[English] 日本語
Yorodumi
- PDB-8qdf: Engineered LmrR with Met-89 replaced by para-boronophenylalanine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qdf
TitleEngineered LmrR with Met-89 replaced by para-boronophenylalanine
ComponentsTranscriptional regulator, PadR-like family
KeywordsTRANSCRIPTION / Artificial enzyme / boron catalysis / unnatural amino acid / 4-boronophenylalanine
Function / homologyTranscription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Transcriptional regulator, PadR-like family
Function and homology information
Biological speciesLactococcus cremoris subsp. cremoris MG1363 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThunnissen, A.M.W.H. / Rozeboom, H.J. / Longwitz, L. / Leveson-Gower, R.B. / Roelfes, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)885396European Union
CitationJournal: Nature / Year: 2024
Title: Boron catalysis in a designer enzyme.
Authors: Longwitz, L. / Leveson-Gower, R.B. / Rozeboom, H.J. / Thunnissen, A.W.H. / Roelfes, G.
History
DepositionAug 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator, PadR-like family
B: Transcriptional regulator, PadR-like family
C: Transcriptional regulator, PadR-like family
D: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)59,2984
Polymers59,2984
Non-polymers00
Water1,54986
1
A: Transcriptional regulator, PadR-like family
B: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)29,6492
Polymers29,6492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-26 kcal/mol
Surface area12400 Å2
MethodPISA
2
C: Transcriptional regulator, PadR-like family
D: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)29,6492
Polymers29,6492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-25 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.674, 53.890, 69.034
Angle α, β, γ (deg.)90.00, 95.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Transcriptional regulator, PadR-like family


Mass: 14824.584 Da / Num. of mol.: 4 / Mutation: M89 replaced with para-boronophenylalanine
Source method: isolated from a genetically manipulated source
Details: LmrR carrying a C-terminal strep-tag, with M89 replaced with para-boronophenylalanine
Source: (gene. exp.) Lactococcus cremoris subsp. cremoris MG1363 (lactic acid bacteria)
Gene: llmg_0323 / Production host: Escherichia coli (E. coli) / References: UniProt: A2RI36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.87 Å3/Da / Density % sol: 34.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein was concentrated to 9 mg/ml in 20 mM Tris-HCl, pH 8.0, 280 mM NaCl and 1 mM EDTA. Reservoir solution contained 25% PEG 1500 in 0.1 M malonate/imidazole/boric acid buffer, pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.2→53.89 Å / Num. obs: 22769 / % possible obs: 99.7 % / Redundancy: 3.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.056 / Rrim(I) all: 0.099 / Χ2: 0.7 / Net I/σ(I): 6.8 / Num. measured all: 70024
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 99.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.376 / Num. measured all: 6099 / Num. unique obs: 1970 / CC1/2: 0.812 / Rpim(I) all: 0.254 / Rrim(I) all: 0.456 / Χ2: 0.78 / Net I/σ(I) obs: 2.3

