[English] 日本語
Yorodumi
- PDB-3up9: Crystal structure of a putative lipoprotein (ACTODO_00931) from A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3up9
TitleCrystal structure of a putative lipoprotein (ACTODO_00931) from Actinomyces odontolyticus ATCC 17982 at 2.35 A resolution
ComponentsPutative uncharacterized protein
KeywordsMETHIONINE-BINDING PROTEIN / MEMBRANE LIPOPROTEIN / L-METHIONINE BINDING PROTEIN / NLPA lipoprotein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Lipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SELENOMETHIONINE / Lipoprotein
Similarity search - Component
Biological speciesActinomyces odontolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein ACTODO_00931 (hypothetical protein ACTODO_00931, SP17422A, P_02044074.1) from Actinomyces odontolyticus ATCC 17982 at 2.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7807
Polymers26,4521
Non-polymers1,3276
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.917, 95.917, 93.781
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Putative uncharacterized protein


Mass: 26452.207 Da / Num. of mol.: 1 / Fragment: UNP residues 33-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomyces odontolyticus (bacteria) / Gene: ACTODO_00931 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7BBB2
#2: Chemical ChemComp-MSE / SELENOMETHIONINE


Type: L-peptide linking / Mass: 196.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2Se
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 34-277 OF THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20.00% polyethylene glycol 1000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.35→29.722 Å / Num. all: 17718 / Num. obs: 17718 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 35.424 Å2 / Rsym value: 0.181 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.35-2.414.90.9590.8641712970.959100
2.41-2.484.90.8450.9620812590.845100
2.48-2.5550.7211.1613012340.72199.9
2.55-2.634.90.5991.3592911990.599100
2.63-2.714.90.4981.5583311790.498100
2.71-2.814.90.451.7550211180.45100
2.81-2.914.90.3512.2536410890.351100
2.91-3.034.90.2842.7524010610.284100
3.03-3.174.90.2253.4507610280.225100
3.17-3.324.90.1734.446029470.173100
3.32-3.54.90.1395.444319050.139100
3.5-3.724.90.1136.643338890.113100
3.72-3.974.80.17.238778020.1100
3.97-4.294.80.0838.636767660.083100
4.29-4.74.70.0739.732576860.073100
4.7-5.254.60.079.929706400.07100
5.25-6.074.60.092826135670.092100
6.07-7.4350.088.924254820.08100
7.43-10.5150.03817.918553700.038100
10.51-29.7224.80.03718.59652000.03795.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
PHENIXrefinement
SCALA3.3.20data scaling
MolProbity3beta29model building
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TQW

3tqw


Resolution: 2.35→29.722 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.78 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A SELENO-METHIONINE AMINO ACID HAS BEEN MODELED AS A LIGAND BASED ON THE ELECTRON DENSITY. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. ANOMALOUS DIFFERENCE FOURIERS MAP SUPPORTS THE MODELING OF MET AS MSE. 6. PEG FRAGMENTS (PE4, PG4) FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTIONS ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 901 5.1 %RANDOM
Rwork0.1565 ---
obs0.1589 17706 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 101.65 Å2 / Biso mean: 46.3306 Å2 / Biso min: 28.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 62 122 2014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021940
X-RAY DIFFRACTIONr_bond_other_d0.0020.021271
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9812625
X-RAY DIFFRACTIONr_angle_other_deg1.07633151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2825243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.57726.62989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39515307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.927153
X-RAY DIFFRACTIONr_chiral_restr0.0990.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 65 -
Rwork0.216 1189 -
all-1254 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 31.491 Å / Origin y: 33.409 Å / Origin z: 57.987 Å
111213212223313233
T0.1591 Å20.034 Å2-0.0037 Å2-0.1864 Å20.0116 Å2--0.0197 Å2
L1.8701 °21.188 °20.154 °2-2.296 °20.2567 °2--1.0186 °2
S0.0668 Å °0.011 Å °0.1263 Å °0.0693 Å °0.0102 Å °0.0038 Å °0.0616 Å °0.0245 Å °-0.077 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