[English] 日本語
Yorodumi
- PDB-3o0y: The crystal structure of the putative lipoprotein from Colwellia ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o0y
TitleThe crystal structure of the putative lipoprotein from Colwellia psychrerythraea
Componentslipoprotein
KeywordsLIPID BINDING PROTEIN / Structural genomics / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / lipoprotein
Function / homologyProtein of unknown function DUF885 / Bacterial protein of unknown function (DUF885) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Putative lipoprotein
Function and homology information
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsZhang, R. / Chhor, G. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the putative lipoprotein from Colwellia psychrerythraea
Authors: Zhang, R. / Chhor, G. / Cobb, G. / Joachimiak, A.
History
DepositionJul 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: lipoprotein
B: lipoprotein
C: lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,82220
Polymers204,1433
Non-polymers1,68017
Water43,2002398
1
A: lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5766
Polymers68,0481
Non-polymers5295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6387
Polymers68,0481
Non-polymers5916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6087
Polymers68,0481
Non-polymers5616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.954, 94.471, 93.894
Angle α, β, γ (deg.)114.32, 91.11, 100.43
Int Tables number1
Space group name H-MP1
DetailsIt looks like the molecules A,B,C form the trimer in the solution.

-
Components

#1: Protein lipoprotein


Mass: 68047.602 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H BAA-681 / Gene: CPS_3202 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q47Z72
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2398 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-tris pH5.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2009 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 1.7→85.13 Å / Num. all: 216434 / Num. obs: 206348 / % possible obs: 95.34 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.85
Reflection shellResolution: 1.703→1.747 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1 / Num. unique all: 16813 / % possible all: 72.08

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→85.13 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.85 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.092
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18545 10876 5 %RANDOM
Rwork0.14599 ---
obs0.14796 206348 95.34 %-
all-216434 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.486 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20.08 Å20.05 Å2
2--1.36 Å20.48 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→85.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13838 0 102 2398 16338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02214228
X-RAY DIFFRACTIONr_bond_other_d0.0010.029581
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.96819281
X-RAY DIFFRACTIONr_angle_other_deg1.037323440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55351751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56325.083665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.446152463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2961572
X-RAY DIFFRACTIONr_chiral_restr0.1340.22119
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02115748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022729
X-RAY DIFFRACTIONr_mcbond_it1.3331.58738
X-RAY DIFFRACTIONr_mcbond_other0.4721.53552
X-RAY DIFFRACTIONr_mcangle_it2.248214071
X-RAY DIFFRACTIONr_scbond_it3.75935490
X-RAY DIFFRACTIONr_scangle_it5.7914.55210
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 589 -
Rwork0.258 11530 -
obs-12119 72.08 %
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)
10.24620.0333-0.01850.2058-0.05750.41320.0171-0.00920.02730.00320.0150.0326-0.035-0.0093-0.03210.0182-0.0010.00110.0062-0.00690.02576.10111.99337.992
20.2924-0.1013-0.02910.47380.09620.20120.0051-0.0211-0.06360.0322-0.0266-0.01070.0080.00450.02150.0091-0.00580.00020.00860.00370.023943.105-24.1494.217
30.1621-0.01210.1530.5575-0.48230.74830.02480.0235-0.0002-0.10830.04230.07880.1239-0.0059-0.06710.0388-0.0047-0.01550.0166-0.00050.0159-1.3388.343-24.111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 100
2X-RAY DIFFRACTION1A101 - 200
3X-RAY DIFFRACTION1A201 - 300
4X-RAY DIFFRACTION1A301 - 400
5X-RAY DIFFRACTION1A401 - 500
6X-RAY DIFFRACTION1A501 - 609
7X-RAY DIFFRACTION2B25 - 100
8X-RAY DIFFRACTION2B101 - 200
9X-RAY DIFFRACTION2B201 - 300
10X-RAY DIFFRACTION2B301 - 400
11X-RAY DIFFRACTION2B401 - 500
12X-RAY DIFFRACTION2B501 - 609
13X-RAY DIFFRACTION3C25 - 100
14X-RAY DIFFRACTION3C101 - 200
15X-RAY DIFFRACTION3C201 - 300
16X-RAY DIFFRACTION3C301 - 400
17X-RAY DIFFRACTION3C401 - 500
18X-RAY DIFFRACTION3C501 - 606

+
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