[English] 日本語
Yorodumi
- PDB-4utw: Structural characterisation of NanE, ManNac6P C2 epimerase, from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4utw
TitleStructural characterisation of NanE, ManNac6P C2 epimerase, from Clostridium perfingens
Components(PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE) x 2
KeywordsISOMERASE / SUGAR 2-EPIMERASE / SIALIC ACID / SUGAR PHOSPHATE / ENZYME MECHANISM / CARBOHYDRATE / MUTAGENESIS / 1H NMR SPECTROSCOPY
Function / homology
Function and homology information


N-acylglucosamine-6-phosphate 2-epimerase / N-acylmannosamine-6-phosphate 2-epimerase activity / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylmannosamine metabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process
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
N-acetyl-D-glucosamine-6-phosphate / Putative N-acetylmannosamine-6-phosphate 2-epimerase / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS STR. 13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPelissier, M.C. / Sebban-Kreuzer, C. / Guerlesquin, F. / Brannigan, J.A. / Davies, G.J. / Bourne, Y. / Vincent, F.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Functional Characterization of the Clostridium Perfringens N-Acetylmannosamine-6-Phosphate 2-Epimerase Essential for the Sialic Acid Salvage Pathway
Authors: Pelissier, M.C. / Sebban-Kreuzer, C. / Guerlesquin, F. / Brannigan, J.A. / Davies, G.J. / Bourne, Y. / Vincent, F.
History
DepositionJul 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
B: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
C: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
D: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,89612
Polymers100,5574
Non-polymers1,3398
Water17,997999
1
A: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
D: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9486
Polymers50,2792
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-56.9 kcal/mol
Surface area19350 Å2
MethodPISA
2
B: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules

C: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9486
Polymers50,2792
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3540 Å2
ΔGint-55.6 kcal/mol
Surface area19360 Å2
MethodPISA
3
C: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules

B: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9486
Polymers50,2792
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3540 Å2
ΔGint-55.6 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.756, 75.584, 82.173
Angle α, β, γ (deg.)89.90, 89.91, 92.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 221
2114B1 - 221
3114C1 - 221
4114D1 - 221

-
Components

#1: Protein PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE / MANNAC-6-P EPIMERASE / N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE


Mass: 25164.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 8 CHLORIDE IONS AND 4 ACTETATE MOLECULES ARE BOUND TO THE 4 MONOMERS
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS STR. 13 (bacteria)
Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: Q0TUP9, UniProt: Q8XNZ3*PLUS, N-acylglucosamine-6-phosphate 2-epimerase
#2: Protein PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE / MANNAC-6-P EPIMERASE / N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE


Mass: 25113.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 8 CHLORIDE IONS AND 4 ACTETATE MOLECULES ARE BOUND TO THE 4 MONOMERS
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS STR. 13 (bacteria)
Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: Q0TUP9, UniProt: Q8XNZ3*PLUS, N-acylglucosamine-6-phosphate 2-epimerase
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-RFW / N-acetyl-D-glucosamine-6-phosphate


Mass: 299.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H14NO9P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.37 Å3/Da / Density % sol: 48.24 % / Description: NONE
Crystal growDetails: 0.1 M NA CACODYLATE PH 6.5, 0.2 M CA ACETATE, 24.5% (W/V) PEG 2K MME AND 5% (V/V) PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→41.1 Å / Num. obs: 63357 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.5 / % possible all: 85.9

-
Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UTT

4utt


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.458 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24805 3129 4.9 %RANDOM
Rwork0.18515 ---
obs0.18832 60227 90.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.44 Å20.23 Å2
2---0.47 Å2-0.03 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7028 0 80 999 8107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227353
X-RAY DIFFRACTIONr_bond_other_d0.0010.024963
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9879966
X-RAY DIFFRACTIONr_angle_other_deg1.005312300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26725.216301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.619151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5051537
X-RAY DIFFRACTIONr_chiral_restr0.0990.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021295
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6811.54625
X-RAY DIFFRACTIONr_mcbond_other0.2421.51887
X-RAY DIFFRACTIONr_mcangle_it1.07627513
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9432728
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8964.52430
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2695 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.330.5
2Bmedium positional0.320.5
3Cmedium positional0.380.5
4Dmedium positional0.380.5
1Amedium thermal0.692
2Bmedium thermal0.712
3Cmedium thermal0.662
4Dmedium thermal0.72
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 212 -
Rwork0.245 4219 -
obs--85.67 %
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)
11.0658-0.04360.07031.16630.1570.88930.01830.0707-0.1002-0.036-0.02530.04120.0787-0.04410.0070.0114-0.0077-0.00120.0202-0.00990.011-5.5589-2.8718-41.151
21.0353-0.036-0.05231.1608-0.14690.79280.01160.07130.1139-0.0412-0.0233-0.035-0.07220.03930.01170.0096-0.00440.0010.01730.00910.0136-0.7133-1.176-0.0141
30.76560.1281-0.04611.1123-0.18330.67-0.003-0.0214-0.16990.0043-0.01580.08480.1179-0.0280.01880.0271-0.0145-0.00010.0351-0.00670.0799-11.9651-34.975-71.6795
40.83640.18170.03261.2070.20760.6091-0.0075-0.01370.17850.0251-0.0124-0.0894-0.10840.04010.01990.0264-0.0145-0.00710.03160.0030.06445.503630.6648-30.537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 220
2X-RAY DIFFRACTION2B-8 - 220
3X-RAY DIFFRACTION3C-8 - 220
4X-RAY DIFFRACTION4D-8 - 220

+
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