[English] 日本語
Yorodumi
- PDB-4a1r: The Structure of Serratia marcescens Lip, a membrane bound compon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a1r
TitleThe Structure of Serratia marcescens Lip, a membrane bound component of the Type VI Secretion System.
ComponentsLIP
KeywordsMEMBRANE PROTEIN / T6SS / BETA-SANDWICH
Function / homologyType VI secretion system, lipoprotein SciN / Type VI secretion system, lipoprotein SciN / Type VI secretion protein SciN-like superfamily / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / Immunoglobulin-like / Sandwich / Mainly Beta / LIP
Function and homology information
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsRao, V.A. / Shepherd, S.M. / English, G. / Coulthurst, S.J. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: The Structure of Serratia Marcescens Lip, a Membrane-Bound Component of the Type Vi Secretion System
Authors: Rao, V.A. / Shepherd, S.M. / English, G. / Coulthurst, S.J. / Hunter, W.N.
History
DepositionSep 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Feb 29, 2012Group: Other
Revision 1.3Mar 20, 2013Group: Derived calculations
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: LIP
B: LIP
C: LIP
D: LIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4476
Polymers65,3624
Non-polymers852
Water6,017334
1
A: LIP


Theoretical massNumber of molelcules
Total (without water)16,3401
Polymers16,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIP


Theoretical massNumber of molelcules
Total (without water)16,3401
Polymers16,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3632
Polymers16,3401
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4022
Polymers16,3401
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: LIP
B: LIP


Theoretical massNumber of molelcules
Total (without water)32,6812
Polymers32,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-17.1 kcal/mol
Surface area14600 Å2
MethodPISA
6
C: LIP
D: LIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7664
Polymers32,6812
Non-polymers852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-25.4 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.730, 77.750, 54.490
Angle α, β, γ (deg.)90.00, 98.31, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
LIP


Mass: 16340.404 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: DB10 / Plasmid: PET15BTEV_SMLIP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: G5EA77*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsETHAN-1,2-DIOL (EDO): EDO D1176
Sequence detailsGENOME IS NOT YET IN ANY DATABASE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45 %
Description: THE MODEL USED FOR MOLECULAR REPLACEMENT WAS INITIALLY SOLVED USING SAD. STRUCTURE NOT DEPOSITED IN PDB.
Crystal growDetails: 15 % PEG 3350, 200 MM NACL.

-
Data collection

DiffractionMean temperature: 86 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.007
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 13, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.92→40 Å / Num. obs: 43478 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL FROM SAD EXPERIMENT

Resolution: 1.92→39.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.853 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED. C,51-52, D,51-54, B,143-146, C,144-146. RESIDUES WITH WEAK SIDE CHAIN ELECTRON DENSITY HAVE OCCUPANCY SET TO 0.01.
RfactorNum. reflection% reflectionSelection details
Rfree0.29158 2200 5.1 %RANDOM
Rwork0.22036 ---
obs0.22392 41277 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.759 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-1.03 Å2
2---0.7 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.92→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4353 0 5 334 4692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9686171
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7895552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31624.11219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34715764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7781533
X-RAY DIFFRACTIONr_chiral_restr0.10.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213476
X-RAY DIFFRACTIONr_gen_planes_other
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: 1.917→1.967 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 147 -
Rwork0.307 2857 -
obs--93.26 %

+
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