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- PDB-4r3a: Erythrobacter litoralis EL346 blue-light activated histidine kinase -

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Basic information

Entry
Database: PDB / ID: 4r3a
TitleErythrobacter litoralis EL346 blue-light activated histidine kinase
ComponentsBlue-light-activated histidine kinase 2
KeywordsSIGNALING PROTEIN / light-activated / LOV domain / histidine kinase / Bergerat fold / signal transduction / sensory transduction / photoreceptor / cell signaling / regulation / two-component system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / 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 / PAS domain / Histidine kinase domain / Histidine kinase domain 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 / PAS domain / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Beta-Lactamase / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RIBOFLAVIN / Blue-light-activated histidine kinase 2
Similarity search - Component
Biological speciesErythrobacter litoralis HTCC2594 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 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 1.3Sep 20, 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 / pdbx_initial_refinement_model / 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_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.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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Blue-light-activated histidine kinase 2
B: Blue-light-activated histidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0588
Polymers77,2452
Non-polymers1,8146
Water00
1
A: Blue-light-activated histidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5294
Polymers38,6221
Non-polymers9073
Water0
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)39,5294
Polymers38,6221
Non-polymers9073
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.882, 98.882, 422.255
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 38622.352 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N4O6
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 293 K / pH: 6
Details: 26% PEG 3350, 0.2 M ammonium sulfate, 0.1 M BisTris, 0.1 mM reduced L-glutathione, 0.1 mM oxidized L-glutathione, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2010 / Details: MONOCHROMATOR
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. obs: 17699 / % possible obs: 99.8 % / Observed criterion σ(I): 50 / Redundancy: 33.6 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.95→3 Å / Redundancy: 27.1 % / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.14data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R38, 4R39

