[English] 日本語
Yorodumi
- PDB-3ru7: Specific recognition of N-acetylated substrates and domain flexib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ru7
TitleSpecific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase
ComponentsWbgU
KeywordsISOMERASE / epimerase / Rossmann fold / UDP-GalNAc / 4-epimerase / UDP-hexose 4-epimerase / UDP-hexoses / NAD(H)
Function / homology
Function and homology information


UDP-N-acetylglucosamine 4-epimerase / UDP-N-acetylglucosamine 4-epimerase activity / O antigen biosynthetic process / nucleotide binding
Similarity search - Function
UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Unknown ligand / UDP-N-acetylglucosamine 4-epimerase
Similarity search - Component
Biological speciesPlesiomonas shigelloides (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBhatt, V.S. / Guan, W. / Wang, P.G.
CitationJournal: TO BE PUBLISHED
Title: Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase
Authors: Bhatt, V.S. / Guan, W. / G Wang, P.
History
DepositionMay 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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: WbgU
B: WbgU
C: WbgU
D: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,37620
Polymers159,2884
Non-polymers3,08816
Water1,72996
1
A: WbgU
C: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,21111
Polymers79,6442
Non-polymers1,5679
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-61 kcal/mol
Surface area26400 Å2
MethodPISA
2
B: WbgU
hetero molecules

D: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1659
Polymers79,6442
Non-polymers1,5217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z+1/31
Buried area4780 Å2
ΔGint-46 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.730, 77.730, 224.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
WbgU


Mass: 39822.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plesiomonas shigelloides (bacteria) / Gene: wbgU / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BJX9

-
Non-polymers , 6 types, 112 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 298.15 K / Method: microbatch under oil / pH: 6.5
Details: 25% PEG 3350, 0.2 M Ammonium Sulfate, 200 mM Bis Tris Propane pH 6.5, microbatch under oil, temperature 298.15K

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 6, 2011
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→74.8 Å / Num. all: 46337 / Num. obs: 45596 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LU1

3lu1


Resolution: 2.6→74.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.887 / SU B: 28.765 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 2307 5.1 %RANDOM
Rwork0.21686 ---
all0.2196 43276 --
obs0.2196 43276 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.547 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.6→74.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10724 0 300 96 11120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211268
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.98215340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31651336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89323.969524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.295151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2361568
X-RAY DIFFRACTIONr_chiral_restr0.0810.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218456
X-RAY DIFFRACTIONr_mcbond_it0.3671.56676
X-RAY DIFFRACTIONr_mcangle_it0.698210796
X-RAY DIFFRACTIONr_scbond_it0.96734592
X-RAY DIFFRACTIONr_scangle_it1.6094.54544
LS refinement shellResolution: 2.605→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 168 -
Rwork0.288 3247 -
obs--99.16 %
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)
10.9945-0.06540.2051.35840.22251.0988-0.0419-0.1694-0.03470.16110.00940.16570.0357-0.10020.03250.03590.01360.0210.03690.00510.021123.165-28.777613.1317
21.2241-0.09050.32911.18060.12181.0937-0.010.14630.119-0.2081-0.0211-0.11-0.05980.10060.03110.05210.00830.01770.02820.01660.020513.345910.445814.1168
30.6073-0.19160.22041.351-0.16390.9459-0.04010.1244-0.0101-0.1523-0.01490.0220.0116-0.00350.05510.024-0.0124-0.00150.0293-0.00260.011710.0187-21.2184-25.1305
40.65630.1724-0.17121.3944-0.11240.8746-0.0278-0.13850.01260.1446-0.03340.026-0.01410.01840.06120.01920.00720.00280.0303-0.00220.010948.9182-1.1898-22.4734
54.6938-2.3032-5.43161.25791.637514.5547-0.1691-0.3549-0.03050.08250.13330.0140.0880.58490.03570.09380.045-0.05340.047-0.01540.039621.8439-21.913711.0784
614.274-14.77694.551150.42996.8235.2380.0004-0.4573-0.5655-0.0725-0.80013.5029-0.0422-0.57220.79970.20910.0754-0.03510.106-0.12480.30287.573-28.077117.8309
70.3165-0.2141-2.11821.24162.282214.835-0.03850.05470.0075-0.06780.1109-0.0170.0931-0.249-0.07240.13510.041-0.02110.0595-0.01040.0437.978115.018216.1711
839.2003-11.365246.167712.48761.363478.0371-0.9311-0.0992.8580.4302-0.05-2.3086-0.8349-0.2340.9810.17790.0604-0.02370.02380.03130.478420.438124.19199.5116
910.807713.69796.9529.90718.268410.32930.18940.0385-0.30890.4115-0.2281-0.20.2893-0.28030.03870.037-0.0029-0.02510.07510.02060.108515.1315-16.9235-21.9059
1032.29479.99381.62513.13130.51940.089-0.03921.9118-1.47270.13720.2851-0.460.04730.0399-0.24590.3393-0.2280.06150.6313-0.01210.253323.0613-29.3862-30.3531
117.6186-8.5737-5.187117.79956.715417.0227-0.0896-0.38450.0385-0.18370.19120.3841-0.1565-0.0807-0.10160.04120.0150.01940.0880.03050.100853.9935-5.494-25.6933
1274.0546-3.9057-5.12910.20650.27080.3554-0.0242-2.21410.8573-0.010.0998-0.0484-0.00390.1494-0.07560.2660.0046-0.01410.26350.15990.212861.90916.9534-17.2739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 341
2X-RAY DIFFRACTION2B1 - 341
3X-RAY DIFFRACTION3C1 - 341
4X-RAY DIFFRACTION4D1 - 341
5X-RAY DIFFRACTION5A349
6X-RAY DIFFRACTION6A350
7X-RAY DIFFRACTION7B349
8X-RAY DIFFRACTION8B350
9X-RAY DIFFRACTION9C349
10X-RAY DIFFRACTION10C350
11X-RAY DIFFRACTION11D349
12X-RAY DIFFRACTION12D350

+
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