[English] 日本語
Yorodumi
- PDB-2qf4: High resolution structure of the major periplasmic domain from th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qf4
TitleHigh resolution structure of the major periplasmic domain from the cell shape-determining filament MreC (orthorhombic form)
ComponentsCell shape determining protein MreC
KeywordsSTRUCTURAL PROTEIN / filament a-lytic protease fold
Function / homology
Function and homology information


regulation of cell shape / plasma membrane
Similarity search - Function
Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC, domain 2 / Cell/Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC / Cell/Rod shape-determining protein MreC, domain 2 / rod shape-determining protein MreC / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cell shape-determining protein MreC
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsLovering, A.L. / Strynadka, N.C.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: High-resolution Structure of the Major Periplasmic Domain from the Cell Shape-determining Filament MreC.
Authors: Lovering, A.L. / Strynadka, N.C.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Cell shape determining protein MreC
B: Cell shape determining protein MreC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7376
Polymers36,4552
Non-polymers2824
Water7,909439
1
A: Cell shape determining protein MreC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4144
Polymers18,2271
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell shape determining protein MreC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3242
Polymers18,2271
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.247, 70.362, 89.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cell shape determining protein MreC


Mass: 18227.457 Da / Num. of mol.: 2 / Fragment: Major Periplasmic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: mreC / Plasmid: pET41 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8DMY2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na Acetate pH 4.6, 0.2M Ammonium sulfate, 12.5% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→55.385 Å / Num. obs: 99707 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 8.3
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.6 / Num. unique all: 14257 / Rsym value: 0.472 / % possible all: 98.8

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→55.385 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.045 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.167 4983 5 %RANDOM
Rwork0.144 ---
all0.145 ---
obs0.145 99637 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.2→55.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 17 439 2954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222620
X-RAY DIFFRACTIONr_bond_other_d0.0020.021650
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9663549
X-RAY DIFFRACTIONr_angle_other_deg3.13134153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.215339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72826.577111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78415493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1841511
X-RAY DIFFRACTIONr_chiral_restr0.1390.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022877
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
X-RAY DIFFRACTIONr_nbd_refined0.2240.2410
X-RAY DIFFRACTIONr_nbd_other0.1960.21822
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21291
X-RAY DIFFRACTIONr_nbtor_other0.0960.21495
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.269
X-RAY DIFFRACTIONr_mcbond_it2.0241.52133
X-RAY DIFFRACTIONr_mcbond_other0.6981.5697
X-RAY DIFFRACTIONr_mcangle_it2.44822734
X-RAY DIFFRACTIONr_scbond_it3.66231036
X-RAY DIFFRACTIONr_scangle_it4.9144.5813
X-RAY DIFFRACTIONr_rigid_bond_restr1.83734985
X-RAY DIFFRACTIONr_sphericity_free7.1693439
X-RAY DIFFRACTIONr_sphericity_bonded3.97334251
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 346 -
Rwork0.249 6779 -
obs-7125 97.42 %

+
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