[English] 日本語
Yorodumi
- PDB-9p1b: P. putida mandelate racemase co-crystallized with tavaborole -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9p1b
TitleP. putida mandelate racemase co-crystallized with tavaborole
ComponentsMandelate racemase
KeywordsISOMERASE / inhibitor / boronic acid
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
: / Mandelate racemase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJabin, A. / Hayden, J.A. / Bearne, S.L. / St Maurice, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-04282 Canada
CitationJournal: Biochemistry / Year: 2026
Title: Inhibition of Mandelate Racemase by Boron-Based Inhibitors: Different Binding Modes for Benzoxaboroles Versus Boronic Acids.
Authors: Hayden, J.A. / Jabin, A. / Kuehm, O.P. / Moncrief, J.G. / St Maurice, M. / Bearne, S.L.
History
DepositionJun 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mandelate racemase
B: Mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,27211
Polymers82,6092
Non-polymers6639
Water11,746652
1
A: Mandelate racemase
B: Mandelate racemase
hetero molecules

A: Mandelate racemase
B: Mandelate racemase
hetero molecules

A: Mandelate racemase
B: Mandelate racemase
hetero molecules

A: Mandelate racemase
B: Mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,08844
Polymers330,4378
Non-polymers2,65136
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area30900 Å2
ΔGint-66 kcal/mol
Surface area83470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.646, 150.646, 177.551
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-792-

HOH

-
Components

#1: Protein Mandelate racemase / MR


Mass: 41304.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: wild-type MR gene product is encoded with an N-terminal StrepII tag
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11444, mandelate racemase
#2: Chemical ChemComp-A1CF8 / Tavaborole / 5-fluoro-2,1-benzoxaborol-1(3H)-ol


Mass: 151.931 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6BFO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Reservoir solution: PEG3350 (9% w/v), HEPES (50mM; pH 8.0) Protein solution: mandelate racemase (10 mg/ml) + 500uM Tavaborole in 100mM HEPES, pH 7.5, 3.3mM MgCl2 2 uL of protein solution was ...Details: Reservoir solution: PEG3350 (9% w/v), HEPES (50mM; pH 8.0) Protein solution: mandelate racemase (10 mg/ml) + 500uM Tavaborole in 100mM HEPES, pH 7.5, 3.3mM MgCl2 2 uL of protein solution was mixed with 2 uL of well solution. Cube-like crystals grew spontaneously over 18-25 days. Crystals were equilibrated in synthetic stabilizing solution (10% w/v PEG3350, 50 mM HEPES, pH 8.0, 5 mM MgCl2, 500 uM Tavaborole, 5% v/v ethylene glycol) for 5 minutes and then transferred directly to cryoprotectant solution (10% w/v PEG3350, 50 mM HEPES, pH 8.0, 5 mM MgCl2, 500 uM Tavaborole, 20% v/v ethylene glycol) for 5 minutes prior to flash freezing in liquid nitrogen.
Temp details: ambient room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.618→114.87 Å / Num. obs: 81806 / % possible obs: 85.6 % / Redundancy: 14.5 % / Biso Wilson estimate: 8.45 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.063 / Rrim(I) all: 0.249 / Net I/σ(I): 7.2
Reflection shellResolution: 1.618→1.833 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4090 / CC1/2: 0.769 / Rpim(I) all: 0.257 / Rrim(I) all: 0.655 / % possible all: 42

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→57.44 Å / SU ML: 0.1927 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 3977 5.02 %
Rwork0.2 75204 -
obs0.2018 79181 84.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→57.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5390 0 44 652 6086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01135602
X-RAY DIFFRACTIONf_angle_d1.0437635
X-RAY DIFFRACTIONf_chiral_restr0.0611889
X-RAY DIFFRACTIONf_plane_restr0.0092978
X-RAY DIFFRACTIONf_dihedral_angle_d15.61582042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.30151780.26713323X-RAY DIFFRACTION37.78
1.86-1.940.25863040.23055765X-RAY DIFFRACTION65.29
1.94-2.030.28083700.22316989X-RAY DIFFRACTION79.25
2.03-2.130.24163920.19757265X-RAY DIFFRACTION81.92
2.13-2.270.23613960.19567514X-RAY DIFFRACTION84.96
2.27-2.440.25744090.21258251X-RAY DIFFRACTION92.68
2.44-2.690.26484810.22558865X-RAY DIFFRACTION99.77
2.69-3.080.2574640.22268942X-RAY DIFFRACTION99.88
3.08-3.880.22234600.18749016X-RAY DIFFRACTION99.95
3.88-57.440.17935230.15949274X-RAY DIFFRACTION99.92

+
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