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- PDB-6ymz: Structure of the CheB methylsterase from P. atrosepticum SCRI1043 -

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Basic information

Entry
Database: PDB / ID: 6ymz
TitleStructure of the CheB methylsterase from P. atrosepticum SCRI1043
ComponentsProtein-glutamate methylesterase/protein-glutamine glutaminase
KeywordsHYDROLASE / BACTERIAL CHEMOTAXIS / METHYLESTERASE / CHEMORECEPTOR
Function / homology
Function and homology information


protein-glutamate methylesterase / protein-glutamate methylesterase activity / protein deamination / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein demethylation / phosphorelay response regulator activity / chemotaxis / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
ACETATE ION / Protein-glutamate methylesterase/protein-glutamine glutaminase
Similarity search - Component
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGavira, J.A. / Krell, T. / Velando-Soriano, F. / Matilla, M.A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2013-4297-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-74875-P Spain
CitationJournal: Int J Mol Sci / Year: 2020
Title: Evidence for Pentapeptide-Dependent and Independent CheB Methylesterases.
Authors: Velando, F. / Gavira, J.A. / Rico-Jimenez, M. / Matilla, M.A. / Krell, T.
History
DepositionApr 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-glutamate methylesterase/protein-glutamine glutaminase
B: Protein-glutamate methylesterase/protein-glutamine glutaminase
C: Protein-glutamate methylesterase/protein-glutamine glutaminase
D: Protein-glutamate methylesterase/protein-glutamine glutaminase
E: Protein-glutamate methylesterase/protein-glutamine glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,06422
Polymers193,0805
Non-polymers98417
Water8,791488
1
A: Protein-glutamate methylesterase/protein-glutamine glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9056
Polymers38,6161
Non-polymers2895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein-glutamate methylesterase/protein-glutamine glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6623
Polymers38,6161
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein-glutamate methylesterase/protein-glutamine glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8465
Polymers38,6161
Non-polymers2304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein-glutamate methylesterase/protein-glutamine glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7313
Polymers38,6161
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protein-glutamate methylesterase/protein-glutamine glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9195
Polymers38,6161
Non-polymers3034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.741, 148.741, 206.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Protein-glutamate methylesterase/protein-glutamine glutaminase


Mass: 38615.965 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (bacteria)
Gene: cheB, ECA1693 / Cell line (production host): D3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6D6I7, protein-glutamate methylesterase, protein-glutamine glutaminase

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Non-polymers , 5 types, 505 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293 K / Method: counter-diffusion
Details: 2.0M NH4 Sulphate,0.1M Tris-HCl pH 8.50 // 1.25M Na Citrate, 0.1M Na-Hepes pH 7.50

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→63.31 Å / Num. obs: 98138 / % possible obs: 98.44 % / Redundancy: 26.2 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.826 / Net I/σ(I): 40.01
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 25.4 % / Mean I/σ(I) obs: 3.41 / Num. unique obs: 9778 / CC1/2: 0.649 / % possible all: 98.13

