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- PDB-8uk7: Periplasmic domain of Escherichia coli CpxA -

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Basic information

Entry
Database: PDB / ID: 8uk7
TitlePeriplasmic domain of Escherichia coli CpxA
ComponentsSensor histidine kinase CpxA
KeywordsSIGNALING PROTEIN / PAS domain / sensor / inner membrane
Function / homology
Function and homology information


cell adhesion involved in biofilm formation / cellular response to cell envelope stress / phosphorelay sensor kinase activity / histidine kinase / phosphoprotein phosphatase activity / response to radiation / signal transduction / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Two-component sensor protein CpxA, periplasmic domain / Two-component sensor protein CpxA, periplasmic domain superfamily / Two-component sensor protein CpxA, periplasmic domain / : / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain ...Two-component sensor protein CpxA, periplasmic domain / Two-component sensor protein CpxA, periplasmic domain superfamily / Two-component sensor protein CpxA, periplasmic domain / : / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / 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 superfamily
Similarity search - Domain/homology
Sensor histidine kinase CpxA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGlover, M.J.N. / Murray, C.R.A. / Edwards, R.A. / Thede, G.L.
Funding support Canada, 4items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2021-02710 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-05163 Canada
Canadian Institutes of Health Research (CIHR)CIHR168972 Canada
Canadian Institutes of Health Research (CIHR)CIHR142347 Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The sensor of the bacterial histidine kinase CpxA is a novel dimer of extracytoplasmic Per-ARNT-Sim domains.
Authors: Cho, T.H.S. / Murray, C. / Malpica, R. / Margain-Quevedo, R. / Thede, G.L. / Lu, J. / Edwards, R.A. / Glover, J.N.M. / Raivio, T.L.
History
DepositionOct 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor histidine kinase CpxA
B: Sensor histidine kinase CpxA


Theoretical massNumber of molelcules
Total (without water)31,7742
Polymers31,7742
Non-polymers00
Water1,58588
1
A: Sensor histidine kinase CpxA


Theoretical massNumber of molelcules
Total (without water)15,8871
Polymers15,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sensor histidine kinase CpxA


Theoretical massNumber of molelcules
Total (without water)15,8871
Polymers15,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.160, 43.163, 186.981
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-IDDetails
d_1ens_1(chain "A" and (resid 2 through 10 or resid 12...
d_2ens_1(chain "B" and (resid 2 through 10 or resid 12...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETGLNGLNAA2 - 1010 - 18
d_12GLNGLNGLNGLNAA1220
d_13GLYGLYASNASNAA13 - 3021 - 38
d_14LEULEUGLNGLNAA32 - 5040 - 58
d_15LEULEUARGARGAA52 - 6060 - 68
d_16ILEILEGLUGLUAA62 - 9470 - 102
d_17VALVALSERSERAA96 - 117104 - 125
d_21METMETGLNGLNBB2 - 1010 - 18
d_22GLNGLNASNASNBB12 - 3020 - 38
d_23LEULEUGLNGLNBB32 - 5040 - 58
d_24LEULEUARGARGBB52 - 6060 - 68
d_25ILEILEGLUGLUBB62 - 9470 - 102
d_26VALVALSERSERBB96 - 117104 - 125

NCS oper: (Code: givenMatrix: (0.185805265651, 0.979821935791, 0.0736571612235), (0.979921998618, -0.19029691311, 0.0594975754542), (0.0723137599657, 0.0611233098258, -0.995507238103)Vector: -27. ...NCS oper: (Code: given
Matrix: (0.185805265651, 0.979821935791, 0.0736571612235), (0.979921998618, -0.19029691311, 0.0594975754542), (0.0723137599657, 0.0611233098258, -0.995507238103)
Vector: -27.8864864409, 30.9595950616, 46.7554720502)

