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- PDB-7x7h: Crystal structure of Fructose regulator/Histidine phosphocarrier ... -

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Basic information

Entry
Database: PDB / ID: 7x7h
TitleCrystal structure of Fructose regulator/Histidine phosphocarrier protein complex from Vibrio cholerae
Components
  • Catabolite repressor/activator
  • HPr family phosphocarrier protein
KeywordsGENE REGULATION/TRANSFERASE / PTS / Vibrio / fructose / transcriptional regulator / GalR/LacI / HPr / GENE REGULATION / GENE REGULATION-TRANSFERASE complex
Function / homology
Function and homology information


response to fructose / phosphoenolpyruvate-dependent sugar phosphotransferase system / transferase activity / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
D-fructose-responsive transcription factor / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site ...D-fructose-responsive transcription factor / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / PTS HPR domain serine phosphorylation site signature. / LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
Phosphocarrier protein HPr / Catabolite repressor/activator
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, M.-K. / Zhang, J. / Yoon, C.-K. / Seok, Y.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1F1A1057780 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: HPr prevents FruR-mediated facilitation of RNA polymerase binding to the fru promoter in Vibrio cholerae.
Authors: Yoon, C.K. / Lee, S.H. / Zhang, J. / Lee, H.Y. / Kim, M.K. / Seok, Y.J.
History
DepositionMar 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: 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 1.2Jul 5, 2023Group: 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catabolite repressor/activator
B: HPr family phosphocarrier protein
C: Catabolite repressor/activator
D: HPr family phosphocarrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0496
Polymers91,9684
Non-polymers802
Water8,035446
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.940, 62.355, 312.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Catabolite repressor/activator


Mass: 36033.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: cra, D6U24_17570, EYB64_06550, FLM02_11955, FXE67_10910, HPY07_16365
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F0B292
#2: Protein HPr family phosphocarrier protein / PTS sugar transporter / Phosphocarrier protein HPr


Mass: 9950.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: ptsH, BC353_05360, D6U24_08050, ERS013138_01023, ERS013165_01775, ERS013166_02939, ERS013186_02269, ERS013193_00498, ERS013198_00582, ERS013199_02080, ERS013200_03874, ERS013201_03670, ...Gene: ptsH, BC353_05360, D6U24_08050, ERS013138_01023, ERS013165_01775, ERS013166_02939, ERS013186_02269, ERS013193_00498, ERS013198_00582, ERS013199_02080, ERS013200_03874, ERS013201_03670, ERS013202_02606, ERS013206_00437, ERS013207_01739, EYB64_14625, F0315_00300, F0H40_04200, F0M16_13080, FLM02_01405, FLM12_04230, FXE67_16935, HPY07_09360
Production host: Escherichia coli (E. coli)
References: UniProt: A0A085PY40, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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

CrystalDescription: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 295 K / Method: microbatch / Details: calcium acetate, PEG 3350, spermidine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 46109 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.996 / Rpim(I) all: 0.036 / Rrim(I) all: 0.138 / Χ2: 0.05 / Net I/av σ(I): 31.294 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.037.60.8014.73342210.8770.9670.2240.8551.381100
2.03-2.077.60.65843111.413100
2.07-2.117.60.56143781.494100
2.11-2.157.60.51142981.519100
2.15-2.27.60.44242671.517100
2.2-2.257.60.41643741.567100
2.25-2.317.60.38642841.588100
2.31-2.377.60.33643231.608100
2.37-2.447.60.30343641.634100
2.44-2.527.60.25842171.686100
2.52-2.617.60.23844121.673100
2.61-2.717.60.21342781.746100
2.71-2.847.70.18143661.816100
2.84-2.997.60.14542241.896100
2.99-3.177.70.11543202.02100
3.17-3.427.60.08743592.141100
3.42-3.767.60.07643072.324100
3.76-4.317.60.06342942.487100
4.31-5.437.60.05943252.403100
5.43-507.30.06143272.74499.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RZR

1rzr


Resolution: 2→31.13 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.91 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2266 2000 4.34 %
Rwork0.1788 --
obs0.1809 46109 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 2 446 5888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.939
X-RAY DIFFRACTIONf_dihedral_angle_d5.589756
X-RAY DIFFRACTIONf_chiral_restr0.049876
X-RAY DIFFRACTIONf_plane_restr0.006978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28811350.23462978X-RAY DIFFRACTION99
2.05-2.110.25041410.19933117X-RAY DIFFRACTION100
2.11-2.170.26611410.19423083X-RAY DIFFRACTION100
2.17-2.240.2481400.18593121X-RAY DIFFRACTION100
2.24-2.320.24561400.19053070X-RAY DIFFRACTION100
2.32-2.410.26621430.18953149X-RAY DIFFRACTION100
2.41-2.520.23481390.18443085X-RAY DIFFRACTION100
2.52-2.660.24911430.18883149X-RAY DIFFRACTION100
2.66-2.820.23161440.18833176X-RAY DIFFRACTION100
2.82-3.040.23911420.19523120X-RAY DIFFRACTION100
3.04-3.340.24721430.17583172X-RAY DIFFRACTION100
3.34-3.830.21041470.15913215X-RAY DIFFRACTION100
3.83-4.820.15281470.14143249X-RAY DIFFRACTION100
4.82-31.130.23461550.19143425X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -8.4218 Å / Origin y: -14.2757 Å / Origin z: 41.0611 Å
111213212223313233
T0.0837 Å20.0052 Å2-0.0074 Å2-0.1443 Å20.0011 Å2--0.1652 Å2
L0.3284 °20.026 °2-0.1031 °2-0.6115 °20.0339 °2--0.8246 °2
S-0.0248 Å °0.0365 Å °0.0338 Å °-0.0523 Å °0.0457 Å °0.0144 Å °-0.0328 Å °-0.0103 Å °-0.0213 Å °
Refinement TLS groupSelection details: all

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