[English] 日本語
Yorodumi
- PDB-9ha0: Crystal structure of Cu(II)-bound LmrR_V15Bpy variant BVS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ha0
TitleCrystal structure of Cu(II)-bound LmrR_V15Bpy variant BVS
ComponentsTranscriptional regulator, PadR-like family
KeywordsMETAL BINDING PROTEIN / artificial metalloenzyme / unnatural amino acid / bipyridine / copper-binding / LmrR / 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 / metal ion binding / COPPER (II) ION / IMIDAZOLE / 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: 1.75 Å
AuthorsThunnissen, A.M.W.H. / Jiang, R. / Casilli, F. / Aalbers, F. / Roelfes, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)885396European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: An Artificial Copper-Michaelase Featuring a Genetically Encoded Bipyridine Ligand for Asymmetric Additions to Nitroalkenes.
Authors: Jiang, R. / Casilli, F. / Thunnissen, A.W.H. / Roelfes, G.
History
DepositionNov 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4946
Polymers30,2002
Non-polymers2944
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-16 kcal/mol
Surface area12450 Å2
Unit cell
Length a, b, c (Å)35.395, 54.313, 145.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 15100.005 Da / Num. of mol.: 2
Mutation: Val15 replaced by (2,2'-bipyridin-5-yl)alanine, A92V, F93S
Source method: isolated from a genetically manipulated source
Details: LmrR with residue Val15 replaced by (2,2'-bipyridin-5-yl)alanine, carrying a C-terminal strep-tag and with evolved mutations A92V, F93S
Source: (gene. exp.) Lactococcus cremoris subsp. cremoris MG1363 (lactic acid bacteria)
Gene: llmg_0323 / Production host: Escherichia coli (E. coli) / References: UniProt: A2RI36
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Copper nitrate, imidazole, PEG 8000

-
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: Jul 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.75→43.55 Å / Num. obs: 29303 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 1.01 / Net I/σ(I): 15.2 / Num. measured all: 377849
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 99.8 % / Redundancy: 13.2 % / Rmerge(I) obs: 2.758 / Num. measured all: 20638 / Num. unique obs: 1567 / CC1/2: 0.502 / Rpim(I) all: 0.78 / Rrim(I) all: 2.868 / Χ2: 0.92 / Net I/σ(I) obs: 1

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.21.1_5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→36.43 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 1437 4.92 %
Rwork0.1981 --
obs0.1999 29233 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 17 105 1924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081907
X-RAY DIFFRACTIONf_angle_d0.8712561
X-RAY DIFFRACTIONf_dihedral_angle_d14.337752
X-RAY DIFFRACTIONf_chiral_restr0.045269
X-RAY DIFFRACTIONf_plane_restr0.012326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.34221450.31022717X-RAY DIFFRACTION100
1.81-1.890.35591490.30272702X-RAY DIFFRACTION100
1.89-1.970.36641380.27232772X-RAY DIFFRACTION100
1.97-2.070.26271180.22582755X-RAY DIFFRACTION100
2.07-2.20.23731610.21452714X-RAY DIFFRACTION100
2.2-2.370.25991500.21072759X-RAY DIFFRACTION100
2.38-2.610.26221410.20322767X-RAY DIFFRACTION100
2.61-2.990.25541450.20622802X-RAY DIFFRACTION100
2.99-3.770.21781300.18762827X-RAY DIFFRACTION100
3.77-36.430.19811600.17242981X-RAY DIFFRACTION100
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)
17.5012-0.5052-3.374.7223-1.95462.5097-0.5235-0.2631-0.61150.80910.35120.4537-0.0419-0.42140.11330.47230.06110.07710.29570.07590.38067.2657-8.9435-30.5125
28.70050.8663-2.05173.8180.62555.32110.0330.05590.36830.1489-0.08430.53270.0636-0.70550.06630.27450.01650.04730.27960.02920.35623.2849-1.2036-39.408
32.3661.3966-1.343.1885-1.04964.1179-0.02820.15880.0498-0.0692-0.0821-0.0380.101-0.03570.10340.26470.00570.04580.2046-0.00250.307117.0871-2.3292-41.4902
46.18651.7762-4.87453.0105-1.41397.1750.0739-0.0847-0.2160.1691-0.40040.23240.1137-0.55650.30520.3153-0.07010.04020.2942-0.12460.31425.9498-22.8217-26.2997
51.8819-0.3236-1.62990.84190.86456.7498-0.1476-0.20170.0629-0.093-0.009-0.04220.5223-0.07730.14870.3068-0.02180.02650.3153-0.07920.3088.2561-20.6122-14.606
66.0966-2.1395-0.05142.30050.47964.0709-0.0138-0.17270.3964-0.00510.1007-0.05480.0861-0.1134-0.03630.2349-0.0516-0.02890.3713-0.11990.26187.675-13.183-2.3083
70.592-0.00570.5818-0.0315-0.25417.6581-0.0182-0.05080.1189-0.0460.05310.0243-0.2411-0.7488-0.05270.30340.00990.04760.5495-0.01550.4534-1.9603-11.3617-24.1729
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 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 112 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 46 )
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 76 )
7X-RAY DIFFRACTION7chain 'B' and (resid 77 through 114 )

+
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