[English] 日本語
Yorodumi
- PDB-3egj: N-acetylglucosamine-6-phosphate deacetylase from Vibrio cholerae. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3egj
TitleN-acetylglucosamine-6-phosphate deacetylase from Vibrio cholerae.
ComponentsN-acetylglucosamine-6-phosphate deacetylase
KeywordsHYDROLASE / N-acetylglucosamine-6-phosphate deacetylase / Carbohydrate metabolism / IDP01616 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


N-acetylglucosamine-6-phosphate deacetylase / N-acetylgalactosamine-6-phosphate deacetylase activity / N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / protein homotetramerization / carbohydrate metabolic process / metal ion binding
Similarity search - Function
N-acetylglucosamine-6-phosphate deacetylase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...N-acetylglucosamine-6-phosphate deacetylase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-acetylglucosamine-6-phosphate deacetylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOsipiuk, J. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of N-acetylglucosamine-6-phosphate deacetylase from Vibrio cholerae.
Authors: Osipiuk, J. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetylglucosamine-6-phosphate deacetylase
B: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8546
Polymers82,5442
Non-polymers3104
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules

B: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8546
Polymers82,5442
Non-polymers3104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2440 Å2
ΔGint-53 kcal/mol
Surface area28570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.001, 77.001, 282.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

-
Components

#1: Protein N-acetylglucosamine-6-phosphate deacetylase / / GlcNAc 6-P deacetylase


Mass: 41272.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar eltor str. N16961 / Gene: nagA, VC_0994 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O32445, N-acetylglucosamine-6-phosphate deacetylase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M ammonium sulfate, 0.1 M Tris, 25% w/v Polyethylene glycol 3,350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→47.2 Å / Num. all: 19809 / Num. obs: 19809 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.211 / Net I/σ(I): 21.618
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 10 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 3.71 / Num. unique all: 957 / Χ2: 1.159 / % possible all: 97.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YRR

1yrr


Resolution: 2.9→47.2 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0.8 / FOM work R set: 0.811 / SU B: 36.805 / SU ML: 0.301 / SU R Cruickshank DPI: 0.335 / SU Rfree: 0.41 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1015 5.1 %RANDOM
Rwork0.189 ---
all0.192 19737 --
obs0.192 19737 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.15 Å2 / Biso mean: 31.293 Å2 / Biso min: 10.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.71 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5603 0 12 15 5630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225704
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9627734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9235737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.98325.542240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.86715973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.641519
X-RAY DIFFRACTIONr_chiral_restr0.1220.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214250
X-RAY DIFFRACTIONr_mcbond_it0.5441.53663
X-RAY DIFFRACTIONr_mcangle_it1.05825905
X-RAY DIFFRACTIONr_scbond_it1.70432041
X-RAY DIFFRACTIONr_scangle_it2.9464.51829
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 88 -
Rwork0.287 1310 -
all-1398 -
obs-1398 97.97 %
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)
12.1474-0.94620.29361.5222-0.12731.89950.0115-0.2960.10290.33120.0753-0.0973-0.47610.0973-0.08670.4453-0.0074-0.0490.0641-0.03740.0807-1.19747.740322.8483
24.06490.56531.58782.6057-0.19262.31160.1239-0.18040.04480.2343-0.07220.6354-0.0805-0.5772-0.05170.37740.08550.11620.1842-0.01930.2643-22.045251.035210.6862
30.7273-0.19940.4311.5913-0.47061.8715-0.02470.00950.0411-0.11020.05230.3012-0.0896-0.2576-0.02770.25980.0365-0.0260.0680.0030.1253-15.861738.30414.9477
48.01990.0107-3.21984.3298-3.2343.7105-0.24560.1657-0.67720.21360.23190.47230.0244-0.21160.01370.4314-0.07350.18370.321-0.11460.182-25.559636.960829.4219
50.9814-0.97370.21581.13740.11821.6485-0.0452-0.07910.05280.18390.0769-0.0635-0.16820.1321-0.03170.3543-0.0343-0.02020.0507-0.02360.0507-0.905839.043420.2538
61.20340.1733-0.52780.60980.35511.39980.0889-0.2228-0.09560.0033-0.0072-0.04450.07020.0173-0.08170.1388-0.0036-0.07510.07510.02870.05755.22673.739823.3003
71.1403-0.33681.84234.06522.40975.18040.18180.2-0.0420.03920.2785-0.56240.33940.569-0.46030.19350.0749-0.09610.073-0.05340.262321.0798-7.04958.6815
80.60130.02290.04251.0610.19951.0515-0.06120.0112-0.061-0.27250.058-0.1295-0.14110.14140.00310.1852-0.0155-0.04660.0265-0.00580.113416.64829.7016-0.6749
96.69985.1570.5598.3933-4.5299.95080.3647-0.7079-0.19590.1988-0.9927-1.1291-0.35361.47050.62790.1048-0.12850.01560.3663-0.00220.320833.732912.212319.1824
101.51630.3426-0.10430.6418-0.27691.41270.0082-0.1495-0.0008-0.10550.0072-0.0466-0.12760.0167-0.01550.13780.0115-0.04090.024-0.01760.03687.301110.185218.6642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 116
2X-RAY DIFFRACTION2A117 - 160
3X-RAY DIFFRACTION3A161 - 275
4X-RAY DIFFRACTION4A276 - 300
5X-RAY DIFFRACTION5A301 - 377
6X-RAY DIFFRACTION6B-1 - 96
7X-RAY DIFFRACTION7B97 - 152
8X-RAY DIFFRACTION8B153 - 275
9X-RAY DIFFRACTION9B276 - 301
10X-RAY DIFFRACTION10B302 - 377

+
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