[English] 日本語
Yorodumi
- PDB-6vva: N-Acetylmannosamine-6-phosphate 2-epimerase from Staphylococcus a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vva
TitleN-Acetylmannosamine-6-phosphate 2-epimerase from Staphylococcus aureus (strain MRSA USA300)
ComponentsN-acetylmannosamine-6-phosphate 2-epimerase
KeywordsISOMERASE / NanE / TIM-barrel / epimerase
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-type TIM barrel
Similarity search - Domain/homology
CITRIC ACID / Putative N-acetylmannosamine-6-phosphate 2-epimerase / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsRenwick, R.C.J. / Currie, M.J.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: N-acetylmannosamine-6-phosphate 2-epimerase uses a novel substrate-assisted mechanism to catalyze amino sugar epimerization.
Authors: Currie, M.J. / Manjunath, L. / Horne, C.R. / Rendle, P.M. / Subramanian, R. / Friemann, R. / Fairbanks, A.J. / Muscroft-Taylor, A.C. / North, R.A. / Dobson, R.C.J.
History
DepositionFeb 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 2.0Aug 11, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_keywords / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entry_details.has_ligand_of_interest / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _software.classification / _software.name / _software.version / _struct_keywords.text
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Apr 20, 2022Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description
Revision 2.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,5976
Polymers49,1422
Non-polymers4554
Water10,539585
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-14 kcal/mol
Surface area20250 Å2
Unit cell
Length a, b, c (Å)44.431, 77.067, 173.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

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


Mass: 24571.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: nanE, BTN44_01590, EP54_02960, EQ90_08785, ERS072840_01491, FA040_00085, HMPREF3211_02501, NCTC10654_00351, NCTC10702_00560, NCTC7878_00328, RK64_02155
Production host: Escherichia coli (E. coli)
References: UniProt: X5EM89, UniProt: Q2G157*PLUS, N-acylglucosamine-6-phosphate 2-epimerase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1 M trisodium citrate, 0.1 M sodium cacodylate, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.84→46.34 Å / Num. obs: 52642 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.995 / Net I/σ(I): 10.8
Reflection shellResolution: 1.84→1.906 Å / Num. unique obs: 5094 / CC1/2: 0.592

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y0E

1y0e


Resolution: 1.84→46.34 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.021 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 1993 3.8 %RANDOM
Rwork0.1797 ---
obs0.1807 50648 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.6 Å2 / Biso mean: 16.312 Å2 / Biso min: 9.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0 Å2
2---0.09 Å20 Å2
3---0.98 Å2
Refinement stepCycle: final / Resolution: 1.84→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 28 585 4053
Biso mean--33.06 30.62 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133793
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173674
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.6385192
X-RAY DIFFRACTIONr_angle_other_deg1.0991.5818526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70324.066182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73915699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0211517
X-RAY DIFFRACTIONr_chiral_restr0.0410.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
LS refinement shellResolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 142 -
Rwork0.305 3618 -
all-3760 -
obs--98.51 %

+
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://pdbjlvh1.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