[English] 日本語
Yorodumi
- PDB-4mzp: MazF from S. aureus crystal form III, C2221, 2.7 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mzp
TitleMazF from S. aureus crystal form III, C2221, 2.7 A
ComponentsMazF mRNA interferase
KeywordsHYDROLASE / CcdB/MazF fold / ribonuclease / MazE / mRNA interferase
Function / homology
Function and homology information


rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Endoribonuclease MazF
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsZorzini, V. / Loris, R. / van Nuland, N.A.J. / Cheung, A.
Citation
Journal: Nucleic Acids Res. / Year: 2014
Title: Structural and biophysical characterization of Staphylococcus aureus SaMazF shows conservation of functional dynamics.
Authors: Zorzini, V. / Buts, L. / Sleutel, M. / Garcia-Pino, A. / Talavera, A. / Haesaerts, S. / Greve, H.D. / Cheung, A. / van Nuland, N.A. / Loris, R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization of the Staphylococcus aureus MazF mRNA interferase.
Authors: Zorzini, V. / Haesaerts, S. / Donegan, N.P. / Fu, Z. / Cheung, A.L. / van Nuland, N.A. / Loris, R.
#2: Journal: Biomol.Nmr Assign. / Year: 2011
Title: 1H, 13C, and 15N backbone and side-chain chemical shift assignment of the staphylococcal MazF mRNA interferase.
Authors: Zorzini, V. / Haesaerts, S. / Cheung, A. / Loris, R. / van Nuland, N.A.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MazF mRNA interferase
B: MazF mRNA interferase
C: MazF mRNA interferase
D: MazF mRNA interferase
E: MazF mRNA interferase
F: MazF mRNA interferase
G: MazF mRNA interferase
H: MazF mRNA interferase


Theoretical massNumber of molelcules
Total (without water)119,6188
Polymers119,6188
Non-polymers00
Water00
1
A: MazF mRNA interferase
B: MazF mRNA interferase


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-9 kcal/mol
Surface area10420 Å2
MethodPISA
2
C: MazF mRNA interferase
D: MazF mRNA interferase


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-8 kcal/mol
Surface area10520 Å2
MethodPISA
3
E: MazF mRNA interferase
F: MazF mRNA interferase


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-8 kcal/mol
Surface area10320 Å2
MethodPISA
4
G: MazF mRNA interferase
H: MazF mRNA interferase


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-8 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.881, 92.636, 222.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:62 or resseq 70:113 )
211chain B and (resseq 1:62 or resseq 70:113 )
311chain C and (resseq 1:62 or resseq 70:113 )
411chain D and (resseq 1:62 or resseq 70:113 )
511chain E and (resseq 1:62 or resseq 70:113 )
611chain F and (resseq 1:62 or resseq 70:113 )
711chain G and (resseq 1:62 or resseq 70:113 )
811chain H and (resseq 1:62 or resseq 70:113 )

-
Components

#1: Protein
MazF mRNA interferase / Endoribonuclease MazF / Toxin MazF


Mass: 14952.206 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: mazF, SA1873 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7A4G9, Hydrolases; Acting on ester bonds

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0 M (NH4)2SO4, 0.1 M NAAC pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0394 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0394 Å / Relative weight: 1
ReflectionResolution: 2.7→39.2 Å / Num. all: 25526 / Num. obs: 25526 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 13.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4(Phaser)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4(Phaser)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MZM

4mzm


Resolution: 2.702→39.2 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 1251 5.08 %random
Rwork0.2085 ---
obs0.2103 24650 94.42 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.18 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4327 Å20 Å2-0 Å2
2--5.7183 Å20 Å2
3----7.151 Å2
Refinement stepCycle: LAST / Resolution: 2.702→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6707 0 0 0 6707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147003
X-RAY DIFFRACTIONf_angle_d1.3289220
X-RAY DIFFRACTIONf_dihedral_angle_d14.2112514
X-RAY DIFFRACTIONf_chiral_restr0.0931153
X-RAY DIFFRACTIONf_plane_restr0.0071181
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A781X-RAY DIFFRACTIONPOSITIONAL
12B781X-RAY DIFFRACTIONPOSITIONAL0.068
13C778X-RAY DIFFRACTIONPOSITIONAL0.061
14D768X-RAY DIFFRACTIONPOSITIONAL0.07
15E782X-RAY DIFFRACTIONPOSITIONAL0.094
16F770X-RAY DIFFRACTIONPOSITIONAL0.051
17G779X-RAY DIFFRACTIONPOSITIONAL0.054
18H793X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7025-2.81060.32591050.27352285X-RAY DIFFRACTION84
2.8106-2.93850.31811440.2452485X-RAY DIFFRACTION92
2.9385-3.09340.27281510.23412528X-RAY DIFFRACTION93
3.0934-3.28710.31631450.23172546X-RAY DIFFRACTION95
3.2871-3.54080.24281400.21052620X-RAY DIFFRACTION96
3.5408-3.89680.22791420.19142655X-RAY DIFFRACTION96
3.8968-4.460.20031410.16812699X-RAY DIFFRACTION98
4.46-5.61650.20161510.1832720X-RAY DIFFRACTION98
5.6165-39.28420.24271320.23092861X-RAY DIFFRACTION98
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)
10.78610.0560.41220.60350.07951.1063-0.0026-0.12230.05330.02190.0198-0.13-0.13220.3708-0.00490.1574-0.0012-0.03770.1686-0.03150.1342-36.51772.807232.1085
20.85580.5654-0.00160.74740.22290.90750.0118-0.0282-0.0679-0.08750.01230.02990.11430.00850.00710.14750.0065-0.01230.0604-0.01060.1226-48.0891-10.065921.8814
30.9390.28020.51190.8519-0.02241.04420.0093-0.01890.0177-0.1341-0.08310.27350.1649-0.1733-0.09830.10870.0419-0.04450.1432-0.02470.1887-55.384319.00097.3381
40.9221-0.0626-0.74981.23830.59750.79320.00450.12550.0755-0.30180.1788-0.1957-0.11470.17670.03970.1354-0.05740.02970.1445-0.02120.1644-36.360825.5597.433
51.17940.0235-0.13751-0.88511.4059-0.0355-0.01960.2485-0.12160.0995-0.0006-0.2846-0.04220.02210.1711-0.0114-0.00680.0497-0.00890.1798-44.030953.335124.6985
61.1962-0.0743-0.42540.56240.54080.94590.1179-0.2206-0.00560.2983-0.1680.26430.2139-0.4292-0.00530.1416-0.07410.06080.1911-0.02130.1619-54.958739.802333.4907
70.4233-0.4026-0.17160.99930.26170.5921-0.1295-0.6150.37060.16740.3929-0.2178-0.12670.08090.06690.17120.055-0.03860.3702-0.31840.2655-19.873452.822448.7273
80.4442-0.3388-0.08880.3973-0.10180.2129-0.2029-0.6667-0.37870.19490.31930.2379-0.0128-0.10360.19240.13440.1831-0.16490.15710.4196-0.1842-25.26933.307146.8429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

+
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