[English] 日本語
Yorodumi
- PDB-3igs: Structure of the Salmonella enterica N-acetylmannosamine-6-phosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3igs
TitleStructure of the Salmonella enterica N-acetylmannosamine-6-phosphate 2-epimerase
ComponentsN-acetylmannosamine-6-phosphate 2-epimerase 2
KeywordsISOMERASE / salmonella / energy metabolism / sugars / CSGID / Carbohydrate metabolism / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


N-acetylmannosamine catabolic process / N-acylglucosamine-6-phosphate 2-epimerase / N-acylmannosamine-6-phosphate 2-epimerase activity / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
Putative N-acetylmannosamine-6-phosphate epimerase / Putative N-acetylmannosamine-6-phosphate epimerase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-16G / Putative N-acetylmannosamine-6-phosphate 2-epimerase 2
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Gordon, E. / Skarina, T. / Papazisi, L. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Structure summary
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetylmannosamine-6-phosphate 2-epimerase 2
B: N-acetylmannosamine-6-phosphate 2-epimerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,90019
Polymers49,1832
Non-polymers1,71717
Water15,817878
1
A: N-acetylmannosamine-6-phosphate 2-epimerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,60010
Polymers24,5911
Non-polymers1,0099
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-acetylmannosamine-6-phosphate 2-epimerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2999
Polymers24,5911
Non-polymers7088
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)183.29, 63.32, 41.80
Angle α, β, γ (deg.)90.00, 91.28, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein N-acetylmannosamine-6-phosphate 2-epimerase 2 / ManNAc-6-P epimerase 2


Mass: 24591.344 Da / Num. of mol.: 2 / Mutation: A129T cloning error
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: nanE2, STM3337 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZLQ7, N-acylglucosamine-6-phosphate 2-epimerase
#2: Sugar ChemComp-16G / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M ammonium sulphate, 5% isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 11, 2009 / Details: beryllium lense
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 77012 / Num. obs: 74625 / % possible obs: 96.9 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 3.3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.095 / Χ2: 1.008 / Net I/σ(I): 26.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.33 / Num. unique all: 5711 / Χ2: 0.979 / % possible all: 74.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
BLU-MAXdata collection
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→37.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.156 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.914 / SU B: 2.164 / SU ML: 0.038 / SU R Cruickshank DPI: 0.067 / SU Rfree: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.177 3757 5 %RANDOM
Rwork0.147 ---
all0.149 77152 --
obs0.148 74621 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.52 Å2 / Biso mean: 10.801 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0.08 Å2
2---0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 91 878 4363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223713
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9965100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3645500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90223.75144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71315594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3371529
X-RAY DIFFRACTIONr_chiral_restr0.0940.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212782
X-RAY DIFFRACTIONr_mcbond_it1.5851.52396
X-RAY DIFFRACTIONr_mcangle_it2.47923867
X-RAY DIFFRACTIONr_scbond_it4.48331317
X-RAY DIFFRACTIONr_scangle_it6.634.51221
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 170 -
Rwork0.233 3750 -
all-3920 -
obs-3396 70.2 %
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)
10.20770.13240.03830.43-0.06350.2306-0.00590.02770.002-0.0010.0050.026-0.04070.00070.00080.02470.00160.0270.0496-0.00720.050136.86336.6412.507
20.46770.1759-0.05760.2770.00620.3040.0081-0.00710.02960.00990.00380.02180.0095-0.056-0.01180.0106-0.00130.02110.0629-0.01220.049416.13210.39110.573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 229
2X-RAY DIFFRACTION2B0 - 229

+
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