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- PDB-7f2h: Crystal structure of the sensor domain of VbrK from Vibrio rotife... -

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Basic information

Entry
Database: PDB / ID: 7f2h
TitleCrystal structure of the sensor domain of VbrK from Vibrio rotiferianus (crystal type 2)
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / sensor domain / beta-lactam antibiotic receptor / S-nitrosylation
Function / homology
Function and homology information


phosphorelay sensor kinase activity / membrane => GO:0016020
Similarity search - Function
Protein of unknown function DUF3404 / Domain of unknown function (DUF3404) / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases ...Protein of unknown function DUF3404 / Domain of unknown function (DUF3404) / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesVibrio rotiferianus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCho, S.Y. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of the antibiotic- and nitrite-responsive histidine kinase VbrK sensor domain from Vibrio rotiferianus.
Authors: Cho, S.Y. / Yoon, S.I.
History
DepositionJun 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine kinase
B: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)50,2312
Polymers50,2312
Non-polymers00
Water18010
1
A: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)25,1161
Polymers25,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)25,1161
Polymers25,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.483, 49.727, 199.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROILEILE(chain 'A' and (resid 21 through 31 or (resid 32...AA21 - 746 - 59
12LEULEUTYRTYR(chain 'A' and (resid 21 through 31 or (resid 32...AA77 - 7862 - 63
13LEULEUILEILE(chain 'A' and (resid 21 through 31 or (resid 32...AA88 - 10473 - 89
14GLYGLYVALVAL(chain 'A' and (resid 21 through 31 or (resid 32...AA107 - 23592 - 220
25PROPROILEILE(chain 'B' and (resid 21 through 158 or (resid 159...BB21 - 746 - 59
26LEULEUTYRTYR(chain 'B' and (resid 21 through 158 or (resid 159...BB77 - 7862 - 63
27LEULEUILEILE(chain 'B' and (resid 21 through 158 or (resid 159...BB88 - 10473 - 89
28GLYGLYVALVAL(chain 'B' and (resid 21 through 158 or (resid 159...BB107 - 23592 - 220

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Components

#1: Protein Histidine kinase /


Mass: 25115.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio rotiferianus (bacteria) / Gene: BI375_20590 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2K7STF1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 23241 / % possible obs: 95.2 % / Redundancy: 5.6 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 39
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.603 / Num. unique obs: 1105 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CUS