4r38

4r39


Resolution: 2.92→46.6 Å / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.33 1693 -
Rwork0.29 --
obs0.294 16909 94.7 %
all-16909 -
Displacement parametersBiso mean: 98.13 Å2
Refine analyzeLuzzati sigma a obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.92→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4615 0 118 0 4733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.05
X-RAY DIFFRACTIONf_dihedral_angle_d14.507
X-RAY DIFFRACTIONf_chiral_restr0.039
X-RAY DIFFRACTIONf_plane_restr0.004
LS refinement shellResolution: 2.92→3.0042 Å
RfactorNum. reflection% reflection
Rfree0.4528 87 -
Rwork0.3677 0 -
obs--1 %
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)
16.4562-3.3744-5.16861.92631.7629.57870.13630.3086-0.2889-0.35980.0169-0.46350.15650.212-0.15381.320.1182-0.34421.22-0.24071.3017-3.885113.575445.0706
22.90210.0062-0.61382.6633-1.2910.75280.0340.5035-0.401-0.36340.13810.20040.25720.1194-0.31060.3213-0.144-0.28550.1586-0.20180.24143.828322.904752.1676
36.7223.32320.04951.6543-0.1583.036-0.0993-0.23110.08850.16640.0351-0.3647-0.0010.32770.11590.29250.287-0.11310.4853-0.03660.612315.441320.162266.7147
42.32130.4753-1.52733.4725-1.29531.2912-0.10970.301-0.1903-0.64860.04370.54950.1487-0.25860.0770.5396-0.0639-0.17550.103-0.02190.65115.908617.838551.9354
51.7837-1.13610.19114.005-0.55594.9751-0.25590.1909-0.4138-0.51940.2994-0.15610.47210.41990.08460.3383-0.06520.06890.2211-0.04340.39816.455518.065552.7699
61.15950.47730.26340.68170.18931.3428-0.0892-0.01310.0878-0.09060.0241-0.1806-0.09590.1738-0.20510.218-0.4225-0.14760.3178-0.08620.331717.722431.638455.9386
70.8385-0.8299-0.73233.69212.14482.268-0.07680.2029-0.0818-0.53230.0918-0.2257-0.05130.2099-0.25430.5033-0.28280.07150.2859-0.24210.191213.383325.14847.5911
84.1234-2.5025-1.49246.2934-1.17882.9503-0.1103-0.4414-0.0930.55720.08320.8031-0.0669-0.71990.02540.29450.0448-0.03670.6451-0.1990.50564.072728.481171.0259
92.04830.72831.30383.59860.07990.8732-0.14220.4879-0.1695-0.65610.2087-0.2342-0.23610.3785-0.11560.2851-0.1681-0.05990.2814-0.18930.242810.605627.026849.1489
100.85570.61760.55510.90910.47141.5263-0.2220.1493-0.0265-0.3503-0.05720.0939-0.0047-0.0635-0.21540.1991-0.3688-0.5604-0.1211-0.24910.4167-1.209529.070653.6612
110.47220.21830.32480.48550.07660.6897-0.0620.1955-0.2652-0.23130.03580.35750.0523-0.0836-0.18370.2273-0.5262-1.1495-0.0397-0.36320.5869-18.526527.58247.6583
122.4291-0.06941.75950.71380.95282.66490.1342-0.0025-0.0339-0.065-0.11370.41440.1459-0.3021-0.12970.4213-0.0495-0.55940.0706-0.07980.8996-25.180730.690258.6055
130.1822-0.76540.41223.3746-1.26352.19230.0544-0.0324-0.0591-0.1745-0.14850.4171-0.005-0.16750.02680.3126-0.1691-0.567-0.0102-0.07870.6176-17.227335.506560.7962
142.94832.2996-1.00162.3936-0.56075.54140.2925-0.170.19520.2089-0.00750.1433-0.39540.5246-0.12440.60040.0134-0.51990.1583-0.05840.823-21.983138.913653.7085
150.3599-0.049-0.75830.00570.10261.5864-0.0080.28940.2375-0.29610.064-0.3186-0.32110.2338-0.08121.99320.0185-0.22711.6306-0.1991.09154.174232.50765.5811
160.49340.79-0.99841.2628-1.59642.01750.0932-0.38810.27290.21510.0982-0.0666-0.39890.4041-0.19652.3982-0.0092-0.37372.0219-0.16871.6650.818636.669210.9923
170.81020.60210.83914.5114-5.15949.10890.17590.57190.8105-0.5085-0.0809-0.0528-0.7837-0.168-0.09131.95290.1099-0.26861.5374-0.22411.31872.922137.355722.2004
182.24780.30311.74310.992-0.71812.30780.01590.01650.1828-0.03330.081-0.0212-0.2555-0.05040.00622.18040.0148-0.271.6611-0.24521.28328.452338.591213.2011
198.07122.22486.95340.61351.91585.99130.1082-0.0784-0.94380.51530.0968-0.48711.12070.0761-0.1821.9059-0.0107-0.19611.6524-0.29071.079919.41627.337817.8051
200.6124-0.03450.49730.64330.57852.36640.07760.185-0.1521-0.1020.02360.07310.1924-0.0904-0.02091.71790.0727-0.22091.4919-0.45671.175911.029623.93613.5422
211.32510.2489-1.88526.10220.67812.85790.08480.3978-0.2299-0.07420.05040.02670.24980.0678-0.13131.53410.0059-0.11291.2998-0.51390.79466.617624.428518.0782
220.95090.6629-1.88084.3534-0.79763.79450.29530.4928-0.0137-0.1892-0.06250.05760.60120.4902-0.19721.5443-0.057-0.15391.2796-0.40110.71152.859627.308614.6976
230.60950.1977-0.22690.71850.34221.0607-0.18320.4011-0.0639-0.12690.19980.071-0.0873-0.1569-0.01191.3592-0.0736-0.59911.2786-0.4170.8256-8.072226.070219.8101
241.9035-0.1250.9751.59740.0331.8505-0.05240.10540.0921-0.1242-0.00210.038-0.10150.01530.03510.8537-0.1892-0.85780.8973-0.13540.8133-17.770629.107432.7887
252.7342-0.62242.09412.1549-0.81834.0612-0.092-0.00650.11590.04030.0602-0.1179-0.1935-0.1210.1111.1778-0.2556-0.6721.4338-0.41830.8497-19.91428.966522.9545
261.1872-0.28660.8040.1913-0.6362.22130.07640.1257-0.16990.0651-0.06880.10660.1747-0.0792-0.11250.9845-0.0616-0.63391.1568-0.20060.86-28.889627.54730.8021
270.145-0.3753-0.29261.07030.51141.0384-0.04490.1572-0.0156-0.07850.11630.124-0.1248-0.15680.05821.491-0.1038-0.77451.8971-0.14620.7907-27.984430.526714.3286
280.94-0.35811.01942.4036-0.20861.94090.03120.0739-0.2162-0.0229-0.03220.04870.260.16-0.29620.9929-0.1472-0.83171.3819-0.3160.811-28.899520.84324.3099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 31 )
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 43 )
5X-RAY DIFFRACTION5chain 'A' and (resid 44 through 64 )
6X-RAY DIFFRACTION6chain 'A' and (resid 65 through 88 )
7X-RAY DIFFRACTION7chain 'A' and (resid 89 through 103 )
8X-RAY DIFFRACTION8chain 'A' and (resid 104 through 112 )
9X-RAY DIFFRACTION9chain 'A' and (resid 113 through 125 )
10X-RAY DIFFRACTION10chain 'A' and (resid 129 through 187 )
11X-RAY DIFFRACTION11chain 'A' and (resid 188 through 271 )
12X-RAY DIFFRACTION12chain 'A' and (resid 272 through 298 )
13X-RAY DIFFRACTION13chain 'A' and (resid 299 through 318 )
14X-RAY DIFFRACTION14chain 'A' and (resid 319 through 338 )
15X-RAY DIFFRACTION15chain 'B' and (resid 19 through 30 )
16X-RAY DIFFRACTION16chain 'B' and (resid 31 through 36 )
17X-RAY DIFFRACTION17chain 'B' and (resid 37 through 43 )
18X-RAY DIFFRACTION18chain 'B' and (resid 44 through 58 )
19X-RAY DIFFRACTION19chain 'B' and (resid 59 through 64 )
20X-RAY DIFFRACTION20chain 'B' and (resid 65 through 93 )
21X-RAY DIFFRACTION21chain 'B' and (resid 94 through 103 )
22X-RAY DIFFRACTION22chain 'B' and (resid 104 through 124 )
23X-RAY DIFFRACTION23chain 'B' and (resid 135 through 188 )
24X-RAY DIFFRACTION24chain 'B' and (resid 189 through 233 )
25X-RAY DIFFRACTION25chain 'B' and (resid 234 through 254 )
26X-RAY DIFFRACTION26chain 'B' and (resid 255 through 282 )
27X-RAY DIFFRACTION27chain 'B' and (resid 283 through 310 )
28X-RAY DIFFRACTION28chain 'B' and (resid 311 through 336 )

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