[English] 日本語
Yorodumi
- PDB-8b2g: SH3-like domain from Penicillium virgatum muramidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b2g
TitleSH3-like domain from Penicillium virgatum muramidase
ComponentsSH3b domain-containing protein
KeywordsHYDROLASE / SH3-like / muramidase / peptidoglycan / cell wall binding domain
Biological speciesPenicillium virgatum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMoroz, O.V. / Blagova, E. / Lebedev, A.A. / Skov, L.K. / Pache, R.A. / Schnorr, K.M. / Kiemer, L. / Nymand-Grarup, S. / Ming, L. / Ye, L. ...Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Skov, L.K. / Pache, R.A. / Schnorr, K.M. / Kiemer, L. / Nymand-Grarup, S. / Ming, L. / Ye, L. / Klausen, M. / Cohn, M.T. / Schmidt, E.G.W. / Davies, G.J. / Wilson, K.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases.
Authors: Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Skov, L.K. / Pache, R.A. / Schnorr, K.M. / Kiemer, L. / Friis, E.P. / Nymand-Grarup, S. / Ming, L. / Ye, L. / Klausen, M. / Cohn, M.T. / Schmidt, ...Authors: Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Skov, L.K. / Pache, R.A. / Schnorr, K.M. / Kiemer, L. / Friis, E.P. / Nymand-Grarup, S. / Ming, L. / Ye, L. / Klausen, M. / Cohn, M.T. / Schmidt, E.G.W. / Davies, G.J. / Wilson, K.S.
History
DepositionSep 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SH3b domain-containing protein
B: SH3b domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8977
Polymers15,5832
Non-polymers3145
Water1,76598
1
A: SH3b domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9814
Polymers7,7921
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3b domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9163
Polymers7,7921
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.142, 59.824, 36.109
Angle α, β, γ (deg.)90.000, 112.131, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 74 / Label seq-ID: 1 - 74

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein SH3b domain-containing protein


Mass: 7791.546 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium virgatum (fungus) / Production host: Aspergillus oryzae (mold)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PACT C9=0.2 M LiCl, 0.1 M Hepes pH 7.0, 20% PEG 6K, MMS (microseed matrix screening) from JCSG, C7=0.2 M zinc acetate dehydrate, 0.1 M sodium acetate, 10%w/v PEG 3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.28249 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28249 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.7624
pseudo-merohedral22-L, -K, -H20.2376
ReflectionResolution: 1.5→59.82 Å / Num. obs: 21381 / % possible obs: 93.8 % / Redundancy: 4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.069 / Rrim(I) all: 0.108 / Χ2: 0.96 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.22-59.823.80.04618.31550.9950.040.0610.7198.9
1.5-1.533.20.96717310.2610.8351.2821.1266.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
xia2data reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0352refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B2S

8b2s


Resolution: 1.5→33.479 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.697 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.015 / ESU R Free: 0.014
Details: Hydrogens have been added in their riding positions twin refinement using structure amplitudes
RfactorNum. reflection% reflection
Rfree0.1725 1052 4.925 %
Rwork0.1631 20307 -
all0.164 --
obs-21359 93.218 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.849 Å2
Baniso -1Baniso -2Baniso -3
1--3.759 Å2-0 Å22.023 Å2
2--3.359 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 17 98 1200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121139
X-RAY DIFFRACTIONr_bond_other_d0.0010.016978
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.6631551
X-RAY DIFFRACTIONr_angle_other_deg0.5651.5712287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.71752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.55810158
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.3351042
X-RAY DIFFRACTIONr_chiral_restr0.0820.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
X-RAY DIFFRACTIONr_nbd_refined0.2120.2181
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.2897
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2579
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.262
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0310.22
X-RAY DIFFRACTIONr_nbd_other0.1180.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.211
X-RAY DIFFRACTIONr_mcbond_it1.9971.703600
X-RAY DIFFRACTIONr_mcbond_other1.9981.701600
X-RAY DIFFRACTIONr_mcangle_it2.8672.55750
X-RAY DIFFRACTIONr_mcangle_other2.8852.553751
X-RAY DIFFRACTIONr_scbond_it2.7351.922539
X-RAY DIFFRACTIONr_scbond_other2.7331.924540
X-RAY DIFFRACTIONr_scangle_it3.8952.778801
X-RAY DIFFRACTIONr_scangle_other3.8932.78802
X-RAY DIFFRACTIONr_lrange_it4.76834.7074882
X-RAY DIFFRACTIONr_lrange_other4.70734.2634836
X-RAY DIFFRACTIONr_ncsr_local_group_10.0930.052243
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.093070.0501
12AX-RAY DIFFRACTIONLocal ncs0.093070.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5370.344510.2731058X-RAY DIFFRACTION66.0119
1.537-1.5790.254740.2271378X-RAY DIFFRACTION88.8073
1.579-1.6250.216570.21459X-RAY DIFFRACTION93.4649
1.625-1.6750.255690.1981355X-RAY DIFFRACTION93.0719
1.675-1.730.217660.1861347X-RAY DIFFRACTION93.8247
1.73-1.790.215690.181297X-RAY DIFFRACTION94.7953
1.79-1.8580.181740.1581248X-RAY DIFFRACTION94.2939
1.858-1.9330.16600.1371250X-RAY DIFFRACTION95.7602
1.933-2.0190.148550.1461188X-RAY DIFFRACTION95.3221
2.019-2.1170.2720.1571137X-RAY DIFFRACTION96.4884
2.117-2.2310.16550.1611079X-RAY DIFFRACTION96.8403
2.231-2.3660.143440.1451030X-RAY DIFFRACTION97.019
2.366-2.5280.206610.161959X-RAY DIFFRACTION97.3282
2.528-2.730.15570.156909X-RAY DIFFRACTION97.5758
2.73-2.9880.123430.145841X-RAY DIFFRACTION97.6796
2.988-3.3380.164500.156779X-RAY DIFFRACTION98.4561
3.338-3.8480.124440.154652X-RAY DIFFRACTION98.8636
3.848-4.6970.188220.134600X-RAY DIFFRACTION99.0446
4.697-6.5780.214170.193470X-RAY DIFFRACTION99.1853
6.578-33.4790.145120.222271X-RAY DIFFRACTION98.951

+
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