7cus


Resolution: 2.25→26.37 Å / SU ML: 0.3533 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6882
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2565 1072 4.63 %
Rwork0.2199 22071 -
obs0.2216 23143 95.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→26.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 0 10 3241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813310
X-RAY DIFFRACTIONf_angle_d1.01394510
X-RAY DIFFRACTIONf_chiral_restr0.0561502
X-RAY DIFFRACTIONf_plane_restr0.0073583
X-RAY DIFFRACTIONf_dihedral_angle_d14.73561986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.350.3721510.29272669X-RAY DIFFRACTION94.76
2.35-2.480.31761000.29042713X-RAY DIFFRACTION94.71
2.48-2.630.36261360.27152698X-RAY DIFFRACTION94.88
2.63-2.830.34231550.27932698X-RAY DIFFRACTION95.83
2.83-3.120.37221310.28312737X-RAY DIFFRACTION94.68
3.12-3.570.29331150.23222795X-RAY DIFFRACTION95.5
3.57-4.490.19551340.18132837X-RAY DIFFRACTION96.96
4.49-26.370.19981500.18492924X-RAY DIFFRACTION95.11
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)
16.134696131771.693282119380.5340868825669.20439060047-4.158029878137.92511612956-0.000422420981216-1.191863258550.249377235861.6533481346-0.334734153273-0.832294592226-0.06194469261161.08996755320.158569882980.570901477553-0.128971168825-0.1733359940940.9022918791210.1942900716150.54652294586415.8384713064-26.1501993327-25.656058524
24.00154382982.93806788195-2.614711888337.56567522209-4.871702294363.35354364467-0.401912225620.115830762667-0.21087471612-0.5122539653440.2012452677470.05326822342470.937224807356-0.2008470226740.1451213486120.572415957109-0.00878827015147-0.0136176016870.211690787661-0.027008519430.43079586889816.2870246645-24.9711901894-47.1900068531
35.175270777980.24700671187-0.6418760123042.016751432570.06434412752913.616738080910.0867869348911-0.3888161944970.1081791923670.623201640080.1037216672480.35788093482-0.3054923746760.215252449282-0.1680901154280.423399189530.00423927520855-0.007216599911440.2481485201510.003636066437520.4581009914514.94222787730.261139864557-49.9408509763
41.68407277052-2.187348131650.812232752323.21660310769-1.948811822372.438383989390.6512713561290.2450800235820.8701873469030.0137562448662-0.2436957881430.100235907374-0.50879743063-0.448782216323-0.3895366193681.075897837550.08321759808360.05298715110320.4318572673050.09478039474310.73840394901214.323518073316.4110988692-58.572037162
52.348415932670.6280436391521.075548555253.68978334606-2.180951407394.65243370584-0.06660741920090.170900738728-0.125442541069-0.4011043915220.2683921054630.2109842173660.278168574018-0.0491942837333-0.2290851022610.3940417651370.0120839494970.008260056812570.226532767015-0.04494025868570.46241850070413.3821726564-3.15705738302-59.9921962406
68.90608918551.51080146789-1.996069554138.092332482820.2324342144318.862672931490.179467130219-0.36627794745-0.0754802585138-0.2113960428380.1299820167070.4020608154750.280818072341-0.326261465379-0.249924551440.380660172771-0.078610339288-0.07131057418470.307235285010.06542551802460.41876237076612.7178632135-21.6972750793-41.0628546458
75.25948831167-1.659523431781.240408508064.21021976111-0.1439605067245.723849361410.041836103476-0.673714141550.1109037061650.7091824703570.05250069811740.744647762137-0.1058543382-0.512374727915-0.2141827452530.593192342186-0.1490747261950.1252006212330.6365251655060.06583194016450.4828961519787.36634602614-19.4474066418-29.0693851691
81.952826940661.402977044562.161972937283.77427849266-0.1726031100958.05721261299-0.0627503326765-0.4589494165320.0655447171625-0.1656803291850.03067954513080.291978831043-0.316009291256-1.54236363653-0.1278456676770.407081524912-0.02760831014730.01982340568810.736981733706-0.05397815467950.440882627102-17.52186018315.97582109455-12.4550585215
92.655704810990.123018901508-1.037224441482.3716960257-0.4642594616910.4499034406850.402880416754-0.6768106831350.2296832470580.562680197204-0.170741138684-0.281006763408-0.3929387541082.04673398154-0.1928848128240.589697971446-0.1147294807940.03093083073881.548777773760.01760668325210.55741970149310.67643064140.7830372899127.99428287469
104.6914778857-1.989475687243.570178688382.45753867813-1.82790451516.34227803505-0.0141283988901-0.256601557908-0.594282328653-0.207228184530.3409327141290.1968736699050.387368925334-0.314679718582-0.2666208635230.402882607506-0.07989062747160.00978151725920.5938565704840.005378056056630.465085506752-8.6888700959-1.10788023595-5.85821875785
115.8402410505-5.40233177104-0.9990653108485.244064977580.4619875772057.002948189980.665467833392-0.11892824342-0.565416616826-0.584624618848-0.333967051699-0.0294959931510.373659708217-0.346419661215-0.2672302206850.719198102768-0.339473674713-0.02997980809720.701057449416-0.0160138658050.523868688607-11.9774942458-0.932848267124-23.4123678954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 92 )
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 176 )
6X-RAY DIFFRACTION6chain 'A' and (resid 177 through 200 )
7X-RAY DIFFRACTION7chain 'A' and (resid 201 through 236 )
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 146 )
10X-RAY DIFFRACTION10chain 'B' and (resid 147 through 200 )
11X-RAY DIFFRACTION11chain 'B' and (resid 201 through 235 )

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