[English] 日本語
Yorodumi
- PDB-3b2m: Crystal Structure of the Major Pilin from Streptococcus pyogenes -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b2m
TitleCrystal Structure of the Major Pilin from Streptococcus pyogenes
ComponentsPutative uncharacterized protein SPy0128
KeywordsCELL ADHESION / STRUCTURAL PROTEIN / All-beta / pili / isopeptide
Function / homology
Function and homology information


pilus / extracellular region
Similarity search - Function
Sortase B signal domain, QVPTGV class / Immunoglobulin-like - #3050 / Streptococcal pilin isopeptide linker / Streptococcal pilin isopeptide linker superfamily / Spy0128-like isopeptide containing domain / Collagen-binding surface protein Cna, B-type domain / Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.22 Å
AuthorsKang, H.J. / Coulibaly, F. / Proft, T. / Baker, E.N.
CitationJournal: Science / Year: 2007
Title: Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure.
Authors: Kang, H.J. / Coulibaly, F. / Clow, F. / Proft, T. / Baker, E.N.
History
DepositionOct 18, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein SPy0128
B: Putative uncharacterized protein SPy0128
C: Putative uncharacterized protein SPy0128


Theoretical massNumber of molelcules
Total (without water)97,4403
Polymers97,4403
Non-polymers00
Water6,215345
1
A: Putative uncharacterized protein SPy0128


Theoretical massNumber of molelcules
Total (without water)32,4801
Polymers32,4801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein SPy0128


Theoretical massNumber of molelcules
Total (without water)32,4801
Polymers32,4801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein SPy0128


Theoretical massNumber of molelcules
Total (without water)32,4801
Polymers32,4801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.309, 52.308, 128.053
Angle α, β, γ (deg.)90.00, 97.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Putative uncharacterized protein SPy0128 / Major Pilin / Fibronectin-binding protein


Mass: 32480.004 Da / Num. of mol.: 3 / Fragment: Residues 18-307 / Mutation: D306V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Species: Streptococcus pyogenes / Strain: M1, SF370 / Gene: spy0128 / Plasmid: pGEX3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9A1S2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCOVALENT BOND IS FORMED BETWEEN THE LYSINE NZ AND ASPARAGINE CG, AND THE ASPARAGINE NH2 IS LOST AS ...COVALENT BOND IS FORMED BETWEEN THE LYSINE NZ AND ASPARAGINE CG, AND THE ASPARAGINE NH2 IS LOST AS AN AMMONIUM ION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium formate, 20% PEG 3350, 0.2M HEPES-HCl pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2006 / Details: Osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionRedundancy: 9.6 % / Av σ(I) over netI: 11.2 / Rmerge(I) obs: 0.083 / Χ2: 1.08 / D res high: 2.7 Å / D res low: 30 Å / Num. obs: 24369 / % possible obs: 97.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.83098.710.0411.119.2
4.615.899.110.0441.159.5
4.034.619910.0511.0259.6
3.664.0398.310.0781.0499.7
3.43.6698.610.1021.0419.7
3.23.498.110.1351.0829.7
3.043.297.910.1981.0969.7
2.913.0497.610.2851.1039.7
2.82.919710.3931.0539.7
2.72.894.110.4981.0648.9
ReflectionResolution: 2.22→66.8 Å / Num. obs: 42842 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.102 / Net I/σ(I): 13.8
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 65.2 / Num. unique all: 4037 / Χ2: 1.055 / % possible all: 92.4

