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- PDB-1a2o: STRUCTURAL BASIS FOR METHYLESTERASE CHEB REGULATION BY A PHOSPHOR... -

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Basic information

Entry
Database: PDB / ID: 1a2o
TitleSTRUCTURAL BASIS FOR METHYLESTERASE CHEB REGULATION BY A PHOSPHORYLATION-ACTIVATED DOMAIN
ComponentsCHEB METHYLESTERASE
KeywordsBACTERIAL CHEMOTAXIS / ADAPTATION / SERINE HYDROLASE
Function / homology
Function and homology information


protein-glutamate methylesterase / protein-glutamate methylesterase activity / protein-glutamine glutaminase activity / protein-glutamine glutaminase / phosphorelay response regulator activity / chemotaxis / cytoplasm
Similarity search - Function
Methylesterase CheB, C-terminal domain / Signal transduction response regulator, chemotaxis, protein-glutamate methylesterase / Protein-glutamate methylesterase/protein-glutamine glutaminase, CheB type / Methylesterase CheB, C-terminal / CheB methylesterase / CheB-type methylesterase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Methylesterase CheB, C-terminal domain / Signal transduction response regulator, chemotaxis, protein-glutamate methylesterase / Protein-glutamate methylesterase/protein-glutamine glutaminase, CheB type / Methylesterase CheB, C-terminal / CheB methylesterase / CheB-type methylesterase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein-glutamate methylesterase/protein-glutamine glutaminase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDjordjevic, S. / Goudreau, P.N. / Xu, Q. / Stock, A.M. / West, A.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain.
Authors: Djordjevic, S. / Goudreau, P.N. / Xu, Q. / Stock, A.M. / West, A.H.
History
DepositionJan 6, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHEB METHYLESTERASE
B: CHEB METHYLESTERASE


Theoretical massNumber of molelcules
Total (without water)75,1982
Polymers75,1982
Non-polymers00
Water7,404411
1
A: CHEB METHYLESTERASE


Theoretical massNumber of molelcules
Total (without water)37,5991
Polymers37,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHEB METHYLESTERASE


Theoretical massNumber of molelcules
Total (without water)37,5991
Polymers37,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.830, 100.460, 53.120
Angle α, β, γ (deg.)90.00, 98.63, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.933, -0.099, -0.346), (0.082, -0.995, 0.062), (-0.35, 0.029, 0.936)84.71128, 153.27753, 37.15702
2given(-0.956, -0.056, -0.29), (0.054, -0.998, 0.012), (-0.29, -0.004, 0.957)81.73852, 154.30302, 38.53921

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Components

#1: Protein CHEB METHYLESTERASE


Mass: 37598.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cellular location: CYTOPLASM / Plasmid: PME30 / Cell (production host): HB101 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P04042, protein-glutamate methylesterase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
21.5 M1dropLi2SO4
30.1 Mimidazole1drop
41.45 M1reservoirLi2SO4
50.1 Mimidazole1reservoir
610 mM1reservoirMgCl2
75 mM1reservoirNaN3
1protein1drop0.001ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 32281 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 38.4 Å2 / Rsym value: 0.054 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.163 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 97667 / Rmerge(I) obs: 0.054

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Processing

Software
NameVersionClassification
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CHD

1chd


Resolution: 2.4→10 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rwork0.222 ---
obs0.225 32281 96.9 %-
Rfree--5 %RANDOM
Displacement parametersBiso mean: 23.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 0 411 5611
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5582
X-RAY DIFFRACTIONp_mcangle_it2.663
X-RAY DIFFRACTIONp_scbond_it1.5332
X-RAY DIFFRACTIONp_scangle_it2.5553
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1070.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.93
X-RAY DIFFRACTIONp_staggered_tor22.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.320
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 32281 / Rfactor all: 0.222 / Rfactor Rfree: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS

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