[English] 日本語
Yorodumi
- PDB-4bug: Pilus-presented adhesin, Spy0125 (Cpa), Cys426Ala mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bug
TitlePilus-presented adhesin, Spy0125 (Cpa), Cys426Ala mutant
ComponentsANCILLARY PROTEIN 1
KeywordsCELL ADHESION
Function / homology
Function and homology information


DNA polymerase; domain 1 - #480 / Thioester domain / Collagen-binding surface protein Cna, B-type domain / Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain ...DNA polymerase; domain 1 - #480 / Thioester domain / Collagen-binding surface protein Cna, B-type domain / Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / SH3 type barrels. / DNA polymerase; domain 1 / Roll / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWalden, M. / Crow, A. / Nelson, M. / Banfield, M.J.
CitationJournal: Proteins / Year: 2014
Title: Intramolecular Isopeptide But not Internal Thioester Bonds Confer Proteolytic and Significant Thermal Stability to the S. Pyogenes Pilus Adhesin Spy0125.
Authors: Walden, M. / Crow, A. / Nelson, M.D. / Banfield, M.J.
History
DepositionJun 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Jun 5, 2024Group: Advisory / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANCILLARY PROTEIN 1
B: ANCILLARY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)102,7382
Polymers102,7382
Non-polymers00
Water30617
1
A: ANCILLARY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)51,3691
Polymers51,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANCILLARY PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)51,3691
Polymers51,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.960, 116.860, 176.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 291 - 719 / Label seq-ID: 25 - 453

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein ANCILLARY PROTEIN 1 / SPY0125


Mass: 51368.961 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 285-723 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ISOPEPTIDE BOND BETWEEN K297 - D595, AND K610 - N715
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: SF370 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GRA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.78 % / Description: NONE
Crystal growpH: 5.75
Details: 38 - 40 % PEG 4000, 200 MM SODIUM ACETATE AND 100 MM TRI - SODIUM CITRATE PH 5.6 REMARK 280 MM MES PH 6.0 - 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→70.51 Å / Num. obs: 24374 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XIC

2xic


Resolution: 2.8→70.61 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 36.348 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26815 1240 5.1 %RANDOM
Rwork0.21102 ---
obs0.21389 23078 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.313 Å2
Baniso -1Baniso -2Baniso -3
1-7.97 Å20 Å20 Å2
2---2.53 Å20 Å2
3----5.44 Å2
Refinement stepCycle: LAST / Resolution: 2.8→70.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 0 0 17 6725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026838
X-RAY DIFFRACTIONr_bond_other_d0.0030.026396
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9669259
X-RAY DIFFRACTIONr_angle_other_deg0.845314821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.40425.767326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.768151216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8891520
X-RAY DIFFRACTIONr_chiral_restr0.0710.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027737
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021475
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6552.9813374
X-RAY DIFFRACTIONr_mcbond_other1.6542.9813373
X-RAY DIFFRACTIONr_mcangle_it2.7714.4654207
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5393.0773464
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 25709 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 91 -
Rwork0.308 1701 -
obs--100 %
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)
11.31131.4217-0.93212.064-0.07792.6113-0.0194-0.18540.0029-0.1063-0.17140.01730.18570.20920.19080.37490.02970.01870.35790.06720.38458.1422-17.7669-26.6197
20.5434-0.64420.68642.1420.42232.0134-0.11270.0663-0.02470.19770.09850.0604-0.10690.12920.01430.2388-0.0171-0.00880.3789-0.00290.45769.7767-13.72851.6972
31.575-0.184-0.4320.6841-1.58535.2533-0.436-0.0963-0.1378-0.15180.1813-0.0404-0.1537-0.59350.25470.72510.0385-0.08250.35310.01370.170939.9635-10.8316-45.1032
40.9287-1.46940.9133.3453-0.39282.4038-0.03450.1972-0.06280.1605-0.05090.0716-0.63960.62810.08540.9845-0.3347-0.13980.19970.03160.074313.433219.3687-19.8069
50.19460.3674-0.64671.261-1.37782.8240.1651-0.05050.01550.0174-0.36650.06670.00880.42310.20150.56720.14480.04850.33090.13630.279817.058313.7596-47.7546
61.4477-0.72280.47121.0631-1.21793.5911-0.1430.0483-0.14240.23370.04530.1687-0.81370.01010.09760.94180.2572-0.04150.1309-0.02190.120842.077916.7264-2.4175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A290 - 387
2X-RAY DIFFRACTION1A586 - 604
3X-RAY DIFFRACTION2A388 - 585
4X-RAY DIFFRACTION3A605 - 720
5X-RAY DIFFRACTION4B287 - 387
6X-RAY DIFFRACTION4B586 - 604
7X-RAY DIFFRACTION5B388 - 585
8X-RAY DIFFRACTION6B605 - 720

+
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