[English] 日本語
Yorodumi
- PDB-9gkt: Crystal structure of artificial enzyme LmrR_pAF variant RGN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gkt
TitleCrystal structure of artificial enzyme LmrR_pAF variant RGN
ComponentsTranscriptional regulator, PadR-like family
KeywordsDNA BINDING PROTEIN / Artificial enzyme / unnatural amino acid / 4-aminophenylalanine / directed evolution
Function / homology: / Transcription 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: 2.45 Å
AuthorsThunnissen, A.M.W.H. / Leveson-Gower, R.B. / Rozeboom, H.J. / Roelfes, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)885396European Union
CitationJournal: Acs Catalysis / Year: 2025
Title: Evolutionary Specialization of a Promiscuous Designer Enzyme.
Authors: Leveson-Gower, R.B. / Tiessler-Sala, L. / Rozeboom, H.J. / Thunnissen, A.W.H. / Marechal, J.D. / Roelfes, G.
History
DepositionAug 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,5012
Polymers29,5012
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-23 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.530, 49.956, 125.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 14750.619 Da / Num. of mol.: 2 / Mutation: V15pAF, L18R, M89N, S95G
Source method: isolated from a genetically manipulated source
Details: LmrR carrying a C-terminal strep-tag, V15 replaced by para-aminophenylalanine (pAF) and with mutations L18R, S95G, M89N (RGN)
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.: 26 / 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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: protein solution: 7-8 mg/ml in 20 mM Tris-HCl, pH 8.0, 280 mM NaCl and 1 mM EDTA, crystallization solution: 25% PEG 1500 in 0.1 M sodium propionate, sodium cacodylate trihydrate, Bis-Tris ...Details: protein solution: 7-8 mg/ml in 20 mM Tris-HCl, pH 8.0, 280 mM NaCl and 1 mM EDTA, crystallization solution: 25% PEG 1500 in 0.1 M sodium propionate, sodium cacodylate trihydrate, Bis-Tris propane (PCTP) buffer, pH 7-8
PH range: 7.0 - 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.45→125.73 Å / Num. obs: 9401 / % possible obs: 99.2 % / Redundancy: 4.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.063 / Rrim(I) all: 0.137 / Χ2: 0.99 / Net I/σ(I): 8.9 / Num. measured all: 40148
Reflection shellResolution: 2.45→2.55 Å / % possible obs: 97 % / Redundancy: 4.3 % / Rmerge(I) obs: 1.005 / Num. measured all: 4383 / Num. unique obs: 1029 / CC1/2: 0.531 / Rpim(I) all: 0.525 / Rrim(I) all: 1.139 / Χ2: 1.03 / Net I/σ(I) obs: 1.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→46.43 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 32.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2858 812 5 %
Rwork0.2149 --
obs0.2184 8126 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 0 26 1766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081766
X-RAY DIFFRACTIONf_angle_d0.9872364
X-RAY DIFFRACTIONf_dihedral_angle_d14.428680
X-RAY DIFFRACTIONf_chiral_restr0.045250
X-RAY DIFFRACTIONf_plane_restr0.007300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.60.39961250.31352496X-RAY DIFFRACTION90
2.6-2.80.32341320.26132566X-RAY DIFFRACTION94
2.8-3.090.3271350.27872571X-RAY DIFFRACTION95
3.09-3.530.31351360.2162638X-RAY DIFFRACTION96
3.53-4.450.28331460.18662568X-RAY DIFFRACTION95
4.45-46.430.22831380.18272602X-RAY DIFFRACTION95
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40740.54980.25140.0979-0.11260.67150.0756-0.02580.03390.0751-0.07240.0872-0.0053-0.02260.3454-0.0014-0.00960.36120.00930.3554.8611-26.695612.2515
20.22860.04720.03880.24670.19270.5367-0.12080.0027-0.00470.00060.09190.1255-0.00050.17490.3435-0.0192-0.02990.3412-0.00350.348911.9554-12.435521.0902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

+
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