[English] 日本語
Yorodumi
- PDB-4z3i: Crystal structure of the lectin domain of PapG from E. coli BI47 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z3i
TitleCrystal structure of the lectin domain of PapG from E. coli BI47 in spacegroup P21212
ComponentsPapG, lectin domain
KeywordsSUGAR BINDING PROTEIN / UPEC / urinary tract infection / fimbrial adhesin / adhesin / type I pili / PapG / carbohydrate binding
Function / homology
Function and homology information


carbohydrate binding / cell adhesion / metal ion binding
Similarity search - Function
Bacterial adhesin receptor binding domain / PapG, carbohydrate-binding domain / PapG, carbohydrate-binding domain superfamily / PapG carbohydrate binding domain / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PapG, lectin domain / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.739 Å
AuthorsJakob, R.P. / Navarra, G. / Zihlmann, P. / Stangier, K. / Preston, R.C. / Rabbani, S. / Maier, T. / Ernst, B.
CitationJournal: Chembiochem / Year: 2017
Title: Carbohydrate-Lectin Interactions: An Unexpected Contribution to Affinity.
Authors: Navarra, G. / Zihlmann, P. / Jakob, R.P. / Stangier, K. / Preston, R.C. / Rabbani, S. / Smiesko, M. / Wagner, B. / Maier, T. / Ernst, B.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 17, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PapG, lectin domain


Theoretical massNumber of molelcules
Total (without water)22,7561
Polymers22,7561
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by software
  • MONOMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.992, 83.981, 45.356
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-402-

HOH

-
Components

#1: Protein PapG, lectin domain


Mass: 22755.660 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: G801_04654, G801_04690 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ADA494 / References: UniProt: T7DCJ2, UniProt: A0A182DW20*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10 % PEG10000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.739→46.006 Å / Num. all: 40944 / Num. obs: 21919 / % possible obs: 98.1 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.5
Reflection shellResolution: 1.739→1.8 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.6 / % possible all: 84.2

-
Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 18JS

18js


Resolution: 1.739→46.006 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 2059 5.03 %
Rwork0.1579 --
obs0.1598 40944 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.739→46.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 0 254 1867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111670
X-RAY DIFFRACTIONf_angle_d1.2932275
X-RAY DIFFRACTIONf_dihedral_angle_d11.879595
X-RAY DIFFRACTIONf_chiral_restr0.056232
X-RAY DIFFRACTIONf_plane_restr0.007293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7388-1.77920.3266980.29961920X-RAY DIFFRACTION72
1.7792-1.82370.27091390.26332634X-RAY DIFFRACTION100
1.8237-1.8730.29421380.23342634X-RAY DIFFRACTION100
1.873-1.92810.21681400.2062637X-RAY DIFFRACTION100
1.9281-1.99040.24451360.20032637X-RAY DIFFRACTION100
1.9904-2.06150.21191360.15672639X-RAY DIFFRACTION100
2.0615-2.1440.19031390.1532657X-RAY DIFFRACTION100
2.144-2.24160.20261390.15722631X-RAY DIFFRACTION100
2.2416-2.35980.19631410.15292628X-RAY DIFFRACTION100
2.3598-2.50760.21241420.15352672X-RAY DIFFRACTION100
2.5076-2.70120.21171420.1552621X-RAY DIFFRACTION100
2.7012-2.9730.2141380.15122646X-RAY DIFFRACTION100
2.973-3.40310.16141420.14592651X-RAY DIFFRACTION100
3.4031-4.28710.19071400.1242636X-RAY DIFFRACTION100
4.2871-46.02230.15621490.15522642X-RAY DIFFRACTION100
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)
10.8971-0.2087-0.78681.11031.01313.6921-0.038-0.0502-0.05570.01170.0011-0.03590.03620.2066-0.02170.08750.00240.00030.10510.03410.14912.76977.882413.572
22.72480.8822-3.79411.6139-1.0918.1470.06010.0095-0.00550.1376-0.0420.0863-0.1134-0.16080.00680.15030.01870.00970.1449-0.01260.15180.373819.228129.0419
32.776-0.5206-0.63171.16470.81443.41950.12040.06180.2093-0.1133-0.09460.089-0.3777-0.15-0.04060.16730.02010.00240.13790.01730.15243.53319.113213.0559
44.8203-1.9871-3.97111.75891.68025.48240.11040.12840.2679-0.15340.0114-0.17-0.15430.067-0.10530.1611-0.0042-0.00850.12150.02310.171113.034112.78595.1267
51.2909-0.0525-0.71440.68290.95172.6197-0.1026-0.0053-0.0648-0.00070.0683-0.07010.22920.470.01470.18650.04920.01850.24910.05880.221419.24342.2399.9173
63.1334-1.7274-4.57961.56962.00297.26790.2191-0.03280.12260.06120.04450.0126-0.37040.1221-0.22620.21-0.01470.00730.182-0.02340.18052.457523.541831.8998
70.4661-0.2755-0.54311.20321.17571.9411-0.0402-0.02120.02330.1404-0.00590.01830.0840.07790.03120.1335-00.00250.13370.01410.13757.509910.766518.6027
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 111 )
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 133 )
6X-RAY DIFFRACTION6chain 'A' and (resid 134 through 146 )
7X-RAY DIFFRACTION7chain 'A' and (resid 147 through 196 )

+
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