[English] 日本語
Yorodumi
- PDB-5xnk: Crystal structure of Microcystis aeruginosa PCC 7806 aspartate ra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xnk
TitleCrystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with DL-methyl-aspartate
ComponentsMcyF
KeywordsISOMERASE / aspartate racemase / McyF / microcystin
Function / homologyamino-acid racemase activity / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / (2S,3S)-3-methyl-aspartic acid / 3-METHYL-BETA-D-ASPARTIC ACID / McyF
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsCao, D.D. / Zhou, K. / Jiang, Y.L. / Zhou, C.Z.
CitationJournal: To Be Published
Title: Structure-function Analyses of a Cyanobacterial Aspartate Racemase Reveal Its Catalytic Mechanism and Substrate Specificity
Authors: Cao, D.D. / Zhou, C.Z.
History
DepositionMay 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: McyF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5243
Polymers29,2301
Non-polymers2942
Water724
1
A: McyF
hetero molecules

A: McyF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0486
Polymers58,4592
Non-polymers5894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2870 Å2
ΔGint-12 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.046, 129.046, 43.898
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein McyF / McyF protein


Mass: 29229.668 Da / Num. of mol.: 1 / Mutation: C87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa PCC 7806 (bacteria)
Gene: mcyF, IPF_371 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RNB4
#2: Chemical ChemComp-2AS / (2S,3S)-3-methyl-aspartic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4 / Comment: antibiotic*YM
#3: Chemical ChemComp-ACB / 3-METHYL-BETA-D-ASPARTIC ACID / (3S)-3-methyl-D-aspartic acid / D-METHYL ASPARTIC ACID


Type: D-beta-peptide, C-gamma linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.61 Å3/Da / Density meas: 34.76 Mg/m3 / Density % sol: 65.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) polyethylene glycol 3350, 0.2 magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 3.4→111.76 Å / Num. obs: 5683 / % possible obs: 96.1 % / Redundancy: 4.8 % / Net I/σ(I): 9.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WXX

5wxx


Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 22.046 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21735 274 4.8 %RANDOM
Rwork0.17895 ---
obs0.18085 5409 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.789 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å2-0.8 Å2-0 Å2
2---1.6 Å2-0 Å2
3---5.19 Å2
Refinement stepCycle: 1 / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 20 4 1810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191836
X-RAY DIFFRACTIONr_bond_other_d0.0020.021808
X-RAY DIFFRACTIONr_angle_refined_deg1.1722.0052485
X-RAY DIFFRACTIONr_angle_other_deg0.85134190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6435226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07525.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.421155
X-RAY DIFFRACTIONr_chiral_restr0.0580.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212021
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02370
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_it2.868.445913
X-RAY DIFFRACTIONr_mcbond_other2.868.445913
X-RAY DIFFRACTIONr_mcangle_it4.7512.651136
X-RAY DIFFRACTIONr_mcangle_other4.74912.651136
X-RAY DIFFRACTIONr_scbond_it2.7058.82923
X-RAY DIFFRACTIONr_scbond_other2.7048.82923
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.67913.0841350
X-RAY DIFFRACTIONr_long_range_B_refined8.50965.7451989
X-RAY DIFFRACTIONr_long_range_B_other8.5165.7591989
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.405→3.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 26 -
Rwork0.255 367 -
obs--94.02 %

+
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