[English] 日本語
Yorodumi
- PDB-4q5t: Crystal structure of an atmB (putative membrane lipoprotein) from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q5t
TitleCrystal structure of an atmB (putative membrane lipoprotein) from Streptococcus mutans UA159 at 1.91 A resolution
ComponentsLipoprotein
KeywordsTRANSPORT PROTEIN / methionine-binding / NLPA lipoprotein / PF03180 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / membrane / Alpha Beta / SELENOMETHIONINE / Lipoprotein
Function and homology information
Biological speciesStreptococcus mutans UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.907 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an atmB (putative membrane lipoprotein) from Streptococcus mutans UA159 at 1.91 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2565
Polymers28,8161
Non-polymers1,4404
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.021, 106.053, 95.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

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

-
Components

#1: Protein Lipoprotein


Mass: 28816.438 Da / Num. of mol.: 1 / Fragment: UNP residues 24-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans UA159 (bacteria) / Strain: ATCC 700610 / UA159 / Gene: atmB, SMU_1941 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: I6L927
#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-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 25-280 OF THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.200M sodium chloride, 50.00% polyethylene glycol 400, 0.0100M Barium Chloride, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979068,0.979338,0.953725
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790681
20.9793381
30.9537251
ReflectionResolution: 1.91→28.777 Å / Num. obs: 23167 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.682 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.11
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.91-1.980.4482101724385196.6
1.98-2.060.312.7102624401199
2.06-2.150.2433.694784093196.4
2.15-2.260.1685.298174212197.7
2.26-2.410.1326.2109374652198.9
2.41-2.590.098899844228199.2
2.59-2.850.07510.6102434367198.5
2.85-3.260.04915.4102774370199.2
3.26-4.10.03124.898974280196.2
4.1-28.7770.02232.3105124406198.1

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
PHENIX1.8.2refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.907→28.777 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.21 / σ(F): 1.22 / Phase error: 23.87 / Stereochemistry target values: MLHL
Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM ...Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. LIGAND SELENOMETHIONINE HAS BEEN MODELED BASED ON DENSITY AND ANOMALOUS DIFFERENCE FOURIER MAP. 6. NONAETHYLENE GLYCOL (2PE) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflection
Rfree0.2302 1189 5.14 %
Rwork0.1827 --
obs0.185 23128 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.53 Å2 / Biso mean: 41.4479 Å2 / Biso min: 17.34 Å2
Refinement stepCycle: LAST / Resolution: 1.907→28.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 49 154 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122103
X-RAY DIFFRACTIONf_angle_d1.2392830
X-RAY DIFFRACTIONf_chiral_restr0.072319
X-RAY DIFFRACTIONf_plane_restr0.005358
X-RAY DIFFRACTIONf_dihedral_angle_d16.777813
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.907-1.99340.29291470.29412685283298
1.9934-2.09850.29891550.23622655281099
2.0985-2.22990.25951400.196627422882100
2.2299-2.4020.23521500.18152710286099
2.402-2.64360.22111530.164827432896100
2.6436-3.02580.22371580.174127552913100
3.0258-3.81080.24551490.16682755290499
3.8108-28.78050.1891370.1722894303199
Refinement TLS params.Method: refined / Origin x: 16.1157 Å / Origin y: 37.3778 Å / Origin z: 37.3935 Å
111213212223313233
T0.2627 Å20.0051 Å20.0313 Å2-0.2262 Å2-0.0008 Å2--0.2316 Å2
L0.0729 °2-0.1657 °20.2717 °2-0.6194 °20.9582 °2--1.6865 °2
S-0.0608 Å °0.0301 Å °0.0402 Å °0.1291 Å °-0.062 Å °0.0894 Å °0.5374 Å °0.0357 Å °-0.0179 Å °
Refinement TLS groupSelection details: chain A

+
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://pdbjlvh1.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