[English] 日本語
Yorodumi
- PDB-4p7n: Structure of Escherichia coli PgaB C-terminal domain in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p7n
TitleStructure of Escherichia coli PgaB C-terminal domain in complex with glucosamine
ComponentsPoly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
KeywordsHYDROLASE / beta alpha barrel / carbohydrate binding / glycosyl hydrolase fold / complex
Function / homology
Function and homology information


macromolecule deacylation / cell adhesion involved in biofilm formation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / single-species biofilm formation / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / hydrolase activity, hydrolyzing O-glycosyl compounds / cell outer membrane / carbohydrate metabolic process / hydrolase activity
Similarity search - Function
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, C-terminal / Hypothetical glycosyl hydrolase family 13 / : / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, C-terminal / Hypothetical glycosyl hydrolase family 13 / : / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-amino-2-deoxy-beta-D-glucopyranose / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsLittle, D.J. / Li, G. / Ing, C. / DiFrancesco, B. / Bamford, N.C. / Robinson, H. / Nitz, M. / Pomes, R. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Modification and periplasmic translocation of the biofilm exopolysaccharide poly-beta-1,6-N-acetyl-D-glucosamine.
Authors: Little, D.J. / Li, G. / Ing, C. / DiFrancesco, B.R. / Bamford, N.C. / Robinson, H. / Nitz, M. / Pomes, R. / Howell, P.L.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9794
Polymers42,4421
Non-polymers5383
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint4 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.967, 78.833, 115.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase / PgaB / Poly-beta-1 / 6-GlcNAc N-deacetylase


Mass: 42441.867 Da / Num. of mol.: 1 / Fragment: UNP residues 310-672
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pgaB, ycdR, b1023, JW5142 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P75906, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Sugar ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO5
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18% PEG3350, 0.1 M Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 31672 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 21.71 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 19.9
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 5 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: dev_1615)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4P7L

4p7l


Resolution: 1.89→39.416 Å / FOM work R set: 0.8908 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 1947 6.34 %Random
Rwork0.147 29650 --
obs0.1496 31597 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.18 Å2 / Biso mean: 26.48 Å2 / Biso min: 9.36 Å2
Refinement stepCycle: final / Resolution: 1.89→39.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 36 388 3384
Biso mean--73.15 35.1 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073078
X-RAY DIFFRACTIONf_angle_d1.0364190
X-RAY DIFFRACTIONf_chiral_restr0.046450
X-RAY DIFFRACTIONf_plane_restr0.005542
X-RAY DIFFRACTIONf_dihedral_angle_d14.131114
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8903-1.91420.28031390.20782058219799
1.9142-1.93940.2041370.201220382175100
1.9394-1.9660.25631400.187820512191100
1.966-1.9940.24161440.184520832227100
1.994-2.02380.24631430.177620762219100
2.0238-2.05540.20671380.166620462184100
2.0554-2.08910.21541410.16420992240100
2.0891-2.12510.25211430.165720702213100
2.1251-2.16380.20721380.161220052143100
2.1638-2.20540.20081450.154920782223100
2.2054-2.25040.21381360.158820672203100
2.2504-2.29930.19611410.152920682209100
2.2993-2.35280.20471410.147320622203100
2.3528-2.41170.24851410.156120552196100
2.4117-2.47690.22421410.146921162257100
2.4769-2.54970.19371340.150520222156100
2.5497-2.6320.19561430.149320812224100
2.632-2.72610.20221400.156420262166100
2.7261-2.83520.2361370.156220572194100
2.8352-2.96420.18441360.154420802216100
2.9642-3.12040.19181410.149820542195100
3.1204-3.31580.19271370.146920772214100
3.3158-3.57170.13561410.144320752216100
3.5717-3.93080.1691380.131120442182100
3.9308-4.49890.17081360.111520632199100
4.4989-5.66540.11731450.119120602205100
5.6654-39.42510.14941330.140620732206100
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)
12.12711.13561.64672.7235-0.78592.50930.01650.0858-0.022-0.08720.0951-0.1703-0.05080.607-0.11040.08910.0038-0.02070.1458-0.00070.16621.5695-11.6819-6.644
20.98290.55050.20771.5410.21781.16190.0586-0.12210.02780.1018-0.0730.0459-0.0367-0.03980.01070.1316-0.00680.00670.12390.0060.11560.7103-9.99951.0953
31.56681.11530.35995.882.7621.93010.0609-0.0946-0.00220.1729-0.17740.0649-0.0037-0.02170.14540.1474-0.00630.00460.12410.00590.09466.5102-1.6091-2.5438
42.1128-2.0795-1.19157.5473-1.46772.97560.15790.1750.0613-0.1496-0.04430.622-0.2354-0.3522-0.09510.17880.0237-0.00870.1681-0.02630.1813.431619.1774-5.7974
50.84790.09880.03744.3586-1.00531.44990.0503-0.08090.00290.1572-0.0252-0.0946-0.07090.0064-0.03330.10130.0060.02780.1625-0.00490.112810.8854.9486-4.3017
62.6782-0.91621.34774.7634-3.29382.7494-0.11590.13490.42020.0895-0.1231-0.1664-0.83460.23070.24540.28160.0079-0.00670.2320.00240.231214.245125.44-16.0254
71.4533-3.08113.17075.7745-6.51436.57010.16880.18580.0241-0.2097-0.3864-0.25090.10520.35610.27350.16150.01340.02040.1860.01870.210716.11447.5354-12.4027
82.73390.98330.60871.87540.51491.4069-0.12790.20660.1004-0.32610.03950.0308-0.0932-0.02280.08920.18820.02470.01520.13770.00560.112.73431.6772-21.9189
93.74610.74190.38413.3809-0.20072.21010.0849-0.07930.3413-0.021-0.07990.1559-0.1484-0.2085-0.05840.17620.0305-0.02720.133-0.02280.1218-4.3671-2.3274-17.967
102.40950.4267-1.07391.8619-1.12584.1059-0.03280.1399-0.1825-0.16440.04430.06420.3224-0.0494-0.01490.1603-0.005-0.01750.1359-0.01410.1296-7.4274-14.3491-18.3607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 306 through 328 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 329 through 391 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 392 through 411 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 412 through 439 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 440 through 477 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 478 through 502 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 503 through 529 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 530 through 595 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 596 through 623 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 624 through 669 )A0

+
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