[English] 日本語
Yorodumi
- PDB-2onq: Gbeta1 stabilization by in vitro evolution and computational design -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2onq
TitleGbeta1 stabilization by in vitro evolution and computational design
ComponentsImmunoglobulin G-binding protein G
KeywordsPROTEIN BINDING / beta sheet / alpha helix / improved hydrophobic packing of core residues
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMax, K.E.A. / Heinemann, U.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Optimization of the gbeta1 domain by computational design and by in vitro evolution: structural and energetic basis of stabilization.
Authors: Wunderlich, M. / Max, K.E. / Roske, Y. / Mueller, U. / Heinemann, U. / Schmid, F.X.
History
DepositionJan 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT the biological unit information is unknown for this isolated domain.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,3271
Polymers6,3271
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.412, 48.412, 107.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
Components

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6326.997 Da / Num. of mol.: 1 / Fragment: residues 373-427 / Mutation: T2Q, Y3F, L7I, T16I, T18I, T25E, V29F, V39I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria) / Strain: G148 / Gene: spg / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19909
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.91 Å3/Da / Density % sol: 35.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 50mM sodium acetate, 20mg/ml protein solution mixed in equal volume of crystallization buffer containing 33% PEG monomethylether, 0.1M calcium chloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 4, 2005 / Details: mirrors / slits
RadiationMonochromator: Graphite Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→39.05 Å / Num. all: 5583 / Num. obs: 5583 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 34.418 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 27.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 7.1 / Num. measured obs: 2733 / Num. unique all: 532 / % possible all: 100

-
Phasing

Phasing MRRfactor: 0.433 / Cor.coef. Fo:Fc: 0.528 / Cor.coef. Io to Ic: 0.555
Highest resolutionLowest resolution
Rotation3 Å8 Å
Translation3 Å8 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PGA

1pga


Resolution: 1.7→19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.212 / SU ML: 0.097 / Isotropic thermal model: ISOTROPIC + TLS Refinement / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.134 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Authors also state that the structure was refined using a combination of isotropic (atomic) and TLS refinement. The whole molecule was ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Authors also state that the structure was refined using a combination of isotropic (atomic) and TLS refinement. The whole molecule was defined as one TLS group. The atomic B-values are reported as anisotropic B-values which were calculated by combining the isotropic B-values and TLS parameters using TLSANL program from the CCP4 suite.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 256 4.6 %RANDOM
Rwork0.205 ---
all0.206 5583 --
obs0.206 5583 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.162 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms446 0 0 34 480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022453
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.941611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.181555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg50.21926.95723
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6261581
X-RAY DIFFRACTIONr_chiral_restr0.1220.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02342
X-RAY DIFFRACTIONr_nbd_refined0.20.2174
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.212
X-RAY DIFFRACTIONr_mcbond_it2.4012288
X-RAY DIFFRACTIONr_mcangle_it3.4373443
X-RAY DIFFRACTIONr_scbond_it5.0884.5194
X-RAY DIFFRACTIONr_scangle_it6.5546168
LS refinement shellResolution: 1.7→1.759 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.281 19 -
Rwork0.248 516 -
obs-535 100 %

+
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