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a2o

1a2o


Resolution: 2.3→63.31 Å / SU ML: 0.258 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5478
RfactorNum. reflection% reflection
Rfree0.2261 4877 5 %
Rwork0.1919 --
obs0.1935 97531 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.93 Å2
Refinement stepCycle: LAST / Resolution: 2.3→63.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12787 0 59 492 13338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413761
X-RAY DIFFRACTIONf_angle_d0.697818680
X-RAY DIFFRACTIONf_chiral_restr0.04552141
X-RAY DIFFRACTIONf_plane_restr0.00472480
X-RAY DIFFRACTIONf_dihedral_angle_d7.051711590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.29481940.2482995X-RAY DIFFRACTION97.7
2.33-2.350.26952150.23773055X-RAY DIFFRACTION98.29
2.35-2.380.28171500.23343082X-RAY DIFFRACTION98.39
2.38-2.410.25741670.23483072X-RAY DIFFRACTION98.27
2.41-2.440.28991510.22833094X-RAY DIFFRACTION97.89
2.44-2.480.26251620.21843033X-RAY DIFFRACTION98.04
2.48-2.510.26281540.21653102X-RAY DIFFRACTION98.64
2.51-2.550.24371500.20363100X-RAY DIFFRACTION99.02
2.55-2.590.24841850.20343117X-RAY DIFFRACTION98.86
2.59-2.630.24261640.20793065X-RAY DIFFRACTION98.66
2.63-2.680.24221540.2113133X-RAY DIFFRACTION98.83
2.68-2.730.21211910.19453049X-RAY DIFFRACTION99.14
2.73-2.780.25291580.20013079X-RAY DIFFRACTION99.14
2.78-2.840.26551590.20223128X-RAY DIFFRACTION99.22
2.84-2.90.25081500.2013104X-RAY DIFFRACTION99.15
2.9-2.970.23151740.18843116X-RAY DIFFRACTION98.89
2.97-3.040.20241630.18933075X-RAY DIFFRACTION98.93
3.04-3.120.25961750.18983064X-RAY DIFFRACTION98.81
3.12-3.210.25771730.18133120X-RAY DIFFRACTION98.59
3.21-3.320.20251240.18293134X-RAY DIFFRACTION99.39
3.32-3.440.24811330.17533158X-RAY DIFFRACTION99.28
3.44-3.570.18641720.1673112X-RAY DIFFRACTION99.06
3.57-3.740.19741590.1663082X-RAY DIFFRACTION98.27
3.74-3.930.20781740.16933021X-RAY DIFFRACTION97.56
3.93-4.180.19251500.16593094X-RAY DIFFRACTION97.74
4.18-4.50.18991520.16353120X-RAY DIFFRACTION98.29
4.5-4.950.20881670.17473090X-RAY DIFFRACTION98.1
4.95-5.670.2241590.20033100X-RAY DIFFRACTION98.58
5.67-7.140.25531620.22493066X-RAY DIFFRACTION97.26
7.14-63.310.20851360.21673094X-RAY DIFFRACTION95.76
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.206240966223-0.09454064235380.02271291712131.1935716146-0.101558430930.149297153666-0.0331027604877-0.0369033589190.04686801543880.009901398469720.04590927850780.000262084901657-0.0415165649235-0.0462165208597-0.02371662551290.114299547368-0.01115471801280.001489847542610.07216023919050.003694954494380.088725886047245.859137115755.01249569920.46412951465
20.5547258149340.77732185235-0.0318214285441.676336018470.5032371375110.119580699011-0.04561903622450.0234130047226-0.1202159917030.04710167805650.114494449782-0.1891783460670.04154123195380.0877831149845-0.008803117873270.148180323621-0.00453054300876-0.01228889128460.112453747202-0.04213009108870.15563191848434.63746238693.49168425579-17.7959315613
31.33608220535-0.280727259524-0.1772571263160.2442782299470.07943210926610.2189880608410.01622123211440.0381889107635-0.0527412675964-0.0296341016499-0.004957309636050.0649296384208-0.0541339951337-0.05802495448250.006581861674130.0997048758463-0.003308663742550.00565452794010.1426676334390.001971480805810.10789075793219.363443778828.545160272429.5909422629
40.543948516381-0.848759655357-0.03142796879161.502886784710.479704818640.180499642936-0.0489396704438-0.03288109097280.133679627714-0.0376110617110.120489002058-0.180033281028-0.02781303460070.09566390749420.002931148399910.1402225490390.004877861807080.005057414872470.10569662859-0.05633970225080.13244494658234.1350356002-3.01457896028-55.3367394025
50.543265816165-0.2019921423170.1137881525730.355048898610.03318183914170.152617051566-0.0765896370761-0.104191204973-0.210801862778-0.02363043279740.05539808960150.148563083263-0.03551776418350.03715887514056.77602659559E-50.528423344331-0.02104123348060.07813201891440.540899117441-0.0006590047746630.36836387835245.681224382456.3807899853-36.5889779798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 356)
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 356)
3X-RAY DIFFRACTION3(chain 'C' and resid 7 through 356)
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 355)
5X-RAY DIFFRACTION5(chain 'E' and resid 7 through 350)

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