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- PDB-4r39: Histidine kinase domain from Erythrobacter litoralis EL346 blue-l... -

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Basic information

Entry
Database: PDB / ID: 4r39
TitleHistidine kinase domain from Erythrobacter litoralis EL346 blue-light activated histidine kinase
ComponentsBlue-light-activated histidine kinase 2
KeywordsTRANSFERASE / light-activated / histidine kinase domain / Bergerat fold / sensory transduction / signal transduction / photoreceptor
Function / homology
Function and homology information


protein histidine kinase activity / response to stimulus / histidine kinase / photoreceptor activity / ATP binding
Similarity search - Function
Signal transduction histidine kinase, subgroup 2, dimerisation and phosphoacceptor domain / Histidine kinase / Histidine kinase-like ATPase domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / PAS repeat profile. ...Signal transduction histidine kinase, subgroup 2, dimerisation and phosphoacceptor domain / Histidine kinase / Histidine kinase-like ATPase domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Blue-light-activated histidine kinase 2
Similarity search - Component
Biological speciesErythrobacter litoralis HTCC2594 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.603 Å
AuthorsTomchick, D.R. / Rivera-Cancel, G. / Gardner, K.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Full-length structure of a monomeric histidine kinase reveals basis for sensory regulation.
Authors: Rivera-Cancel, G. / Ko, W.H. / Tomchick, D.R. / Correa, F. / Gardner, K.H.
History
DepositionAug 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Blue-light-activated histidine kinase 2
B: Blue-light-activated histidine kinase 2
C: Blue-light-activated histidine kinase 2
D: Blue-light-activated histidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,85412
Polymers99,7324
Non-polymers2,1228
Water4,936274
1
A: Blue-light-activated histidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4643
Polymers24,9331
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Blue-light-activated histidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4643
Polymers24,9331
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Blue-light-activated histidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4643
Polymers24,9331
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Blue-light-activated histidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4643
Polymers24,9331
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.503, 120.503, 192.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Blue-light-activated histidine kinase 2 / EL346-LOV-histidine kinase / EL346-LOV-HK


Mass: 24933.115 Da / Num. of mol.: 4 / Fragment: C-terminal histidine kinase, UNP residues 121-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacter litoralis HTCC2594 (bacteria)
Strain: HTCC2594 / Gene: ELI_04860 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2NB77, histidine kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.564.86
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop68% PEG 8000, 0.2 M sodium chloride, 0.1 M sodium cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop76% PEG 8000, 0.2 M magnesium chloride, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97934
SYNCHROTRONAPS 19-ID20.97912
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDAug 8, 2012monochromator
ADSC QUANTUM 315r2CCDOct 18, 2012monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979121
ReflectionResolution: 2.6→50 Å / Num. all: 43630 / Num. obs: 43630 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.095 / Χ2: 1.101
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.644.40.83521650.9771,299.4
2.64-2.694.70.70721561.0131,299.6
2.69-2.744.80.57821720.9971,299.7
2.74-2.84.90.52621801.031,299.7
2.8-2.864.90.45321540.9571,2100
2.86-2.934.90.39621641.0331,299.7
2.93-34.90.30521620.9481,299.6
3-3.084.90.24221821.0341,299.4
3.08-3.174.90.21221511.0921,299.1
3.17-3.284.90.1621911.1631,299.5
3.28-3.394.90.12221491.1371,299.4
3.39-3.534.80.10821851.1321,299.3
3.53-3.694.80.09221681.2011,298.7
3.69-3.884.80.07621891.1821,298.5
3.88-4.134.70.06421901.1381,299.1
4.13-4.454.70.05921691.1511,297.8
4.45-4.894.60.05421851.1831,297.8
4.89-5.64.50.0622021.2131,297.6
5.6-7.054.50.05322121.291,296.5
7.05-504.40.03123041.1641,294

