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- PDB-7en7: The crystal structure of Escherichia coli MurR in complex with N-... -

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Basic information

Entry
Database: PDB / ID: 7en7
TitleThe crystal structure of Escherichia coli MurR in complex with N-acetylmuramic-acid-6-phosphate
ComponentsHTH-type transcriptional regulator MurR
KeywordsGENE REGULATION / regulator / N-acetylmuramic-acid-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-J79 / HTH-type transcriptional regulator MurR
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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)21,7302
Polymers21,3571
Non-polymers3731
Water4,702261
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)86,9198
Polymers85,4264
Non-polymers1,4934
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 area16860 Å2
ΔGint-88 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.411, 72.759, 81.765
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-441-

HOH

21A-455-

HOH

31A-556-

HOH

41A-607-

HOH

51A-653-

HOH

61A-661-

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: Chemical ChemComp-J79 / (2R)-2-[(2R,3R,4R,5S,6R)-3-acetamido-2,5-bis(oxidanyl)-6-(phosphonooxymethyl)oxan-4-yl]oxypropanoic acid


Mass: 373.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20NO11P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 40.62 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane pH 8.8, 16% 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: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 58134 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.03 / Rrim(I) all: 0.108 / Net I/σ(I): 23
Reflection shellResolution: 1.22→1.26 Å / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 2 / Num. unique obs: 5733 / CC1/2: 0.82 / CC star: 0.949 / Rpim(I) all: 0.245 / Rrim(I) all: 0.864

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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: 1.22→29.206 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1692 2592 4.98 %
Rwork0.1533 49499 -
obs0.1541 52091 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.43 Å2 / Biso mean: 17.6402 Å2 / Biso min: 6.8 Å2
Refinement stepCycle: final / Resolution: 1.22→29.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 24 261 1751
Biso mean--14.35 31.95 -
Num. residues----191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.22-1.24210.19081220.172605
1.2421-1.2660.18261460.16932560
1.266-1.29180.18031380.16632572
1.2918-1.31990.17211430.16062568
1.3199-1.35060.20011150.16352601
1.3506-1.38440.16881380.16182564
1.3844-1.42180.19021320.16652563
1.4218-1.46370.19621380.16582592
1.4637-1.51090.1761430.14862596
1.5109-1.56490.16161570.14382563
1.5649-1.62750.15551170.14992610
1.6275-1.70160.17611350.14652596
1.7016-1.79130.14931402602
1.7913-1.90350.17571330.15442606
1.9035-2.05050.16621440.15062603
2.0505-2.25670.16761570.14792597
2.2567-2.58310.17531190.15122670
2.5831-3.25380.19691360.15382662
3.2538-90.14181392769
Refinement TLS params.Method: refined / Origin x: -8.355 Å / Origin y: -5.215 Å / Origin z: -14.262 Å
111213212223313233
T0.0835 Å2-0.0051 Å2-0.009 Å2-0.0804 Å2-0.0004 Å2--0.0765 Å2
L0.7232 °20.2114 °2-0.0506 °2-0.6366 °2-0.0719 °2--0.6041 °2
S-0.0364 Å °0.0552 Å °-0.0172 Å °-0.0463 Å °0.0436 Å °0.0235 Å °0.0172 Å °-0.0737 Å °-0.0084 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 95:191 )

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