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- PDB-7en6: The crystal structure of Escherichia coli MurR in apo form -

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Basic information

Entry
Database: PDB / ID: 7en6
TitleThe crystal structure of Escherichia coli MurR in apo form
ComponentsHTH-type transcriptional regulator MurR
KeywordsGENE REGULATION / regulator / Apo-form / sugar-binding
Function / homologyGlucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.276 Å
AuthorsZhang, Y. / Chen, W. / Ji, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21922705, 22077083, 21907066 China
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Molecular basis for cell-wall recycling regulation by transcriptional repressor MurR in Escherichia coli.
Authors: Zhang, Y. / Chen, W. / Wu, D. / Liu, Y. / Wu, Z. / Li, J. / Zhang, S.Y. / Ji, Q.
History
DepositionApr 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: 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 1.2Jun 22, 2022Group: 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
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator MurR
B: HTH-type transcriptional regulator MurR
C: HTH-type transcriptional regulator MurR
D: HTH-type transcriptional regulator MurR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8006
Polymers78,6104
Non-polymers1902
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-75 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.558, 77.583, 144.333
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
HTH-type transcriptional regulator MurR / MurPQ operon repressor


Mass: 19652.518 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: murR, E4K61_08440 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6C9BRR1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M L-proline, 0.1 M HEPES pH 7.5, 10% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 32333 / % possible obs: 99.8 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.023 / Rrim(I) all: 0.082 / Net I/σ(I): 27.7
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1549 / CC1/2: 0.943 / CC star: 0.985 / Rpim(I) all: 0.169 / Rrim(I) all: 0.594 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IVN

4ivn


Resolution: 2.276→38.792 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 1618 5.02 %
Rwork0.1894 30588 -
obs0.1929 32206 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.41 Å2 / Biso mean: 59.2619 Å2 / Biso min: 25.81 Å2
Refinement stepCycle: final / Resolution: 2.276→38.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 0 10 134 5436
Biso mean--107.15 53.05 -
Num. residues----698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2762-2.34320.35241280.2577241297
2.3432-2.41880.31121340.23812521100
2.4188-2.50530.31081440.2212512100
2.5053-2.60560.25161290.20832544100
2.6056-2.72410.31141440.21332498100
2.7241-2.86770.28341370.20422534100
2.8677-3.04730.29831500.21472520100
3.0473-3.28250.3041330.1972570100
3.2825-3.61260.25531340.19192568100
3.6126-4.13480.24941230.1666258899
4.1348-5.20740.22641230.15682632100
5.2074-90.23321390.1887268998
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)
11.42880.57160.48421.88430.23932.2308-0.0295-0.0345-0.04280.1083-0.04720.0650.2812-0.01320.01950.66480.0001-0.00860.2494-0.03680.27421.286-4.896-32.119
21.7616-0.51660.56761.3425-0.20892.10930.024-0.0394-0.03790.1704-0.14560.0869-0.1361-0.10250.09920.5761-0.01060.05820.3108-0.05570.35661.9277.833-0.581
31.893-0.20810.06722.3463-0.22722.10830.03320.1033-0.2387-0.0902-0.0456-0.0370.52450.0589-0.02360.81210.0719-0.03890.32430.00510.337119.79-6.7190.024
41.2740.24530.56251.16030.23342.5446-0.0520.12250.0791-0.1667-0.0452-0.0199-0.17640.55870.06730.6095-0.01760.02110.39980.02390.297619.7799.408-30.047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 94:270 )A94 - 270
2X-RAY DIFFRACTION2( CHAIN B AND RESID 91:267 )B91 - 267
3X-RAY DIFFRACTION3( CHAIN C AND RESID 92:271 )C92 - 271
4X-RAY DIFFRACTION4( CHAIN D AND RESID 91:267 )D91 - 267

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