[English] 日本語
Yorodumi
- PDB-5xnj: Crystal structure of Microcystis aeruginosa PCC 7806 aspartate/gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xnj
TitleCrystal structure of Microcystis aeruginosa PCC 7806 aspartate/glutamate racemase in complex with L-glutamate
ComponentsMcyF
KeywordsISOMERASE / aspartate/glutamate racemase / McyF / microcystin
Function / homologyracemase activity, acting on amino acids and derivatives / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / GLUTAMIC ACID / McyF
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsCao, D.D. / Zhou, K. / Jiang, Y.L. / Zhou, C.Z.
CitationJournal: To Be Published
Title: Structure-function Analyses of a Cyanobacterial Aspartate/Glutamate 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)29,3612
Polymers29,2141
Non-polymers1471
Water23413
1
A: McyF
hetero molecules

A: McyF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7214
Polymers58,4272
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2900 Å2
ΔGint-11 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.247, 129.247, 44.292
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein McyF / McyF protein


Mass: 29213.605 Da / Num. of mol.: 1 / Mutation: C87S, C195S
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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.66 Å3/Da / Density % sol: 66.35 %
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: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.82→111.93 Å / Num. obs: 10438 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Χ2: 1.402 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.82-2.875.80.4620.9190.2050.5090.84599.8
2.87-2.9260.4730.930.2030.5170.88599.8
2.92-2.986.10.410.9540.1740.4470.90298.3
2.98-3.046.40.3030.9580.1270.330.96899.6
3.04-3.16.30.2710.9710.1140.2951.02499.8
3.1-3.186.20.2360.9760.10.2571.0397.8
3.18-3.266.30.1990.9830.0850.2171.01799.4
3.26-3.346.20.180.9850.0770.1961.18799.6
3.34-3.446.10.1540.9880.0660.1681.27798.3
3.44-3.556.50.1280.9920.0530.1391.32299.8
3.55-3.6860.1040.9930.0450.1141.684100
3.68-3.8360.0970.9960.0420.1061.54399.8
3.83-45.80.0820.9960.0360.091.91299.6
4-4.216.50.0730.9970.030.0791.91199.4
4.21-4.487.10.0620.9980.0240.0661.91299.8
4.48-4.828.10.0560.9980.020.061.962100
4.82-5.318.20.0540.9980.0190.0571.67199.8
5.31-6.078.40.0520.9980.0180.0551.41999.6
6.07-7.657.40.040.9990.0150.0431.27199.8
7.65-507.80.0360.9940.0140.0391.72299.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WXX
Resolution: 2.82→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.201 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.443 / ESU R Free: 0.258
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 525 5 %RANDOM
Rwork0.1867 ---
obs0.1879 9892 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.6 Å2 / Biso mean: 68.508 Å2 / Biso min: 43.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.39 Å2-
2---0.77 Å2-0 Å2
3---2.51 Å2
Refinement stepCycle: final / Resolution: 2.82→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 10 13 1809
Biso mean--82.56 59.76 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191827
X-RAY DIFFRACTIONr_bond_other_d0.0020.021801
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9972472
X-RAY DIFFRACTIONr_angle_other_deg0.88734176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51125.78976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5715343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.675155
X-RAY DIFFRACTIONr_chiral_restr0.0650.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212011
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02368
LS refinement shellResolution: 2.817→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 40 -
Rwork0.268 699 -
all-739 -
obs--96.1 %

+
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