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.603→41.25 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 21.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 2180 5.01 %RANDOM
Rwork0.1831 ---
all0.185 43544 --
obs0.185 43544 98.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.15 Å2 / Biso mean: 35.99 Å2 / Biso min: 0.9 Å2
Refine analyzeLuzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.603→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6346 0 128 274 6748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076556
X-RAY DIFFRACTIONf_angle_d0.8998925
X-RAY DIFFRACTIONf_chiral_restr0.0461063
X-RAY DIFFRACTIONf_plane_restr0.0031152
X-RAY DIFFRACTIONf_dihedral_angle_d16.2892445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.603-2.65920.31931510.27162512266399
2.6592-2.72110.31221360.243925692705100
2.7211-2.78910.2821370.23892569270699
2.7891-2.86450.27861300.232525832713100
2.8645-2.94880.29281370.22962566270399
2.9488-3.04390.26991310.208625602691100
3.0439-3.15270.25721350.20392593272899
3.1527-3.27890.24241300.1962582271299
3.2789-3.4280.23111310.20082571270299
3.428-3.60870.23271240.18392586271099
3.6087-3.83460.19411470.17072573272099
3.8346-4.13040.20241440.15342598274299
4.1304-4.54560.18131360.14752574271098
4.5456-5.20230.18841430.14912595273898
5.2023-6.55010.21021330.19942623275697
6.5501-41.2550.18761350.16862710284595
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)
15.52822.19111.98044.09012.98197.35050.3039-0.72690.06990.32570.11440.41180.1626-0.2058-0.27520.2591-0.04010.02340.46650.10520.285547.220819.261693.788
23.83540.9619-0.43651.9046-2.11862.51320.0801-0.2117-0.26270.18870.0038-0.0461-0.00680.2813-0.08450.14490.0477-0.01350.37260.00020.374657.024421.053988.4124
32.2981-1.00170.64011.25411.06962.58350.0705-0.4229-0.1740.242-0.00450.19980.1281-0.2443-0.06510.1572-0.0475-0.00350.34840.07610.213941.429720.523184.875
41.24790.314-0.52431.7041-0.3960.79810.0538-0.1241-0.16860.09930.0204-0.1312-0.0820.1123-0.03920.0639-0.0355-0.0120.2605-0.0270.134646.652228.644975.1886
52.75222.23390.49714.3040.17320.94360.00070.2043-0.0913-0.23490.08490.0407-0.04170.152-0.08290.0731-0.00190.03770.2538-0.07780.193747.35829.022465.3074
61.7645-2.25471.52155.9159-2.83791.57460.18070.36880.0022-0.3858-0.2236-0.65330.22260.42170.06290.1570.064-0.00820.4761-0.0560.374562.986125.623765.4986
71.384-0.40240.53641.2049-0.50041.71360.11290.0202-0.4532-0.14770.0381-0.02790.31270.14540.0640.12050.03770.02570.3024-0.09840.295650.091915.59169.8017
83.3554-0.3295-1.85072.56931.5213.5389-0.018-0.12670.33810.16550.1126-0.1745-0.4080.3571-0.0870.3653-0.09450.04010.2545-0.12110.359945.946556.993182.0297
91.5637-0.30750.15861.66360.00591.7250.0624-0.13250.44530.0305-0.02690.1272-0.3008-0.036-0.05830.16060.00360.06570.2179-0.0480.230233.453747.385773.282
102.61560.64490.50061.43910.31241.6945-0.03490.1410.2079-0.2451-0.0040.0426-0.24270.06490.01750.64810.02320.14060.94660.14020.325839.325740.904828.6737
110.48240.1267-1.24351.47930.07324.8566-0.15330.1234-0.1135-0.3820.0814-0.21910.05240.17040.02920.54570.10730.16451.0201-0.0810.341544.752831.527828.741
120.2307-0.02230.13841.8050.54722.60180.00580.2112-0.0111-0.1561-0.01230.014-0.05490.03660.00350.23090.09820.00270.77860.01410.186436.254236.69836.6148
133.5418-0.4726-0.86853.7416-1.71556.6186-0.0440.52940.661-0.32280.0375-0.077-0.46830.279-0.00390.40950.01270.06130.65090.1710.387944.099150.080941.4634
141.56680.7277-0.46261.8524-0.66291.7440.17470.3489-0.0563-0.0577-0.00560.0965-0.19940.1864-0.08350.11230.01690.01340.3876-0.07330.183935.034931.819148.6969
150.36470.1375-0.31191.75570.10570.5551-0.07560.1764-0.0821-0.28690.0301-0.15590.08870.03060.07630.22370.05260.05340.551-0.08930.167643.292129.519643.0679
163.00121.76940.38812.93790.61451.46760.27810.1449-0.24710.0571-0.053-0.16480.00770.1193-0.12350.12760.03720.01690.2772-0.13040.225542.684327.377354.6583
172.13131.1198-2.15420.5882-1.13122.1763-0.2096-0.1024-0.401-0.493-0.142-0.5480.41580.42390.34960.38850.17110.10050.7262-0.24070.619650.335215.874346.5153
180.0968-0.3603-0.18852.39071.91831.7768-0.12830.1614-0.2353-0.27290.0037-0.20640.11640.0704-0.05190.38320.14450.19510.7457-0.14560.366652.427828.990439.5296
195.83044.5777-5.0233.662-4.19085.2209-0.1814-0.0343-0.5777-0.5696-0.1876-0.81380.4270.39940.41840.17810.07270.0510.3132-0.10250.281851.283522.611952.7919
201.42931.4839-1.01382.6369-0.57341.23080.13810.29310.2714-0.2-0.0542-0.2642-0.21560.2667-0.10990.1742-0.01050.05850.53040.07420.288852.925139.30748.1705
213.2093-1.030.84073.33320.26553.86660.25740.1492-0.1168-0.2359-0.02940.14850.16250.0295-0.14830.13410.0193-0.09190.3583-0.08720.36517.787921.030346.6526
221.71260.1340.30140.6318-0.02631.31630.11480.1796-0.1082-0.01730.00190.1153-0.019-0.0909-0.09610.08630.0514-0.00630.2531-0.03150.177619.708831.295156.3971
232.57840.3164-0.62761.01-0.64012.44620.124-0.2232-0.11610.0886-0.00050.60780.0037-0.4422-0.07930.08730.04080.00190.3616-0.01530.194515.357330.913367.3733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 145 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 171 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 200 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 201 through 254 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 255 through 282 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 283 through 298 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 299 through 343 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 130 through 189 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 190 through 341 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 130 through 145 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 146 through 170 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 171 through 189 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 190 through 200 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 201 through 233 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 234 through 254 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 255 through 282 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 283 through 298 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 299 through 311 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 312 through 324 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 325 through 340 )C0
21X-RAY DIFFRACTION21chain 'D' and (resid 127 through 169 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 170 through 311 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 312 through 343 )D0

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