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Components

#1: Protein Sensor histidine kinase CpxA


Mass: 15886.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: cpxA, ecfB, eup, ssd, b3911, JW3882 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AE82, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris-HCl pH 7.5, 350 mM NaCl, 20% v/v 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.03316 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.8→39.2 Å / Num. obs: 28337 / % possible obs: 98.1 % / Redundancy: 8 % / Biso Wilson estimate: 34.85 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Net I/σ(I): 13.75
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 2769 / CC1/2: 0.958 / CC star: 0.989 / Rpim(I) all: 0.408 / Rrim(I) all: 1.16 / % possible all: 96.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
Cootmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.19 Å / SU ML: 0.1873 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.6725
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 1345 4.75 %
Rwork0.2043 26992 -
obs0.2062 28337 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 0 88 1989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311988
X-RAY DIFFRACTIONf_angle_d1.15042695
X-RAY DIFFRACTIONf_chiral_restr0.0658280
X-RAY DIFFRACTIONf_plane_restr0.0078364
X-RAY DIFFRACTIONf_dihedral_angle_d19.6376779
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.798007206057 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.34891330.30322602X-RAY DIFFRACTION96.64
1.86-1.940.31191380.28962610X-RAY DIFFRACTION97.62
1.94-2.030.28511460.25562637X-RAY DIFFRACTION98.17
2.03-2.130.27891320.2332670X-RAY DIFFRACTION98.35
2.13-2.270.24531490.2222678X-RAY DIFFRACTION98.6
2.27-2.440.26481240.21932688X-RAY DIFFRACTION98.53
2.44-2.690.29031180.22432742X-RAY DIFFRACTION98.72
2.69-3.080.25881350.22842718X-RAY DIFFRACTION98.45
3.08-3.880.26451270.18762779X-RAY DIFFRACTION99.21
3.88-39.190.20491430.17952868X-RAY DIFFRACTION96.69
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)
12.30120470265-2.01407825493-2.606165255915.12047646334.068979154733.886291425520.4701585530970.2091528765450.0873441337661-0.3799448828230.0344990898617-0.223779576739-1.29335530336-0.917632723857-0.270238808011.020020926020.3129748394020.3327877546590.5355880716960.1892977092580.521618805574-12.636964741836.472958164219.842455736
22.521928503240.233182629403-1.354287818042.936125339280.2334923344223.693980724690.1864133373240.429994949677-0.08829396654640.0230383933648-0.1399471539830.08687524493960.468711230315-0.511163364978-0.1170945873750.448480403608-0.008407820173680.04216637419540.30016187765-0.04248517381640.319773476876-16.904060480619.263576321331.5170251706
36.253754508670.472531374688-3.54399811125.24767472413-0.5878196056099.63431570641-0.0893013940352-0.227816232773-0.8827693520531.30107711631-0.3685049021010.09718355569581.020032847190.6087352053260.3039073282720.640589108649-0.005202435218560.07197713407210.2233983511180.0257125387050.373845923858-14.122583173619.662244532141.0608315994
45.91520522024-2.02113288627-4.81465696628.430143547734.616827294689.570062522870.4303254750410.2701410547870.2226595276440.436528465848-0.230892663149-0.261881087321-0.124309674910.0879315572612-0.1898025524240.4107597398320.02935472482680.01008144744180.2187844509060.002727279289210.365308565825-12.802589338828.795491213137.3762759674
57.89786586602-0.886044466144-3.217862862722.551312153372.215654245062.707031870120.387248736457-0.3450228440411.059510427760.06264219674990.0766898476332-0.888400253356-1.78471741256-0.0579686649745-0.5837745400570.911993471941-0.06284751722950.2166555100780.343515446928-0.09230577541840.639559149481-11.631307896839.404711517237.102310921
65.850069963281.90403707550.664381585328.676821399661.062103616388.28830831990.5365519460740.5498495976940.413774365589-0.430972044198-0.102185282180.432552473625-1.49452461358-0.00259633120545-0.2385228400440.7218014211650.108701119730.2186044520740.2791058566960.05775621954170.515283173192-12.131340525436.459975751726.7435707561
