 %RANDOM
Rwork0.19536 ---
all0.1976 39150 --
obs0.1976 39150 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.378 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.27 Å2
2---0.43 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.19→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 126 234 5685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9557550
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.66423.626273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.419151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4021541
X-RAY DIFFRACTIONr_chiral_restr0.1160.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024105
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5991.53120
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13725065
X-RAY DIFFRACTIONr_scbond_it2.13732487
X-RAY DIFFRACTIONr_scangle_it3.3094.52481
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.192→2.249 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 119 -
Rwork0.241 2695 -
obs-2191 90.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.02530.3022-0.60463.7624-0.3771.292-0.0151-0.0478-0.0076-0.06160.01840.15190.1216-0.0122-0.00330.0362-0.0145-0.00890.1869-0.00540.0091-8.14640.50856.661
20.9636-0.5146-0.51053.33680.02181.50070.01250.00740.14240.04070.058-0.0162-0.0765-0.0144-0.07050.0054-0.00080.00060.1681-0.00330.026-6.2671.19857.147
32.52780.40381.39940.99760.73594.9326-0.13680.16390.0123-0.01690.0839-0.0899-0.09360.78570.05290.011-0.0293-0.00230.29040.02380.012721.72358.43438.991
43.01210.37541.06141.30350.21232.9559-0.02830.21370.0301-0.31070.06170.22860.0696-0.1964-0.03340.1116-0.021-0.06680.19410.0160.0446-3.2953.76622.044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A341 - 502
2X-RAY DIFFRACTION2B351 - 502
3X-RAY DIFFRACTION3C349 - 502
4X-RAY DIFFRACTION4D341 - 502

+
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