[English] 日本語
Yorodumi
- PDB-4a1j: Ykud L,D-transpeptidase from B.subtilis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a1j
TitleYkud L,D-transpeptidase from B.subtilis
ComponentsPUTATIVE L, D-TRANSPEPTIDASE YKUD
KeywordsTRANSFERASE
Function / homology
Function and homology information


spore wall / Transferases / peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / sporulation resulting in formation of a cellular spore / glycosyltransferase activity / cell wall organization / regulation of cell shape
Similarity search - Function
Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / LysM domain superfamily ...Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / LysM domain superfamily / Lysin motif / LysM domain / LysM domain profile. / LysM domain / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Putative L,D-transpeptidase YkuD
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBlaise, M. / Fuglsang Midtgaard, S. / Roi Midtgaard, S. / Boesen, T. / Thirup, S.
CitationJournal: To be Published
Title: Structure of Ykud
Authors: Blaise, M. / Fuglsang Midtgaard, S. / Roi Midtgaard, S. / Boesen, T. / Thirup, S.
History
DepositionSep 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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 / 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 / _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: PUTATIVE L, D-TRANSPEPTIDASE YKUD
B: PUTATIVE L, D-TRANSPEPTIDASE YKUD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7858
Polymers35,2082
Non-polymers5766
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-111.6 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.240, 86.280, 74.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein PUTATIVE L, D-TRANSPEPTIDASE YKUD / YKUD L\ / D TRANSPEPTIDASE / SPORE PROTEIN YKUD


Mass: 17604.230 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O34816, Transferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 117 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 118 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, LYS 117 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 118 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 117 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 118 TO ALA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.85 % / Description: NONE
Crystal growDetails: 100 MM BIS-TRIS PH 5.5, 200 MM AMSO4, 25 % PEG 3350 AND 2 MM MURNAC MONOSACCHARIDE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.28
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.2→74.4 Å / Num. obs: 18649 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Biso Wilson estimate: 20.81 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 6.5 / % possible all: 88.7

-
Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y7M

1y7m


Resolution: 2.2→47.115 Å / SU ML: 0.47 / σ(F): 1.99 / Phase error: 24.26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2437 1862 10 %
Rwork0.1922 --
obs0.1974 18627 98.34 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.704 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0528 Å20 Å20 Å2
2--2.5823 Å20 Å2
3---1.7376 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 30 166 2673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082554
X-RAY DIFFRACTIONf_angle_d1.0723486
X-RAY DIFFRACTIONf_dihedral_angle_d12.917922
X-RAY DIFFRACTIONf_chiral_restr0.072406
X-RAY DIFFRACTIONf_plane_restr0.005444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25960.48921360.43631218X-RAY DIFFRACTION94
2.2596-2.32610.53511250.42791123X-RAY DIFFRACTION88
2.3261-2.40120.2591420.20521286X-RAY DIFFRACTION100
2.4012-2.4870.25541430.18531285X-RAY DIFFRACTION100
2.487-2.58650.30621430.18881295X-RAY DIFFRACTION100
2.5865-2.70420.26331440.19981290X-RAY DIFFRACTION100
2.7042-2.84680.25851430.20291292X-RAY DIFFRACTION100
2.8468-3.02510.24741450.19541300X-RAY DIFFRACTION100
3.0251-3.25870.24881450.18411310X-RAY DIFFRACTION100
3.2587-3.58650.21551460.16921304X-RAY DIFFRACTION100
3.5865-4.10520.21441450.16021310X-RAY DIFFRACTION98
4.1052-5.17110.15961480.12561338X-RAY DIFFRACTION100
5.1711-47.12540.17711570.1581414X-RAY DIFFRACTION99
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)
11.91340.8044-0.3731.3226-0.00681.9347-0.21890.0913-0.2328-0.1164-0.0301-0.14810.0527-0.095-0.01090.095-0.0185-0.00190.0740.01280.0853-12.537816.4547-1.8673
21.06880.6157-0.72790.7048-0.16180.6852-0.0646-0.0591-0.22310.1813-0.2083-0.4196-0.01210.3185-0.42920.14990.0363-0.06380.14030.04110.1846-8.797614.63066.6728
30.48240.1580.65910.10990.28360.99230.0213-0.16920.0133-0.0371-0.0149-0.051-0.0805-0.3750.10230.0899-0.00540.03260.10.0150.0667-26.58215.3025-5.5686
41.8723-0.5517-0.62291.11460.29771.788-0.03830.0397-0.181-0.10130.00790.03040.0806-0.12010.06990.08140.00470.03950.0747-0.02290.0938-27.16828.1999-20.7412
51.2927-0.12520.46491.04080.64571.56280.0940.17240.2318-0.26010.0569-0.0799-0.38570.039-0.05950.10850.00220.06420.09980.02280.1443-19.898417.1001-22.0451
63.6393-0.7212-3.50671.57640.59293.38730.06710.4574-0.0727-0.2727-0.19390.01930.0522-0.283-0.29050.25620.04350.01860.14380.06690.1469-30.583921.1605-23.0132
72.0564-0.8081-0.33095.81021.01743.5507-0.0731-0.3482-0.27490.0725-0.095-0.04770.3320.051-0.17180.0456-0.00720.0090.19750.04350.112-25.809511.042-12.6694
84.3482-0.81861.94191.3332-0.75062.2463-0.10220.16840.3249-0.14470.03520.1288-0.0698-0.12530.07160.16320.0189-0.14680.15510.0240.2281-6.087138.8615-16.1261
90.9373-0.1595-0.79040.68180.84551.5633-0.03490.02050.10830.2031-0.00470.19540.0236-0.14670.02860.07940.089-0.00330.0189-0.05780.083-11.758333.0601-9.9616
101.3036-0.2597-0.54670.8298-0.10570.859-0.0999-0.00180.24080.120.0832-0.0435-0.04520.0076-0.04850.0863-0.00840.00280.11560.01980.05071.220933.3634-15.9256
113.7663.76112.54485.58382.86752.58860.06040.20680.5084-0.0619-0.051-0.13020.15030.1994-0.1220.1697-0.0068-0.02490.2685-0.04170.226415.585423.1038-21.4974
122.42291.12990.38742.62240.56890.6188-0.22090.6102-0.0218-0.75590.22820.6843-0.1477-0.37910.11240.2922-0.0122-0.06950.3580.01530.2506-4.47321.5728-31.3368
132.04730.4466-0.02182.85940.66761.56960.18120.0072-0.15910.1648-0.2167-0.0180.062-0.3169-0.01710.11410.0008-0.00520.1379-0.02790.1358-2.632419.9753-15.9359
140.85210.02470.04641.87080.06891.1716-0.02790.1918-0.2283-0.0658-0.0495-0.210.0832-0.1518-0.01840.12250.02370.01950.1545-0.07520.15112.875917.3258-22.2084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 0:29)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 30:41)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 42:61)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 62:92)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 93:143)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 144:153)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 154:164)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 0:11)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 12:29)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 30:71)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 72:80)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 81:92)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 93:120)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 121:164)

+
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