[English] 日本語
Yorodumi
- PDB-6vim: P. putida mandelate racemase co-crystallized with phenylboronic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vim
TitleP. putida mandelate racemase co-crystallized with phenylboronic acid
ComponentsMandelate racemase
KeywordsISOMERASE/INHIBITOR / Inhibitor / Boronate / ISOMERASE / ISOMERASE-INHIBITOR complex
Function / homology
Function and homology information


mandelate racemase / mandelate racemase activity / mandelate catabolic process / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
Mandelate racemase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like ...Mandelate racemase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily
Similarity search - Domain/homology
PHENYL BORONIC ACID / Mandelate racemase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGrandinetti, L. / Sharma, A.N. / Bearne, S.L. / St Maurice, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-05083 Canada
CitationJournal: Biochemistry / Year: 2020
Title: Potent Inhibition of Mandelate Racemase by Boronic Acids: Boron as a Mimic of a Carbon Acid Center.
Authors: Sharma, A.N. / Grandinetti, L. / Johnson, E.R. / St Maurice, M. / Bearne, S.L.
History
DepositionJan 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mandelate racemase
B: Mandelate racemase
C: Mandelate racemase
D: Mandelate racemase
E: Mandelate racemase
F: Mandelate racemase
G: Mandelate racemase
H: Mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,53839
Polymers330,4378
Non-polymers2,10131
Water60,3143348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33580 Å2
ΔGint-184 kcal/mol
Surface area82790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.988, 150.356, 150.275
Angle α, β, γ (deg.)90.000, 129.252, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
Mandelate racemase / MR


Mass: 41304.621 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlA / Production host: Escherichia coli (E. coli) / References: UniProt: P11444, mandelate racemase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PBC / PHENYL BORONIC ACID


Mass: 121.930 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C6H7BO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.42 % / Description: cube-like crystals (~50 um x 40 um x 40 um)
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The reservoir solution consisted of PEG 4000 (10% w/v) and Bis-Tris Propane (BTP; 50 mM, pH 7.0). The protein solution consisted of 6 mg/mL P. putida MR, 1.0 mM phenylboronic acid, 3.3 mM ...Details: The reservoir solution consisted of PEG 4000 (10% w/v) and Bis-Tris Propane (BTP; 50 mM, pH 7.0). The protein solution consisted of 6 mg/mL P. putida MR, 1.0 mM phenylboronic acid, 3.3 mM MgCl2, and 50 mM HEPES buffer (pH 7.5). The protein solution and reservoir solution were mixed in a 1:1 ratio to a final volume of 10 uL
PH range: 7.0 - 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→116.57 Å / Num. obs: 262707 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.69 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 26100 / CC1/2: 0.782 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UXK

3uxk


Resolution: 2→116.37 Å / SU ML: 0.204 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6143 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1983 13014 4.96 %
Rwork0.1581 249577 -
obs0.1602 262591 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.94 Å2
Refinement stepCycle: LAST / Resolution: 2→116.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21539 0 140 3348 25027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006522310
X-RAY DIFFRACTIONf_angle_d0.757430407
X-RAY DIFFRACTIONf_chiral_restr0.04733556
X-RAY DIFFRACTIONf_plane_restr0.00523898
X-RAY DIFFRACTIONf_dihedral_angle_d3.793318183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.31924340.23898249X-RAY DIFFRACTION99.4
2.03-2.050.27954350.22378266X-RAY DIFFRACTION99.59
2.05-2.070.24474180.20468295X-RAY DIFFRACTION99.51
2.07-2.10.25424550.20128239X-RAY DIFFRACTION99.5
2.1-2.130.23924670.19748252X-RAY DIFFRACTION99.55
2.13-2.160.25144170.19458336X-RAY DIFFRACTION99.59
2.16-2.190.24584100.18998299X-RAY DIFFRACTION99.63
2.19-2.220.25093930.18498382X-RAY DIFFRACTION99.61
2.22-2.260.25933740.18848329X-RAY DIFFRACTION99.5
2.26-2.290.23374360.18478287X-RAY DIFFRACTION99.69
2.29-2.330.25513860.17338372X-RAY DIFFRACTION99.6
2.33-2.380.22684120.16528303X-RAY DIFFRACTION99.71
2.38-2.420.23114610.17448256X-RAY DIFFRACTION99.73
2.42-2.470.22214390.16628334X-RAY DIFFRACTION99.77
2.47-2.520.22443980.16678297X-RAY DIFFRACTION99.62
2.52-2.580.23184720.16658332X-RAY DIFFRACTION99.71
2.58-2.650.2154490.1638289X-RAY DIFFRACTION99.77
2.65-2.720.21014420.168279X-RAY DIFFRACTION99.78
2.72-2.80.2034170.15488421X-RAY DIFFRACTION99.81
2.8-2.890.19884580.14648255X-RAY DIFFRACTION99.76
2.89-2.990.18934090.14258369X-RAY DIFFRACTION99.82
2.99-3.110.1874520.15348331X-RAY DIFFRACTION99.76
3.11-3.250.1944460.15628298X-RAY DIFFRACTION99.74
3.25-3.430.19444840.15998312X-RAY DIFFRACTION99.69
3.43-3.640.2064830.15928247X-RAY DIFFRACTION99.78
3.64-3.920.16094420.1438372X-RAY DIFFRACTION99.88
3.92-4.320.14733930.1228431X-RAY DIFFRACTION99.91
4.32-4.940.13234650.11448348X-RAY DIFFRACTION99.95
4.94-6.220.16464130.14088445X-RAY DIFFRACTION99.91
6.22-116.370.14684540.14158352X-RAY DIFFRACTION98.19

+
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