[English] 日本語
Yorodumi
- PDB-3tlb: Microcin C7 self immunity protein MccF in complex aspartyl sulfam... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tlb
TitleMicrocin C7 self immunity protein MccF in complex aspartyl sulfamoyl adenosine
ComponentsMccF
KeywordsHYDROLASE / serine protease
Function / homology
Function and homology information


bacteriocin immunity / hydrolase activity / identical protein binding
Similarity search - Function
Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain / LD-carboxypeptidase A C-terminal domain-like / Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Glucose Oxidase; domain 1 ...Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain / LD-carboxypeptidase A C-terminal domain-like / Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Glucose Oxidase; domain 1 / Class I glutamine amidotransferase-like / 3-Layer(bba) Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-O-(L-alpha-aspartylsulfamoyl)adenosine / MccF / Microcin C7 self-immunity protein MccF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsAgarwal, V. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure and function of a serine carboxypeptidase adapted for degradation of the protein synthesis antibiotic microcin C7.
Authors: Agarwal, V. / Tikhonov, A. / Metlitskaya, A. / Severinov, K. / Nair, S.K.
History
DepositionAug 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 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_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: MccF
B: MccF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3564
Polymers83,4332
Non-polymers9232
Water15,565864
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-1 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.431, 85.675, 72.892
Angle α, β, γ (deg.)90.000, 101.310, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein MccF


Mass: 41716.586 Da / Num. of mol.: 2 / Mutation: S168A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mccF / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2KKH9, UniProt: Q47511*PLUS
#2: Chemical ChemComp-DSZ / 5'-O-(L-alpha-aspartylsulfamoyl)adenosine


Mass: 461.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N7O9S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 864 / 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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 8% ethylene glycol, 0.1 M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 282K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 99681 / % possible obs: 95.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.058 / Χ2: 0.877 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.555.30.24488600.659185
1.55-1.625.90.19798270.668194.9
1.62-1.695.90.15498600.704194.9
1.69-1.785.90.12198550.762194.8
1.78-1.895.90.09498560.808195.1
1.89-2.045.90.071100600.935196.1
2.04-2.245.90.059101510.973197.5
2.24-2.566.10.054102951.066198.6
2.56-3.236.40.051103661.06199.2
3.23-506.40.046105511.011199.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0056refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TLA

3tla


Resolution: 1.501→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.225 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.202 4974 5 %RANDOM
Rwork0.1796 ---
obs0.1807 99640 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 14.5943 Å2 / Biso min: 6.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.27 Å2
2--1.21 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.501→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5261 0 62 864 6187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225447
X-RAY DIFFRACTIONr_bond_other_d0.0020.021
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9857386
X-RAY DIFFRACTIONr_angle_other_deg0.77532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3125668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26223.929224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70515934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2331528
X-RAY DIFFRACTIONr_chiral_restr0.0670.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214046
X-RAY DIFFRACTIONr_mcbond_it0.2761.53336
X-RAY DIFFRACTIONr_mcangle_it0.5725401
X-RAY DIFFRACTIONr_scbond_it1.01132111
X-RAY DIFFRACTIONr_scangle_it1.6984.51985
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 288 -
Rwork0.237 5750 -
all-6038 -
obs--78.57 %

+
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