-
Processing

Software
NameVersionClassification
PHENIX(1.20rc1_4395: ???)refinement
xia23.8.6data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.37 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2774 1194 5.26 %
Rwork0.2063 --
obs0.2101 22682 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 0 86 3578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143570
X-RAY DIFFRACTIONf_angle_d1.3224803
X-RAY DIFFRACTIONf_dihedral_angle_d13.5791395
X-RAY DIFFRACTIONf_chiral_restr0.063509
X-RAY DIFFRACTIONf_plane_restr0.012618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.290.33081230.25372392X-RAY DIFFRACTION99
2.29-2.390.32811210.23862373X-RAY DIFFRACTION99
2.39-2.520.28741380.22862339X-RAY DIFFRACTION99
2.52-2.670.34481280.2482376X-RAY DIFFRACTION99
2.67-2.880.30711370.25112394X-RAY DIFFRACTION100
2.88-3.170.31011400.23862370X-RAY DIFFRACTION100
3.17-3.630.30251460.20922376X-RAY DIFFRACTION99
3.63-4.570.26211330.16382406X-RAY DIFFRACTION99
4.57-43.370.19241280.17072462X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.03830.00010.02890.01390.04520.0599-0.1476-0.05120.15560.04270.1104-0.1701-0.0296-0.023400.21560.02070.01120.10580.00340.20035.23918.8429-32.5258
20.05870.0115-0.04370.01250.00720.0680.2182-0.0916-0.0009-0.11250.0653-0.1285-0.23190.22640.00740.2156-0.0121-0.02030.17390.00020.222213.98899.6928-41.1547
30.00610.01380.00270.0169-0.03080.03990.04990.19520.066-0.1382-0.0074-0.11830.21160.0619-00.2879-0.02240.02760.1756-0.02950.23232.26650.4682-41.1872
40.096-0.0064-0.06380.11270.11420.1418-0.07220.1242-0.19120.0594-0.3829-0.0238-0.12930.0451-0.00890.24570.0705-0.02370.23920.02470.25463.46636.8932-52.4912
50.37030.0342-0.15150.0394-0.02090.06260.3923-0.0317-0.14660.6108-0.33360.9356-0.5049-0.12720.01550.4020.01960.0490.1795-0.01320.2778-3.413418.1144-27.9881
60.0025-0.0601-0.02880.029-0.03230.14030.07270.0311-0.0674-0.07960.06240.0593-0.22880.03010.00340.27660.00890.04760.1721-0.01520.1836-4.306412.3464-14.7611
70.1144-0.01720.06980.0364-0.00210.04830.01930.0558-0.2035-0.0254-0.2138-0.04010.1632-0.31420.00110.34610.05230.12020.14220.03140.3011-1.71851.0283-11.6997
80.3338-0.1432-0.36960.35780.01210.7037-0.0704-0.48160.0948-0.07740.0705-0.1034-0.09040.5140.06780.21730.0174-0.00640.35030.00320.19116.739611.1273-13.9791
90.1469-0.1419-0.01050.25940.0680.13180.1861-0.1255-0.0678-0.14760.08560.0039-0.0539-0.22880.01070.1885-0.0158-0.03340.30850.01920.250923.463133.99562.7494
100.01820.02280.01860.01060.00950.02270.18110.0013-0.18640.1095-0.06820.26670.1899-0.0768-00.28630.0354-0.02520.28120.0320.367932.206126.21827.1351
110.3983-0.5094-0.0330.67890.23260.35740.1103-0.45270.1052-0.3361-0.0512-0.5202-0.0506-0.29750.21590.1256-0.0949-0.12560.45310.02110.265633.006138.75733.6746
120.0581-0.0482-0.0406-0.00940.01540.0702-0.00860.203-0.0727-0.0175-0.0994-0.36860.2404-0.1285-0.00330.34330.04020.00230.30530.03320.293833.748334.8083-15.5469
130.0545-0.0188-0.03010.0828-0.05530.04180.44430.11520.09680.1442-0.11-0.0061-0.0767-0.2384-0.00010.22270.02490.04010.24130.00350.300139.943540.7106-24.0817
140.0034-0.00460.0030.02960.00860.008-0.03060.1418-0.0080.0323-0.0650.00340.1474-0.0309-00.4246-0.0590.03370.310.06610.386736.745326.1931-23.5153
150.15150.1413-0.02290.773-0.40290.5202-0.1070.64390.18310.04540.15260.09540.1498-0.26630.20290.1261-0.0736-0.04960.61720.03030.254926.732235.1581-21.412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 82 )
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 107 )
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 46 )
7X-RAY DIFFRACTION7chain 'B' and (resid 47 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 110 )
9X-RAY DIFFRACTION9chain 'C' and (resid 4 through 46 )
10X-RAY DIFFRACTION10chain 'C' and (resid 47 through 59 )
11X-RAY DIFFRACTION11chain 'C' and (resid 60 through 109 )
12X-RAY DIFFRACTION12chain 'D' and (resid 4 through 23 )
13X-RAY DIFFRACTION13chain 'D' and (resid 24 through 46 )
14X-RAY DIFFRACTION14chain 'D' and (resid 47 through 59 )
15X-RAY DIFFRACTION15chain 'D' and (resid 60 through 109 )

+
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