72.622608922813.09292877196-1.117984090594.16734929417-2.393360090592.763282421210.757450680180.4944246154050.5140297631590.331541803705-0.09709646725061.33085272323-0.724019981098-1.55608047896-0.5341152536670.4399959338540.005014621708270.101408385130.485628591682-0.03546406955790.694061763176-23.500719137123.990201355532.4930916958
89.835954072530.0583414447811-0.6968123420996.827093959380.2429234288474.705461183850.344815366407-0.4869961700891.130444085890.0286658035925-0.0494663742717-0.0451890359721-0.51142856965-0.127754664377-0.2779391859430.4017284885710.05998625287160.03355263625290.45312716922-0.03934128732360.365976890384-13.849922170529.478949805231.6776983567
97.16650557333-0.113680360278-7.783073277475.22894894897-0.2565011313998.48853774203-1.34074519604-0.9608289068310.5139330588140.7926488256280.836510276995-1.303927403320.228757845521.35397610310.1027391156830.7162579107780.355020260112-0.2470752890281.30488854669-0.3680349064460.6979477000768.678479504512.527521443627.9069309448
102.080947291330.0756742448604-0.4903354942.55483694532.580088259096.81747058891-0.2234119983050.113389504946-0.03384508006640.400376853673-0.02742942243640.1676614343720.370360927705-0.5084734372280.1635283959670.2960710513160.06116208638680.03459027891070.508156342891-0.1253141471880.387620400686-9.8347387909912.35381396315.3041063332
113.04523594192-0.752556669397-3.89758621223.372373722450.2373703913167.57606689952-0.1852848058281.09563419953-0.06473600928630.2197866032560.2614455620530.256583056776-0.458369833849-0.286397194099-0.2891514606440.1261208666210.02363913261090.01822446175970.821764452135-0.1455234314830.397030607057-7.9382224551915.96007943016.02334770284
124.81090550638-2.76790269523-2.46591098655.934922267723.142788502876.812275653340.1182705631990.3881074873620.2236432485170.1091137433030.194251718714-0.2648455135670.02701813021270.0892319775802-0.3572195429610.282235795850.021831248309-0.01397354531340.598788570606-0.1314021774340.427544477990.41179124350714.842278202510.3108746616
135.82292940629-0.209962429543-1.41084348336.27590441851-0.8808994995617.49619461963-0.1395654608220.3718893243490.39676946776-0.4220970832620.463270136732-0.7165953747160.06575147029721.17578884999-0.120208218020.357631929077-0.04507560213820.02054782598180.870778026412-0.2856845939620.72354980114611.217462536514.102854050111.1617198778
146.532356842215.32788429129-5.04065598588.22857440183-4.957900124664.08478750405-0.906865617698-1.27334767825-2.251605930840.4546344938820.647876489484-2.002413319171.266091600161.526311778340.4930340689961.182704246560.4006874353529.06569965501E-51.004897666660.05850447202150.962053126344.260054025494.5676668615423.2541276161
153.76520967829-0.8296513585181.496042576087.497601622863.289761911878.68714201505-0.37276723848-0.3290919631510.05236745640050.2453790196810.523204671685-0.625899795404-0.279131156040.543018684673-0.1498058211350.3326595074110.107819554859-0.02811503998660.605704504573-0.1783689442780.4417640697833.2509808911513.304564777618.121294598
164.809129181533.475504071475.01156325312.997086828634.160670101027.82286667766-0.5403226766760.2351097829930.43602683891-0.09589687037420.1166416882390.420985245076-0.114051411868-0.02767313155570.2234595884440.2984876781350.05894318178010.009008542872620.472547008865-0.123529342970.4877597156670.68035652704813.763533957516.1123457193
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 6 )AA2 - 61 - 5
22chain 'A' and (resid 7 through 33 )AA7 - 336 - 36
33chain 'A' and (resid 34 through 45 )AA34 - 4537 - 48
44chain 'A' and (resid 46 through 65 )AA46 - 6549 - 69
55chain 'A' and (resid 66 through 78 )AA66 - 7870 - 82
66chain 'A' and (resid 79 through 97 )AA79 - 9783 - 102
77chain 'A' and (resid 98 through 105 )AA98 - 105103 - 110
88chain 'A' and (resid 106 through 117 )AA106 - 117111 - 122
99chain 'B' and (resid 1 through 6 )BB1 - 61 - 6
1010chain 'B' and (resid 7 through 33 )BB7 - 337 - 33
1111chain 'B' and (resid 34 through 45 )BB34 - 4534 - 45
1212chain 'B' and (resid 46 through 65 )BB46 - 6546 - 67
1313chain 'B' and (resid 66 through 78 )BB66 - 7868 - 80
1414chain 'B' and (resid 79 through 85 )BB79 - 8581 - 87
1515chain 'B' and (resid 86 through 105 )BB86 - 10588 - 107
1616chain 'B' and (resid 106 through 117 )BB106 - 117108 - 119

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