[English] 日本語
Yorodumi
- PDB-9blp: T450S mutant of repeat domain 2 from Clostridium perfringens adhe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9blp
TitleT450S mutant of repeat domain 2 from Clostridium perfringens adhesin CPE0147 with intramolecular ester bond
ComponentsSurface anchored protein
KeywordsUNKNOWN FUNCTION / repeat domain / adhesin / bacterial adhesion / Ig-like domain
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
T-Q ester bond containing domain / T-Q ester bond containing domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Putative surface anchored protein
Similarity search - Component
Biological speciesClostridium perfringens B str. ATCC 3626 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSquire, C.J. / Yosaatmadja, Y.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: To Be Published
Title: T450C mutant of repeat domain 2 from Clostridium perfringens adhesin CPE0147 without intramolecular ester bond
Authors: Squire, C.J. / Yosaatmadja, Y.
History
DepositionMay 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Surface anchored protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1294
Polymers16,9871
Non-polymers1423
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.907, 44.166, 64.704
Angle α, β, γ (deg.)90.000, 110.107, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Surface anchored protein


Mass: 16986.559 Da / Num. of mol.: 1 / Fragment: Repeat domain 2, residues 439-587 / Mutation: T450S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens B str. ATCC 3626 (bacteria)
Gene: AC1_0147 / Plasmid: pPROEXHTa / Production host: Escherichia coli (E. coli) / References: UniProt: B1R775
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium thiocyanate and 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→17.86 Å / Num. obs: 44396 / % possible obs: 97.7 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rpim(I) all: 0.018 / Net I/σ(I): 20.2
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2119 / CC1/2: 0.947 / Rpim(I) all: 0.186 / % possible all: 93.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→17.86 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.068 / SU ML: 0.022 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1584 2117 4.769 %random selection
Rwork0.142 42278 --
all0.143 ---
obs-44395 97.449 %-
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: 13.799 Å2
Baniso -1Baniso -2Baniso -3
1-0.042 Å20 Å20.018 Å2
2---0.019 Å20 Å2
3----0.029 Å2
Refinement stepCycle: LAST / Resolution: 1.2→17.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 6 197 1275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131241
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161166
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.6431707
X-RAY DIFFRACTIONr_angle_other_deg1.4031.5952710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.76127.74262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48815220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.984151
X-RAY DIFFRACTIONr_chiral_restr0.0630.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021516
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02258
X-RAY DIFFRACTIONr_nbd_refined0.2810.2225
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.21068
X-RAY DIFFRACTIONr_nbtor_refined0.150.2557
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2568
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2124
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.24
X-RAY DIFFRACTIONr_nbd_other0.1860.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.217
X-RAY DIFFRACTIONr_mcbond_it0.7041.205639
X-RAY DIFFRACTIONr_mcbond_other0.7021.205638
X-RAY DIFFRACTIONr_mcangle_it1.0141.818812
X-RAY DIFFRACTIONr_mcangle_other1.0131.818813
X-RAY DIFFRACTIONr_scbond_it1.0751.435602
X-RAY DIFFRACTIONr_scbond_other1.081.437603
X-RAY DIFFRACTIONr_scangle_it1.3932.064882
X-RAY DIFFRACTIONr_scangle_other1.3922.065883
X-RAY DIFFRACTIONr_lrange_it2.36216.4821362
X-RAY DIFFRACTIONr_lrange_other1.94515.3631305
X-RAY DIFFRACTIONr_rigid_bond_restr0.71932407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.2211590.1882975X-RAY DIFFRACTION94.1707
1.231-1.2650.2161440.1693003X-RAY DIFFRACTION95.7117
1.265-1.3020.1781430.1582928X-RAY DIFFRACTION96.0588
1.302-1.3420.1731370.1352807X-RAY DIFFRACTION96.3036
1.342-1.3860.171360.1322761X-RAY DIFFRACTION96.7279
1.386-1.4340.1511400.1172677X-RAY DIFFRACTION97.1379
1.434-1.4880.1411230.1122573X-RAY DIFFRACTION97.1532
1.488-1.5490.1561390.1142500X-RAY DIFFRACTION97.8495
1.549-1.6180.1491350.1172405X-RAY DIFFRACTION97.9183
1.618-1.6970.1341120.1232313X-RAY DIFFRACTION98.2577
1.697-1.7880.1431100.1212204X-RAY DIFFRACTION98.51
1.788-1.8970.1551280.1272073X-RAY DIFFRACTION98.9213
1.897-2.0280.1331080.1271980X-RAY DIFFRACTION99.0982
2.028-2.190.146870.1331853X-RAY DIFFRACTION99.182
2.19-2.3990.163810.1341709X-RAY DIFFRACTION99.5551
2.399-2.6810.162670.151562X-RAY DIFFRACTION99.694
2.681-3.0950.194600.1521381X-RAY DIFFRACTION99.8614
3.095-3.7880.156540.1431168X-RAY DIFFRACTION99.5925
3.788-5.3470.118340.165908X-RAY DIFFRACTION97.4147
5.347-17.860.255200.241498X-RAY DIFFRACTION93.8406

+
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