[English] 日本語
Yorodumi
- PDB-3g74: Crystal structure of a functionally unknown protein from Eubacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g74
TitleCrystal structure of a functionally unknown protein from Eubacterium ventriosum ATCC 27560
ComponentsProtein of unknown function
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC21008.1 / Eubacterium ventriosum ATCC 27560 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyeubacterium ventriosum atcc fold / eubacterium ventriosum atcc domain / Stage V sporulation protein AA / Stage V sporulation protein AA, N-terminal domain superfamily / Stage V sporulation protein AA / Sandwich / Mainly Beta / membrane / Stage V sporulation protein AA
Function and homology information
Biological speciesEubacterium ventriosum ATCC 27560 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.43 Å
AuthorsTan, K. / Sather, A. / Marshall, N. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown protein from Eubacterium ventriosum ATCC 27560
Authors: Tan, K. / Sather, A. / Marshall, N. / Freeman, L. / Joachimiak, A.
History
DepositionFeb 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein of unknown function
B: Protein of unknown function
C: Protein of unknown function
D: Protein of unknown function
E: Protein of unknown function
F: Protein of unknown function
G: Protein of unknown function
H: Protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,88625
Polymers93,2538
Non-polymers1,63317
Water1,74797
1
A: Protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0415
Polymers11,6571
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8493
Polymers11,6571
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein of unknown function


Theoretical massNumber of molelcules
Total (without water)11,6571
Polymers11,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7532
Polymers11,6571
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0415
Polymers11,6571
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8493
Polymers11,6571
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8493
Polymers11,6571
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8493
Polymers11,6571
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.996, 107.961, 67.691
Angle α, β, γ (deg.)90.00, 92.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-101-

SO4

21A-180-

HOH

DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN.

-
Components

#1: Protein
Protein of unknown function


Mass: 11656.649 Da / Num. of mol.: 8 / Fragment: UNP residues 1-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium ventriosum ATCC 27560 (bacteria)
Gene: EUBVEN_02336 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A5Z9E1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.5M Ammonium sulfate, 0.1M Sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918, 0.97940
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2008 / Details: Mirrors
RadiationMonochromator: Si(111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.97941
ReflectionResolution: 2.43→33.5 Å / Num. all: 30092 / Num. obs: 30092 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 24.3
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.83 / Num. unique all: 1460 / % possible all: 98.4

-
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: MAD / Resolution: 2.43→33.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 22.593 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.552 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26347 1476 4.9 %RANDOM
Rwork0.20865 ---
all0.21137 28466 --
obs0.21137 28466 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.713 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-0.02 Å2
2---0.72 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.43→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5624 0 85 97 5806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225734
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9917684
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9545698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09727.203236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.692151260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1371517
X-RAY DIFFRACTIONr_chiral_restr0.1020.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023885
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_it1.0323515
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76135766
X-RAY DIFFRACTIONr_scbond_it1.24622219
X-RAY DIFFRACTIONr_scangle_it1.86331916
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.43→2.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 97 -
Rwork0.235 1724 -
obs-1959 80.22 %
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)
14.62992.04261.50833.5873-0.05655.63690.1102-0.42410.39870.4813-0.04590.7946-0.3154-0.3595-0.06430.08480.02550.09150.4283-0.00590.46135.77575.8513.217
24.52640.78481.57846.3268-1.894.92070.2524-0.4978-0.08260.6543-0.019-0.0080.4004-0.2808-0.23340.17680.030.01260.40740.02660.239820.62663.69329.853
32.8390.8734-0.78465.74370.18598.28970.00550.2278-0.39610.10820.5387-1.21290.81.7456-0.54420.08330.2175-0.07290.8304-0.25490.549838.06361.97911.42
44.6159-1.36160.93059.01531.47763.7497-0.12720.33480.4436-1.18810.13270.0076-0.48880.1715-0.00550.2029-0.04240.01990.4684-0.03340.241923.25474.71-3.842
57.92011.53191.25563.83981.02732.4926-0.0449-0.27640.31040.5337-0.06720.3955-0.0668-0.20170.11210.10920.0210.09850.374-0.01790.263821.74190.91533.778
64.58770.0754-1.96887.44390.84917.2788-0.3836-0.1328-0.40341.1198-0.0458-0.8210.7010.25220.42940.23370.0396-0.11120.5102-0.08550.498144.3581.38930.03
79.23010.46952.74396.2709-2.35543.50960.07321.9907-0.7362-0.43020.1799-0.9730.03561.1027-0.25320.0459-0.03230.1010.9808-0.19860.434343.32590.1626.652
84.10921.5023-0.32017.84481.21945.3725-0.31160.41430.234-0.82830.0791.0485-0.4339-0.4330.23270.1305-0.0188-0.07150.44380.03510.340320.9599.93711.103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 90
2X-RAY DIFFRACTION2B1 - 90
3X-RAY DIFFRACTION3C0 - 90
4X-RAY DIFFRACTION4D-1 - 90
5X-RAY DIFFRACTION5E-1 - 90
6X-RAY DIFFRACTION6F2 - 89
7X-RAY DIFFRACTION7G1 - 91
8X-RAY DIFFRACTION8H1 - 90

+
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