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- PDB-2o3o: Crystal Structure of the sensor histidine kinase regulator YycI f... -

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Basic information

Entry
Database: PDB / ID: 2o3o
TitleCrystal Structure of the sensor histidine kinase regulator YycI from Bacillus subtitlis
ComponentsYycI protein
KeywordsSIGNALING PROTEIN / two-component system
Function / homology
Function and homology information


membrane => GO:0016020 / plasma membrane
Similarity search - Function
YycH protein, domain 3-like / Regulatory protein YycH-like / YycI protein / YycH protein, domain 2 / Regulatory protein YycH/YycI , domain 2 / TATA-Binding Protein / Lipocalin / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Two-component system WalR/WalK regulatory protein YycI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.89 Å
AuthorsSantelli, E. / Liddington, R.C.
CitationJournal: J.Bacteriol. / Year: 2007
Title: The Crystal Structure of Bacillus subtilis YycI Reveals a Common Fold for Two Members of an Unusual Class of Sensor Histidine Kinase Regulatory Proteins.
Authors: Santelli, E. / Liddington, R.C. / Mohan, M.A. / Hoch, J.A. / Szurmant, H.
History
DepositionDec 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YycI protein
B: YycI protein
C: YycI protein
D: YycI protein
E: YycI protein
F: YycI protein
G: YycI protein
H: YycI protein
I: YycI protein
J: YycI protein
K: YycI protein
L: YycI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,84918
Polymers355,63612
Non-polymers2136
Water00
1
A: YycI protein
C: YycI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3083
Polymers59,2732
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-29 kcal/mol
Surface area25330 Å2
MethodPISA
2
B: YycI protein
D: YycI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3083
Polymers59,2732
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-27 kcal/mol
Surface area25560 Å2
MethodPISA
3
E: YycI protein
G: YycI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3083
Polymers59,2732
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-27 kcal/mol
Surface area25200 Å2
MethodPISA
4
F: YycI protein
H: YycI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3083
Polymers59,2732
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-26 kcal/mol
Surface area25500 Å2
MethodPISA
5
I: YycI protein
K: YycI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3083
Polymers59,2732
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-30 kcal/mol
Surface area25450 Å2
MethodPISA
6
J: YycI protein
L: YycI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3083
Polymers59,2732
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-28 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.792, 161.922, 180.156
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
31I
41A
51E
61I
71A
81E
91I
12B
22F
32J
42B
52F
62J
72B
82F
92J
13C
23G
33K
43C
53G
63K
73C
83G
93K
14D
24H
34L
44D
54H
64L
74D
84H
94L
15A
25B
35C
45D
55A
65B
75C
85D
95A
105B
115C
125D
16A
26E
36I
17B
27F
37J
18C
28G
38K
19D
29H
39L

