[English] 日本語
Yorodumi
- PDB-6e12: Crystal Structure of the Alr8543 protein in complex with Oleic Ac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6000000000000
TitleCrystal Structure of the Alr8543 protein in complex with Oleic Acid and magnesium ion from Nostoc sp. PCC 7120, Northeast Structural Genomics Consortium Target NsR141
ComponentsAlr8543 protein
KeywordsLIPID BINDING PROTEIN / alpha-beta protein / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homologyUbiquinone biosynthesis protein Coq4 / Coenzyme Q (ubiquinone) biosynthesis protein Coq4 / ubiquinone biosynthetic process / OLEIC ACID / Alr8543 protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Xiao, R. / Ciccosanti, C. / Patel, D. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Xiao, R. / Ciccosanti, C. / Patel, D. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P50 GM62413 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)U54 GM074958 United States
CitationJournal: To Be Published
Title: Crystal Structure of the Alr8543 protein in complex with Oleic Acid and magnesium ion from Nostoc sp. PCC 7120, Northeast Structural Genomics Consortium Target NsR141
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Xiao, R. / Ciccosanti, C. / Patel, D. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J. ...Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Xiao, R. / Ciccosanti, C. / Patel, D. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionJul 9, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJul 25, 2018ID: 3KB4
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alr8543 protein
B: Alr8543 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7587
Polymers52,1092
Non-polymers6495
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-63 kcal/mol
Surface area19120 Å2
MethodPISA
2
A: Alr8543 protein
B: Alr8543 protein
hetero molecules

A: Alr8543 protein
B: Alr8543 protein
hetero molecules

A: Alr8543 protein
B: Alr8543 protein
hetero molecules

A: Alr8543 protein
B: Alr8543 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,03328
Polymers208,4378
Non-polymers2,59620
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area28690 Å2
ΔGint-285 kcal/mol
Surface area69520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.308, 112.918, 167.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Alr8543 protein


Mass: 26054.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr8543 / Cell (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YJY7
#2: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 5.2 Å3/Da / Density % sol: 76 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 100mM Citric Acid (pH 5) and 1.6M (NH4)2SO4, microbatch under oil, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97885 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 14, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2.4→37.536 Å / Num. obs: 39307 / % possible obs: 92.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1 / Net I/σ(I): 19.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 7913 / Χ2: 0.61 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→37.536 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.53
RfactorNum. reflection% reflection
Rfree0.199 3931 10 %
Rwork0.1715 --
obs0.1743 39307 92.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→37.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 43 211 3618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083483
X-RAY DIFFRACTIONf_angle_d0.9134724
X-RAY DIFFRACTIONf_dihedral_angle_d20.2722102
X-RAY DIFFRACTIONf_chiral_restr0.05535
X-RAY DIFFRACTIONf_plane_restr0.006599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42930.26391540.22071289X-RAY DIFFRACTION97
2.4293-2.460.22121420.2051321X-RAY DIFFRACTION98
2.46-2.49240.22641310.19311321X-RAY DIFFRACTION97
2.4924-2.52650.20891360.18631327X-RAY DIFFRACTION97
2.5265-2.56260.2251520.17361308X-RAY DIFFRACTION98
2.5626-2.60080.17531440.17061297X-RAY DIFFRACTION97
2.6008-2.64150.20571500.18181309X-RAY DIFFRACTION96
2.6415-2.68480.20891340.18421301X-RAY DIFFRACTION97
2.6848-2.7310.23121390.18921304X-RAY DIFFRACTION97
2.731-2.78070.20131320.18211317X-RAY DIFFRACTION96
2.7807-2.83420.22211460.17631310X-RAY DIFFRACTION96
2.8342-2.8920.20341530.19391297X-RAY DIFFRACTION97
2.892-2.95480.25011430.20311275X-RAY DIFFRACTION96
2.9548-3.02360.23591590.19321282X-RAY DIFFRACTION95
3.0236-3.09910.21721450.20621288X-RAY DIFFRACTION95
3.0991-3.18290.25511310.20731307X-RAY DIFFRACTION95
3.1829-3.27650.24591450.19521263X-RAY DIFFRACTION94
3.2765-3.38220.23511340.19191274X-RAY DIFFRACTION93
3.3822-3.5030.21771480.17981256X-RAY DIFFRACTION92
3.503-3.64310.17731410.16481212X-RAY DIFFRACTION89
3.6431-3.80880.20871390.16391201X-RAY DIFFRACTION89
3.8088-4.00940.18971390.14721206X-RAY DIFFRACTION88
4.0094-4.26020.15541190.1381182X-RAY DIFFRACTION86
4.2602-4.58860.15071560.13151180X-RAY DIFFRACTION87
4.5886-5.04940.16031420.13311201X-RAY DIFFRACTION87
5.0494-5.77780.18011210.16091221X-RAY DIFFRACTION87
5.7778-7.27080.16041250.17521199X-RAY DIFFRACTION85
7.2708-37.54040.21171310.18431128X-RAY DIFFRACTION77
Refinement TLS params.Method: refined / Origin x: 65.4527 Å / Origin y: 39.2986 Å / Origin z: 24.2245 Å
111213212223313233
T0.2346 Å20.0489 Å20.0351 Å2-0.2298 Å20.0303 Å2--0.218 Å2
L0.6233 °2-0.0872 °20.12 °2-0.7634 °2-0.2833 °2--0.6393 °2
S-0.0872 Å °-0.0508 Å °0.0229 Å °0.0619 Å °-0.0333 Å °-0.0776 Å °0.0795 Å °0.0671 Å °-0.0079 Å °
Refinement TLS groupSelection details: all

+
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