[English] 日本語
Yorodumi
- PDB-1qwy: Latent LytM at 1.3 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qwy
TitleLatent LytM at 1.3 A resolution
Componentspeptidoglycan hydrolase
KeywordsHYDROLASE / LytM lysostaphin metalloprotease asparagine switch
Function / homology
Function and homology information


lysostaphin / cobalt ion binding / peptide catabolic process / nickel cation binding / cell wall organization / metalloendopeptidase activity / manganese ion binding / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #290 / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Glycyl-glycine endopeptidase LytM
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsOdintsov, S.G. / Sabala, I. / Marcyjaniak, M. / Bochtler, M.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Latent LytM at 1.3A resolution.
Authors: Odintsov, S.G. / Sabala, I. / Marcyjaniak, M. / Bochtler, M.
#1: Journal: J.Bacteriol. / Year: 1997
Title: Molecular cloning, sequencing and expression of LytM, a unique autolytic gene of Staphylococcus aureus
Authors: Ramadurai, L. / Jayaswal, R.
#2: Journal: Microbiology (Reading, Engl.) / Year: 1999
Title: Characterization of a chromosomally encoded glycylglycine endopeptidase of Staphylococcus aureus
Authors: Ramadurai, L. / Lockwood, K.J. / Nadakavukaren, M.J. / Jayaswal, R.K.
History
DepositionSep 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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_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
Remark 999SEQUENCE At the time of processing, no database sequence was available for this protein. The ...SEQUENCE At the time of processing, no database sequence was available for this protein. The sequence here is from Staphylococcus aureus NCTC8325.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: peptidoglycan hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8282
Polymers31,7621
Non-polymers651
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.332, 53.232, 51.603
Angle α, β, γ (deg.)90.00, 104.02, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe monomer in the asymmetric unit is the biological unit

-
Components

#1: Protein peptidoglycan hydrolase


Mass: 31762.350 Da / Num. of mol.: 1 / Fragment: residues 26-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Species: Staphylococcus aureus / Strain: NCTC8325 / Gene: LytM / Plasmid: pET15bmod / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O33599, lysostaphin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 1.9 Å3/Da / Density % sol: 35.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 170 mM ammonium sulfate, 25.5% (w/v) PEG 8K, 15% (v/v) glycerol, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
25 mMTris1droppH7.5
3170 mMammonium sulfate1reservoir
425.5 %(w/v)PEG80001reservoir
515 %(v/v)glycerol1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONBESSY 14.211.28335
ROTATING ANODERIGAKU21.54179
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.283351
21.541791
ReflectionResolution: 1.3→15 Å / Num. all: 54733 / Num. obs: 54733 / % possible obs: 94.05 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 6.4
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 3.5 / Num. unique all: 7719 / Rsym value: 0.174 / % possible all: 91.1
Reflection
*PLUS
% possible obs: 94 %

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.661 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.049 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18084 2781 5.1 %RANDOM
Rwork0.16271 ---
all0.16362 51945 --
obs0.16362 51945 93.76 %-
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 mean: 12.723 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-0.44 Å2
2---0.25 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 1 354 2177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211878
X-RAY DIFFRACTIONr_bond_other_d0.0020.021421
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.8842561
X-RAY DIFFRACTIONr_angle_other_deg0.77533338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022222
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02401
X-RAY DIFFRACTIONr_nbd_refined0.2040.2359
X-RAY DIFFRACTIONr_nbd_other0.2570.21720
X-RAY DIFFRACTIONr_nbtor_other0.0860.2980
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8271.51150
X-RAY DIFFRACTIONr_mcangle_it1.53421827
X-RAY DIFFRACTIONr_scbond_it2.0083728
X-RAY DIFFRACTIONr_scangle_it3.0464.5734
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.335 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.233 191
Rwork0.236 3479
Refinement
*PLUS
Highest resolution: 1.3 Å / Rfactor Rfree: 0.181 / Rfactor Rwork: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3

+
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