-
Phasing

PhasingMethod: SIR
Phasing set
ID
1
2
Phasing MIR der

Native set-ID: 1 / Resolution: 2.22→40.36 Å

IDDer set-IDPower acentricPower centricReflection acentricReflection centric
ISO_1100400242171
ISO_220.7470.79822192687
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDPower acentricPower centricReflection acentricReflection centric
9.6740.36ISO_100435130
6.949.67ISO_100820126
5.696.94ISO_1001057123
4.945.69ISO_1001270114
4.434.94ISO_1001416109
4.054.43ISO_1001578105
3.754.05ISO_100172590
3.513.75ISO_1001868101
3.313.51ISO_1001987100
3.143.31ISO_1002106105
33.14ISO_1002196106
2.873ISO_1002275108
2.762.87ISO_1002350103
2.662.76ISO_1002482110
2.572.66ISO_1002574108
2.492.57ISO_1002601103
2.412.49ISO_1002753101
2.342.41ISO_1002806115
2.282.34ISO_1002875106
2.222.28ISO_1002850108
9.6740.36ISO_22.0191.37441354
6.949.67ISO_21.7331.48681862
5.696.94ISO_21.4651.042104960
4.945.69ISO_20.9850.864126156
4.434.94ISO_20.6870.576140252
4.054.43ISO_20.6010.527155349
3.754.05ISO_20.5630.51169442
3.513.75ISO_20.5030.531184047
3.313.51ISO_20.4980.535195648
3.143.31ISO_20.4770.618206947
33.14ISO_20.5170.557215850
2.873ISO_20.5290.513223149
2.762.87ISO_20.5390.536228644
2.662.76ISO_20.5160.723146227
2.572.66ISO_20000
2.492.57ISO_20000
2.412.49ISO_20000
2.342.41ISO_20000
2.282.34ISO_20000
2.222.28ISO_20000

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SIR / Resolution: 2.22→66.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 15.051 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic, TLS refinement / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2157 5 %RANDOM
Rwork0.2 ---
all0.203 40580 --
obs0.203 42739 97.18 %-
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: 58.205 Å2
Refinement stepCycle: LAST / Resolution: 2.22→66.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6680 0 0 345 7025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226887
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9569351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0725882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.17326.877301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.731151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.81153
X-RAY DIFFRACTIONr_chiral_restr0.0820.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025145
X-RAY DIFFRACTIONr_nbd_refined0.20.22438
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2473
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.216
X-RAY DIFFRACTIONr_mcbond_it0.6261.54421
X-RAY DIFFRACTIONr_mcangle_it1.03827058
X-RAY DIFFRACTIONr_scbond_it1.61232783
X-RAY DIFFRACTIONr_scangle_it2.6334.52280
LS refinement shellResolution: 2.223→2.281 Å / Rfactor Rfree error: 0.26 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 134 -
Rwork0.267 2754 -
all-2888 -
obs-42739 89.8 %
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)
11.68030.127-3.08321.534-0.99848.7161-0.15410.1928-0.161-0.2926-0.1996-0.04190.31570.18620.3537-0.2545-0.0193-0.0756-0.131-0.0394-0.295210.63612.44346.035
21.8164-0.4978-2.10831.78921.52697.43530.10260.33160.0843-0.3090.11880.0677-0.4092-0.2033-0.2214-0.2277-0.0603-0.0592-0.18750.0275-0.2156-2.02317.19869.449
31.4443-0.3555-4.18170.08751.029212.1074-0.0116-0.1769-0.00850.1817-0.00640.11210.29370.1640.0179-0.07370.05470.1022-0.10.0168-0.1408-10.55342.989123.145
42.64030.3469-2.32151.8705-0.39324.23270.1245-0.33230.03430.28280.01460.1612-0.14290.2136-0.139-0.22130.0001-0.0402-0.24750.0194-0.25841.55141.38794.19
52.3128-0.5447-3.91581.01481.499910.2317-0.0465-0.0556-0.02350.04130.0143-0.04660.04180.32830.0322-0.2630.0377-0.052-0.24670.023-0.304925.30915.83284.746
62.1380.5813-3.65931.4648-1.445115.5885-0.0249-0.4461-0.13050.2895-0.00330.0607-0.43170.41160.0282-0.00450.07310.0702-0.07170.0213-0.202613.0920.089128.12
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA28 - 17215 - 159
2X-RAY DIFFRACTION2AA173 - 307160 - 294
3X-RAY DIFFRACTION3BB28 - 17215 - 159
4X-RAY DIFFRACTION4BB173 - 307160 - 294
5X-RAY DIFFRACTION5CC28 - 17215 - 159
6X-RAY DIFFRACTION6CC173 - 307160 - 294

+
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