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUMSEMSE4AA55 - 9129 - 65
211GLUGLUMSEMSE4EE55 - 9129 - 65
311GLUGLUMSEMSE4II55 - 9129 - 65
421VALVALGLUGLU4AA98 - 25072 - 224
521VALVALGLUGLU4EE98 - 25072 - 224
621VALVALGLUGLU4II98 - 25072 - 224
731THRTHRSERSER4AA261 - 273235 - 247
831THRTHRSERSER4EE261 - 273235 - 247
931THRTHRSERSER4II261 - 273235 - 247
112GLUGLUMSEMSE4BB55 - 9129 - 65
212GLUGLUMSEMSE4FF55 - 9129 - 65
312GLUGLUMSEMSE4JJ55 - 9129 - 65
422VALVALGLUGLU4BB98 - 25072 - 224
522VALVALGLUGLU4FF98 - 25072 - 224
622VALVALGLUGLU4JJ98 - 25072 - 224
732THRTHRSERSER4BB261 - 273235 - 247
832THRTHRSERSER4FF261 - 273235 - 247
932THRTHRSERSER4JJ261 - 273235 - 247
113GLUGLUMSEMSE4CC55 - 9129 - 65
213GLUGLUMSEMSE4GG55 - 9129 - 65
313GLUGLUMSEMSE4KK55 - 9129 - 65
423VALVALGLUGLU4CC98 - 25072 - 224
523VALVALGLUGLU4GG98 - 25072 - 224
623VALVALGLUGLU4KK98 - 25072 - 224
733THRTHRSERSER4CC261 - 273235 - 247
833THRTHRSERSER4GG261 - 273235 - 247
933THRTHRSERSER4KK261 - 273235 - 247
114GLUGLUMSEMSE4DD55 - 9129 - 65
214GLUGLUMSEMSE4HH55 - 9129 - 65
314GLUGLUMSEMSE4LL55 - 9129 - 65
424VALVALGLUGLU4DD98 - 25072 - 224
524VALVALGLUGLU4HH98 - 25072 - 224
624VALVALGLUGLU4LL98 - 25072 - 224
734THRTHRSERSER4DD261 - 273235 - 247
834THRTHRSERSER4HH261 - 273235 - 247
934THRTHRSERSER4LL261 - 273235 - 247
115LYSLYSMSEMSE6AA34 - 918 - 65
215LYSLYSMSEMSE6BB34 - 918 - 65
315LYSLYSMSEMSE6CC34 - 918 - 65
415LYSLYSMSEMSE6DD34 - 918 - 65
525VALVALGLUGLU6AA98 - 25072 - 224
625VALVALGLUGLU6BB98 - 25072 - 224
725VALVALGLUGLU6CC98 - 25072 - 224
825VALVALGLUGLU6DD98 - 25072 - 224
935THRTHRSERSER6AA261 - 273235 - 247
1035THRTHRSERSER6BB261 - 273235 - 247
1135THRTHRSERSER6CC261 - 273235 - 247
1235THRTHRSERSER6DD261 - 273235 - 247
116LYSLYSTYRTYR4AA34 - 548 - 28
216LYSLYSTYRTYR4EE34 - 548 - 28
316LYSLYSTYRTYR4II34 - 548 - 28
117LYSLYSTYRTYR4BB34 - 548 - 28
217LYSLYSTYRTYR4FF34 - 548 - 28
317LYSLYSTYRTYR4JJ34 - 548 - 28
118LYSLYSTYRTYR4CC34 - 548 - 28
218LYSLYSTYRTYR4GG34 - 548 - 28
318LYSLYSTYRTYR4KK34 - 548 - 28
119LYSLYSTYRTYR4DD34 - 548 - 28
219LYSLYSTYRTYR4HH34 - 548 - 28
319LYSLYSTYRTYR4LL34 - 548 - 28

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
Detailspairs of chains (A, C) (B, D) (E, G) (F, H) (I, K) (J, L) each define a dimeric assembly

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Components

#1: Protein
YycI protein


Mass: 29636.318 Da / Num. of mol.: 12 / Fragment: Periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yycI / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q45612
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl

