[English] 日本語
Yorodumi
- PDB-2pl9: Crystal Structure of CheY-Mg(2+)-BeF(3)(-) in Complex with CheZ(C... -

+
Open data


ID or keywords:

Loading...

-
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 / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of chemotaxis / bacterial-type flagellum / 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 ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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).

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more