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- PDB-5xlx: Crystal structure of the C-terminal domain of CheR1 containing SAH -

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Basic information

Entry
Database: PDB / ID: 5xlx
TitleCrystal structure of the C-terminal domain of CheR1 containing SAH
ComponentsChemotaxis protein methyltransferase 1
KeywordsTRANSFERASE / signaling / methyltransferase
Function / homology
Function and homology information


protein-glutamate O-methyltransferase / protein-glutamate O-methyltransferase activity / methylation
Similarity search - Function
: / Chemotaxis protein methyltransferase CheR / Chemotaxis receptor methyltransferase CheR, N-terminal domain superfamily / MCP methyltransferase, CheR-type / Chemotaxis receptor methyltransferase CheR, N-terminal / MCP methyltransferase, CheR-type, SAM-binding domain, C-terminal / CheR methyltransferase, SAM binding domain / CheR methyltransferase, all-alpha domain / CheR-type methyltransferase domain profile. / Methyltransferase, chemotaxis proteins / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Chemotaxis protein methyltransferase 1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.969 Å
AuthorsYuan, Z. / Zhu, Y. / Gu, L.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Structural basis for the regulation of chemotaxis by MapZ in the presence of c-di-GMP
Authors: Zhu, Y. / Yuan, Z. / Gu, L.
History
DepositionMay 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemotaxis protein methyltransferase 1
B: Chemotaxis protein methyltransferase 1
C: Chemotaxis protein methyltransferase 1
D: Chemotaxis protein methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5608
Polymers127,0224
Non-polymers1,5384
Water13,007722
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-18 kcal/mol
Surface area34550 Å2
Unit cell
Length a, b, c (Å)36.237, 78.392, 140.808
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chemotaxis protein methyltransferase 1


Mass: 31755.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: cheR1, PA3348 / Production host: Escherichia coli (E. coli)
References: UniProt: O87131, protein-glutamate O-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O

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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: 1.57 Å3/Da / Density % sol: 21.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15%(w/v)PEG10,000 100mM Sodium citrate PH5.5 2%(V/V)Dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.969→50 Å / Num. obs: 52220 / % possible obs: 98.8 % / Redundancy: 6.3 % / Net I/σ(I): 24.29

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Processing

Software
NameVersionClassification
PHENIXdev_2719refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.969→40.111 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1980 3.79 %
Rwork0.1909 --
obs0.1923 52219 93.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.969→40.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6328 0 104 722 7154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026575
X-RAY DIFFRACTIONf_angle_d0.6528881
X-RAY DIFFRACTIONf_dihedral_angle_d2.5843951
X-RAY DIFFRACTIONf_chiral_restr0.045964
X-RAY DIFFRACTIONf_plane_restr0.0031127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9686-2.01780.31591060.22862720X-RAY DIFFRACTION71
2.0178-2.07240.29871240.22222991X-RAY DIFFRACTION80
2.0724-2.13340.25711220.21163384X-RAY DIFFRACTION87
2.1334-2.20220.30191480.20413483X-RAY DIFFRACTION93
2.2022-2.28090.26911450.21233621X-RAY DIFFRACTION95
2.2809-2.37220.23631450.19923674X-RAY DIFFRACTION97
2.3722-2.48020.25691500.19933715X-RAY DIFFRACTION98
2.4802-2.61090.24851500.19733769X-RAY DIFFRACTION98
2.6109-2.77450.23661400.19943755X-RAY DIFFRACTION98
2.7745-2.98860.2311500.19853774X-RAY DIFFRACTION99
2.9886-3.28930.22081500.19873833X-RAY DIFFRACTION100
3.2893-3.76490.19931500.17813789X-RAY DIFFRACTION100
3.7649-4.74220.18251500.16033844X-RAY DIFFRACTION100
4.7422-40.11930.22641500.18563887X-RAY DIFFRACTION99

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