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- PDB-7en5: The crystal structure of Escherichia coli MurR in complex with N-... -

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Basic information

Entry
Database: PDB / ID: 7en5
TitleThe crystal structure of Escherichia coli MurR in complex with N-acetylglucosamine-6-phosphate
ComponentsHTH-type transcriptional regulator MurR
KeywordsGENE REGULATION / regulator / N-acetylglucosamine-6-phosphate / sugar-binding
Function / homology
Function and homology information


N-acetylmuramic acid catabolic process / regulation of carbohydrate catabolic process / carbohydrate derivative metabolic process / carbohydrate derivative binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription regulator HTH, MurR / Helix-turn-helix protein RpiR / : / Helix-turn-helix domain, rpiR family / RpiR-type HTH domain profile. / RpiR-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily ...Transcription regulator HTH, MurR / Helix-turn-helix protein RpiR / : / Helix-turn-helix domain, rpiR family / RpiR-type HTH domain profile. / RpiR-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4QY / 2-METHOXYETHANOL / HTH-type transcriptional regulator MurR
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,8264
Polymers21,3571
Non-polymers4693
Water3,729207
1
A: HTH-type transcriptional regulator MurR
hetero molecules

A: HTH-type transcriptional regulator MurR
hetero molecules

A: HTH-type transcriptional regulator MurR
hetero molecules

A: HTH-type transcriptional regulator MurR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,30416
Polymers85,4264
Non-polymers1,87812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area18070 Å2
ΔGint-96 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.257, 72.751, 82.069
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-461-

HOH

31A-525-

HOH

41A-584-

HOH

51A-592-

HOH

61A-605-

HOH

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Components

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


Mass: 21356.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: murR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P77245
#2: Sugar ChemComp-4QY / 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose / beta-N-acetylglucosamine-6-phosphate / N-acetyl-6-O-phosphono-beta-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 301.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.68 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% v/v 2-Propanol, 0.1 M Tris pH 8.0, 5% w/v Polyethylene glycol 8,000

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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: Jun 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 48028 / % possible obs: 98.9 % / Redundancy: 11.3 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.053 / Rrim(I) all: 0.154 / Net I/σ(I): 13.6
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 4 / Num. unique obs: 4718 / CC1/2: 0.914 / CC star: 0.977 / Rpim(I) all: 0.147 / Rrim(I) all: 0.54 / % possible all: 97.7

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Processing

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

4ivn


Resolution: 1.25→28.881 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2159 2265 4.84 %
Rwork0.1976 44527 -
obs0.1985 46792 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.32 Å2 / Biso mean: 19.4291 Å2 / Biso min: 8.49 Å2
Refinement stepCycle: final / Resolution: 1.25→28.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 30 207 1697
Biso mean--19.55 30.62 -
Num. residues----190
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.25-1.27720.25991090.2442222477
1.2772-1.30690.26111270.2303252488
1.3069-1.33960.21451460.208264993
1.3396-1.37580.24711200.2127276796
1.3758-1.41630.22431330.2025281298
1.4163-1.4620.21681530.1949277998
1.462-1.51430.21651270.1931285599
1.5143-1.57490.20751430.1999279198
1.5749-1.64660.21931590.1965283599
1.6466-1.73340.20531370.1935286799
1.7334-1.8420.1871660.1964283099
1.842-1.98410.22771410.1971287499
1.9841-2.18380.20511590.19242864100
2.1838-2.49960.21071470.1969290999
2.4996-3.14860.24811390.1996291699
3.1486-90.20471590.194303199
Refinement TLS params.Method: refined / Origin x: -8.6457 Å / Origin y: -5.351 Å / Origin z: -14.4785 Å
111213212223313233
T0.0983 Å2-0.0074 Å2-0.0073 Å2-0.0979 Å20.0042 Å2--0.0829 Å2
L0.4273 °20.0991 °20.1428 °2-0.9722 °2-0.1461 °2--0.5144 °2
S-0.0224 Å °0.0434 Å °-0.011 Å °-0.0467 Å °0.0542 Å °0.0317 Å °-0.0014 Å °-0.0502 Å °-0.0315 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA95 - 285
2X-RAY DIFFRACTION1allW1 - 359
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1

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