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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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / pH: 3.2
Details: 18% PEG1500, 100 MM CITRATE BUFFER, 200 mM lithium sulfate, pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 3.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.94645, 0.97969, 0.97955
DetectorDetector: CCD / Date: May 20, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979691
30.979551
ReflectionResolution: 2.89→90 Å / Num. obs: 71733 / % possible obs: 92.7 % / Observed criterion σ(I): -4 / Redundancy: 3.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.4
Reflection shellResolution: 2.89→2.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1.4 / % possible all: 53.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.89→90 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.885 / SU B: 40.89 / SU ML: 0.352 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.464
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3605 5 %RANDOM
Rwork0.212 ---
obs0.214 68065 92.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.23 Å2
2---1.22 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.89→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23395 0 6 0 23401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02223820
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215971
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.96232140
X-RAY DIFFRACTIONr_angle_other_deg0.764339512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65552848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07126.5451146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.733154614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8121524
X-RAY DIFFRACTIONr_chiral_restr0.0690.23598
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0225880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024252
X-RAY DIFFRACTIONr_nbd_refined0.2060.24282
X-RAY DIFFRACTIONr_nbd_other0.180.214972
X-RAY DIFFRACTIONr_nbtor_refined0.1840.211218
X-RAY DIFFRACTIONr_nbtor_other0.0850.213090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2375
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.276
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.2117
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.925117374
X-RAY DIFFRACTIONr_mcbond_other0.38615743
X-RAY DIFFRACTIONr_mcangle_it2.796223314
X-RAY DIFFRACTIONr_scbond_it4.6362.510963
X-RAY DIFFRACTIONr_scangle_it6.39448826
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2776medium positional0.280.5
12E2776medium positional0.250.5
13I2776medium positional0.280.5
21B2776medium positional0.280.5
22F2776medium positional0.30.5
23J2776medium positional0.360.5
31C2776medium positional0.540.5
32G2776medium positional0.370.5
33K2776medium positional0.530.5
41D2776medium positional0.390.5
42H2776medium positional0.340.5
43L2776medium positional0.530.5
61A286medium positional0.230.5
62E286medium positional0.260.5
63I286medium positional0.330.5
71B286medium positional0.350.5
72F286medium positional0.330.5
73J286medium positional0.530.5
81C286medium positional0.250.5
82G286medium positional0.290.5
83K286medium positional0.260.5
91D286medium positional0.240.5
92H286medium positional0.270.5
93L286medium positional0.260.5
51A3062loose positional0.55
52B3062loose positional0.555
53C3062loose positional0.815
54D3062loose positional0.655
11A2776medium thermal0.472
12E2776medium thermal0.442
13I2776medium thermal0.492
21B2776medium thermal0.462
22F2776medium thermal0.432
23J2776medium thermal0.452
31C2776medium thermal0.472
32G2776medium thermal0.442
33K2776medium thermal0.442
41D2776medium thermal0.472
42H2776medium thermal0.422
43L2776medium thermal0.452
61A286medium thermal0.522
62E286medium thermal0.512
63I286medium thermal0.622
71B286medium thermal0.512
72F286medium thermal0.462
73J286medium thermal0.552
81C286medium thermal0.42
82G286medium thermal0.342
83K286medium thermal0.362
91D286medium thermal0.362
92H286medium thermal0.452
93L286medium thermal0.412
51A3062loose thermal3.1710
52B3062loose thermal3.1410
53C3062loose thermal3.2310
54D3062loose thermal3.0210
LS refinement shellResolution: 2.89→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 129 -
Rwork0.327 2506 -
obs--46.6 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.25110.8230.43671.78090.13851.712-0.12050.4488-0.9292-0.0229-0.02760.14710.1642-0.0860.148-0.31820.05680.076-0.4019-0.1021-0.19425.248720.9211154.855
26.53480.3629-0.86221.64520.00161.79660.00210.47940.7124-0.0297-0.0134-0.038-0.22580.07230.0113-0.28010.0294-0.0149-0.38650.0825-0.340291.116946.5085152.8989
32.32532.5846-0.85.5158-2.91424.2987-0.0298-0.16160.34310.9066-0.0356-0.0314-0.31180.27180.06540.04870.099-0.016-0.4452-0.0042-0.373940.7299.2039187.2543
42.71471.82371.05144.55642.67454.5419-0.0448-0.1295-0.33270.25450.04530.06540.1187-0.2386-0.0005-0.22490.09560.0407-0.41830.0143-0.409575.555262.1317183.431
57.8861.4840.67212.0040.25852.0521-0.10020.1995-0.9389-0.0620.0198-0.00470.2224-0.08720.0804-0.27670.07330.1063-0.436-0.064-0.221827.125821.788592.9892
65.86081.3602-0.48141.93720.27152.102-0.18580.21820.8515-0.09390.08650.2192-0.32110.08030.0993-0.2420.0492-0.0516-0.43060.069-0.216993.228447.347992.0666
72.02042.4353-1.67474.6469-3.10225.58050.036-0.12360.41250.08880.12890.08350.20140.3411-0.1649-0.06240.1424-0.0531-0.2389-0.0395-0.297441.61437.5205123.8412
82.83952.02720.88654.76782.37834.87070.01820.0192-0.44360.3378-0.06160.0668-0.0741-0.4150.0434-0.06420.09560.0967-0.345-0.0011-0.246378.320460.361124.1545
95.94171.12531.06661.9328-0.11531.8017-0.02340.2544-0.497-0.0917-0.0041-0.09620.33660.03650.0275-0.27770.03790.0403-0.4194-0.0205-0.408925.199622.404731.8043
106.12911.2207-0.56691.7594-0.21742.0692-0.10740.20830.8177-0.01460.0767-0.064-0.25610.0680.0307-0.29860.0311-0.0584-0.44560.0726-0.2275
113.39591.9606-0.72534.7188-2.54234.7592-0.1447-0.08930.34810.40880.05380.02080.06480.31830.09090.06290.16520.0377-0.3772-0.0097-0.413240.08758.257763.7913
122.33442.74041.24674.39553.29945.65830.2722-0.0919-0.12190.5393-0.1068-0.0338-0.0033-0.3855-0.1655-0.03290.08390.0318-0.285-0.0025-0.151675.124560.50266.1438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 273
2X-RAY DIFFRACTION2B34 - 273
3X-RAY DIFFRACTION3C34 - 273
4X-RAY DIFFRACTION4D34 - 273
5X-RAY DIFFRACTION5E34 - 273
6X-RAY DIFFRACTION6F34 - 273
7X-RAY DIFFRACTION7G34 - 273
8X-RAY DIFFRACTION8H34 - 273
9X-RAY DIFFRACTION9I34 - 273
10X-RAY DIFFRACTION10J34 - 273
11X-RAY DIFFRACTION11K34 - 273
12X-RAY DIFFRACTION12L34 - 273

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