[English] 日本語
Yorodumi
- PDB-4b6i: Crystal structure Rap2b (SMA2266) from Serratia marcescens -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b6i
TitleCrystal structure Rap2b (SMA2266) from Serratia marcescens
ComponentsSMA2266
KeywordsSIGNALING PROTEIN
Function / homologyType VI secretion system (T6SS), amidase immunity protein / T6SS superfamily / Type VI secretion system (T6SS), amidase immunity protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1620 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Sma2266
Function and homology information
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.95 Å
AuthorsSrikannathasan, V. / Hunter, W.N.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: New Secreted Toxins and Immunity Proteins Encoded within the Type Vi Secretion System Gene Cluster of Serratia Marcescens.
Authors: English, G. / Trunk, K. / Rao, V.A. / Srikannathasan, V. / Hunter, W.N. / Coulthurst, S.J.
History
DepositionAug 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Jul 17, 2013Group: Database references
Revision 1.4Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SMA2266
B: SMA2266
C: SMA2266
D: SMA2266


Theoretical massNumber of molelcules
Total (without water)45,8984
Polymers45,8984
Non-polymers00
Water2,882160
1
A: SMA2266
D: SMA2266


Theoretical massNumber of molelcules
Total (without water)22,9492
Polymers22,9492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-16.1 kcal/mol
Surface area10100 Å2
MethodPISA
2
B: SMA2266
C: SMA2266


Theoretical massNumber of molelcules
Total (without water)22,9492
Polymers22,9492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-15.7 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.055, 56.894, 122.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11D-2006-

HOH

-
Components

#1: Protein
SMA2266


Mass: 11474.593 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: J9PBR6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.77 % / Description: NONE
Crystal growpH: 4 / Details: 1 M LICL2, 20% PEG 6K, 0.1 M CITRIC ACID PH 4.0

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 19, 2011
RadiationMonochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→44.78 Å / Num. obs: 23682 / % possible obs: 10 % / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 2→44.78 Å / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 11.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.95→61.1 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.301 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22873 1269 5.1 %RANDOM
Rwork0.17558 ---
obs0.17824 23682 99.01 %-
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 mean: 14.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2---0.64 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.95→61.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 0 160 3344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023263
X-RAY DIFFRACTIONr_bond_other_d0.0010.022218
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.954391
X-RAY DIFFRACTIONr_angle_other_deg1.0533.0035411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.13525.595168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80315601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1561516
X-RAY DIFFRACTIONr_chiral_restr0.1150.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02642
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 79 -
Rwork0.19 1388 -
obs--87.37 %
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)
12.2211-1.027-0.36861.70760.25851.3593-0.0122-0.05220.00720.04350.0739-0.02610.1240.1599-0.06170.01230.0157-0.00560.055-0.01330.021635.788849.197911.444
21.3727-0.4490.71632.0856-0.36852.21370.05170.035-0.132-0.09410.00710.08870.25190.0808-0.05880.04350.0137-0.01780.0058-0.00820.02697.409216.624619.0653
30.9593-0.05380.01242.12760.15521.07160.08880.0386-0.0155-0.1985-0.06590.15640.0141-0.0316-0.02290.02810.0136-0.01580.0241-0.00160.01314.321832.522214.6894
41.54230.11730.07461.28670.17261.4159-0.0214-0.10840.1159-0.0129-0.01930.02710.03310.02530.04070.02020.00690.01740.021-0.00780.029420.389554.21416.0695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 119
2X-RAY DIFFRACTION2B20 - 119
3X-RAY DIFFRACTION3C18 - 119
4X-RAY DIFFRACTION4D18 - 119

+
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