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- PDB-2pl9: Crystal Structure of CheY-Mg(2+)-BeF(3)(-) in Complex with CheZ(C... -

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Basic information

Entry
Database: PDB / ID: 2pl9
TitleCrystal Structure of CheY-Mg(2+)-BeF(3)(-) in Complex with CheZ(C19) Peptide solved from a P2(1)2(1)2 Crystal
Components(Chemotaxis protein ...) x 2
KeywordsSIGNALING PROTEIN / CHEMOTAXIS / CHEY-CHEZ PEPTIDE COMPLEX / CHEY-BEF(3)(-)
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum / regulation of chemotaxis / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphorelay signal transduction system / phosphoprotein phosphatase activity / chemotaxis / metal ion binding / cytoplasm
Similarity search - Function
Chemotaxis phosphatase, CheZ / Chemotaxis phosphatase, CheZ / : / 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 ...Chemotaxis phosphatase, CheZ / Chemotaxis phosphatase, CheZ / : / 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
BERYLLIUM TRIFLUORIDE ION / Protein phosphatase CheZ / Chemotaxis protein CheY
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGuhaniyogi, J. / Stock, A.M.
CitationJournal: J.Bacteriol. / Year: 2008
Title: Interaction of CheY with the C-terminal peptide of CheZ.
Authors: Guhaniyogi, J. / Wu, T. / Patel, S.S. / Stock, A.M.
History
DepositionApr 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 6, 2013Group: Advisory / Other
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Sep 2, 2020Group: Data collection / Derived calculations / Structure summary
Category: struct_biol / struct_keywords / struct_site
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text ..._struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemotaxis protein cheY
B: Chemotaxis protein cheY
C: Chemotaxis protein cheY
D: Chemotaxis protein cheZ
E: Chemotaxis protein cheZ
F: Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,34113
Polymers47,8756
Non-polymers4667
Water97354
1
A: Chemotaxis protein cheY
D: Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0494
Polymers15,9582
Non-polymers902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chemotaxis protein cheY
E: Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2445
Polymers15,9582
Non-polymers2863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chemotaxis protein cheY
F: Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0494
Polymers15,9582
Non-polymers902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.058, 162.972, 37.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 6 / Auth seq-ID: 2 - 129 / Label seq-ID: 1 - 128

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsThe asymmetric unit contains three biological units (chains A & D, chains B & E and chains C & F).

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Components

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Chemotaxis protein ... , 2 types, 6 molecules ABCDEF

#1: Protein Chemotaxis protein cheY


Mass: 14009.188 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: cheY / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P0A2D5
#2: Protein/peptide Chemotaxis protein cheZ


Mass: 1949.078 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: This sequence corresponds to the C-terminal 19 residues of the CheZ protein occurring naturally in Salmonella enterica serovar Typhumurium.
References: UniProt: P07800

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Non-polymers , 4 types, 61 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 37.5 % PEG 8000, 0.1 M ammonium thiocyanate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 11, 2006 / Details: vertical mirrors
RadiationMonochromator: Horizontally deflecting and focusing crystal before a vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 15119 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.137 / Χ2: 1.068 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.598.60.35514381.093199.2
2.59-2.698.60.29514971.079199.5
2.69-2.828.60.27514631.097199.5
2.82-2.968.50.21714901.074199.7
2.96-3.158.50.18314981.091199.4
3.15-3.398.50.14115091.039199.7
3.39-3.738.40.11215071.078199.6
3.73-4.278.20.0915261.049199.7
4.27-5.388.20.08115521.051199.7
5.38-307.60.08116391.027199.1

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.4 Å
Translation2.5 Å29.4 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 15016
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.06-10048.30.585504
6.33-8.0658.90.655502
5.51-6.3356.80.691507
5-5.5153.60.732503
4.62-5570.752505
4.34-4.6256.60.78508
4.11-4.3452.20.767508
3.93-4.1150.60.762502
3.77-3.9351.40.72505
3.63-3.7753.30.749531
3.51-3.6349.50.755540
3.39-3.5152.90.743531
3.29-3.3952.40.694607
3.2-3.29470.71575
3.11-3.2480.743576
3.03-3.1152.20.721641
2.96-3.0354.20.701623
2.89-2.9653.60.685633
2.83-2.89560.688667
2.77-2.8352.20.711687
2.71-2.77500.71679
2.66-2.7151.80.677670
2.61-2.6651.10.699735
2.56-2.6151.30.705729
2.5-2.5658.10.6671048

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DM5phasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345345 mmdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FQW

1fqw


Resolution: 2.6→29.4 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.852 / SU B: 31.499 / SU ML: 0.351 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1371 10.3 %RANDOM
Rwork0.213 ---
all0.22 ---
obs0.22 13375 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 27 54 3389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223365
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.9884527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33326.327147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28615620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7261512
X-RAY DIFFRACTIONr_chiral_restr0.1530.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022474
X-RAY DIFFRACTIONr_nbd_refined0.2090.21602
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22279
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2149
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.29
X-RAY DIFFRACTIONr_mcbond_it0.6361.52223
X-RAY DIFFRACTIONr_mcangle_it0.61523408
X-RAY DIFFRACTIONr_scbond_it1.41231284
X-RAY DIFFRACTIONr_scangle_it2.0654.51119
Refine LS restraints NCS

Ens-ID: 1 / Number: 981 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.535
2BLOOSE POSITIONAL0.55
3CLOOSE POSITIONAL0.545
1ALOOSE THERMAL1.3110
2BLOOSE THERMAL1.3410
3CLOOSE THERMAL1.3910
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 101 -
Rwork0.21 881 -
obs-982 98.99 %
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)
15.85220.2318-0.23954.5412-0.76271.7075-0.0229-0.452-0.06280.2425-0.0994-0.21090.0280.33680.1222-0.0368-0.0109-0.0125-0.05460.0187-0.0933-8.259941.69011.6596
22.34381.6771-0.67633.19810.36851.42190.00570.1970.2562-0.2645-0.02990.0226-0.0835-0.16360.0242-0.09340.00950.0061-0.02320.0042-0.0782-11.650546.1235-10.4398
322.952521.296-0.912120.220.06921.85450.12050.77180.1456-0.29890.1294-0.41830.06740.5855-0.24990.07620.03810.05660.0368-0.0190.1203-0.13536.4858-10.5376
43.62290.604-1.07212.97691.28251.87150.00120.6144-0.3054-0.3719-0.10410.2715-0.1438-0.44970.1029-0.03930.0231-0.01240.0467-0.0254-0.0022-21.738668.1618-1.8774
53.00970.7647-1.59734.56740.59842.191-0.11530.02930.17170.33940.0195-0.1834-0.03330.10120.0958-0.05040.01790.009-0.053-0.0351-0.0888-17.524575.95969.0659
61.2118-1.4215-1.30364.847-0.52782.7332-0.3686-0.2992-0.31620.04810.27310.55250.1291-0.38290.09550.010.002-0.02170.0174-0.0553-0.0254-23.119263.185111.4293
70.8272-0.20772.0164.16360.03054.98360.17710.05570.57920.157-0.20460.2409-0.3101-0.19510.0275-0.04220.03070.0406-0.1144-0.0181-0.05411.656168.57681.0478
83.1394-0.37660.62814.1010.06192.018-0.06890.1579-0.0093-0.0973-0.00730.18040.0176-0.07350.0762-0.0759-0.0068-0.03-0.08340.0135-0.062114.547661.9583-5.3815
96.8248-2.05852.3581.3498-1.84532.8841-0.38930.4457-0.0333-0.17710.40380.7183-0.0767-0.4044-0.01450.1599-0.0236-0.02320.05870.02110.03438.79871.8057-11.2943
104.5399-5.674311.01187.8176-13.119727.2809-1.35631.3791-1.61780.78661.38811.4368-2.1248-1.5398-0.03180.2770.1639-0.0760.1867-0.03860.2838-19.342235.4048-19.1818
115.0237-0.2079-5.509913.6212-9.767713.3829-0.28490.1859-0.3553-0.3080.1848-0.56330.36330.5680.10010.07970.0532-0.0570.1537-0.09340.0021-10.221138.6245-22.6327
125.03196.14693.372331.5967-0.17483.0257-0.9875-0.4152-0.97761.01450.0230.34460.37070.65360.96450.19240.0933-0.01380.1151-0.01520.0906-13.840962.043120.1226
1326.8753-3.9059-21.918614.076-10.255831.25070.1006-0.9692-0.3195-0.2223-1.06731.65580.2947-0.0510.96670.3447-0.0179-0.0960.17090.07910.1222-20.294868.692423.3915
149.1197.4684-4.45516.1259-3.272517.4963-0.82221.3334-0.0663-0.84320.91060.4892-0.39611.239-0.08840.1831-0.022-0.01460.1560.15010.075318.575175.4964-18.8187
1510.6745.86641.43795.56667.774221.016-0.36880.8587-0.2192-0.01310.82811.24591.0464-0.3936-0.45930.12810.0251-0.08950.15590.10590.258713.864968.0794-23.5446
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 601 - 59
22AA61 - 11460 - 113
33AA115 - 129114 - 128
44BB2 - 461 - 45
55BB47 - 10546 - 104
66BB106 - 129105 - 128
77CC2 - 211 - 20
88CC22 - 10521 - 104
99CC106 - 129105 - 128
1010DD196 - 2021 - 7
1111DD203 - 2148 - 19
1212EE200 - 2085 - 13
1313EE209 - 21414 - 19
1414FF200 - 2055 - 10
1515FF206 - 21411 - 19

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