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- PDB-3v67: Periplasmic domain of Vibrio parahaemolyticus CpxA -

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Basic information

Entry
Database: PDB / ID: 3v67
TitlePeriplasmic domain of Vibrio parahaemolyticus CpxA
ComponentsSensor protein CpxA
KeywordsSIGNALING PROTEIN / PAS fold / Signal sensing / MEROHEDRAL TWINNING
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / plasma membrane
Similarity search - Function
Two-component sensor protein CpxA, periplasmic 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 ...Two-component sensor protein CpxA, periplasmic 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. / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsKwon, E. / Kim, D.Y. / Ngo, T.D. / Gross, J.D. / Kim, K.K.
CitationJournal: Protein Sci. / Year: 2012
Title: The crystal structure of the periplasmic domain of Vibrio parahaemolyticus CpxA
Authors: Kwon, E. / Kim, D.Y. / Ngo, T.D. / Gross, C.A. / Gross, J.D. / Kim, K.K.
History
DepositionDec 19, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein CpxA
B: Sensor protein CpxA


Theoretical massNumber of molelcules
Total (without water)32,4652
Polymers32,4652
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-7 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.583, 148.583, 32.314
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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
11LYSLYSTHRTHRchain A and (resseq 43:105 or resseq 108:161 )AA43 - 1058 - 70
12ARGARGASNASNchain A and (resseq 43:105 or resseq 108:161 )AA108 - 16173 - 126
21LYSLYSTHRTHRchain B and (resseq 43:105 or resseq 108:161 )BB43 - 1058 - 70
22ARGARGASNASNchain B and (resseq 43:105 or resseq 108:161 )BB108 - 16173 - 126

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Components

#1: Protein Sensor protein CpxA


Mass: 16232.465 Da / Num. of mol.: 2 / Fragment: Sensor domain, residues 38-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP2859 / Plasmid: PVFT1A - PET28A(+) DERIVED / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q87KW6, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7
Details: 0.1M Tris-HCl, 18-24% PEG 3000, 0.2M Ca(OAc)2, 3%(v/v) 1,6-hexanediol, 2mM tris(2-carboxyethyl)phosphine, pH 7.0, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97943, 0.97970, 0.98751, 0.97176
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 10, 2009
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979431
20.97971
30.987511
40.971761
Reflection twinOperator: h,-h-k,-l / Fraction: 0.064
ReflectionResolution: 2.3→30 Å / Num. all: 11802 / Num. obs: 11802 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.5 / Redundancy: 5.1 % / Rsym value: 0.098 / Net I/σ(I): 24.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 594 / Rsym value: 0.276 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX2011_12_05_2329refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→28.876 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2.27 / Phase error: 32.77 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2736 562 4.78 %
Rwork0.2302 11158 -
obs0.2336 11757 99.56 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.585 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 150.01 Å2 / Biso mean: 48.4194 Å2 / Biso min: 10.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.3497 Å2-0 Å2-0 Å2
2--1.3497 Å2-0 Å2
3----2.6994 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 0 100 2291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042244
X-RAY DIFFRACTIONf_angle_d0.9113029
X-RAY DIFFRACTIONf_chiral_restr0.067313
X-RAY DIFFRACTIONf_plane_restr0.003401
X-RAY DIFFRACTIONf_dihedral_angle_d15.727880
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A972X-RAY DIFFRACTIONPOSITIONAL0.018
12B972X-RAY DIFFRACTIONPOSITIONAL0.018
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3024-2.53370.30381440.27922787293194
2.5337-2.89930.3181420.26912775291795
2.8993-3.64880.30091370.24762794293195
3.6488-19.4310.23891360.19362802293895
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)
13.5595-1.0677-1.4451.82980.08052.1406-0.0748-0.00560.0263-0.4779-0.0239-0.82610.09540.23450.0680.17760.02930.0930.17460.02590.22750.021559.74246.6331
21.8267-1.2123-1.41025.75732.65084.57860.09480.06990.233-0.57470.0076-0.113-0.3826-0.023-0.18680.3667-0.0409-0.1998-0.1550.12230.3228-7.874372.68451.7966
30.6038-0.1672-0.30380.46651.32373.7528-0.07440.2451-0.1369-0.1822-0.1378-0.09710.1357-0.0869-0.1860.53380.05720.0522-0.0536-0.2386-0.1608-8.821361.4723-3.6423
40.48420.3434-0.86042.23511.74394.3789-0.01470.3204-0.0284-0.8107-0.2260.7649-0.6728-0.59780.18160.41260.2565-0.13530.2579-0.14520.2865-14.702264.20016.6154
54.29730.65410.5916.6386-3.79584.68790.04670.04370.5644-0.64130.19841.19320.198-0.8253-0.1390.2492-0.1037-0.16160.16240.02130.529-16.38955.32514.8117
65.68350.0301-3.045.8693.78026.1770.0073-0.7846-0.82941.1889-0.02090.02841.4586-0.06720.11170.5175-0.04290.03030.22670.02370.1757-6.689352.134616.9211
74.91330.6128-0.2553.87031.83270.9304-0.04680.4303-0.421-0.8621-0.07520.43910.3585-0.1029-0.12590.58420.0696-0.0556-0.0174-0.1130.0797-9.364949.3092.94
86.3898-1.0858-0.01631.3055-1.91823.5493-0.1376-0.33-0.0386-0.05550.0755-0.16320.26990.0879-0.04720.14740.03510.03430.10880.03160.0671-4.968162.71519.5643
90.83760.3436-0.24496.87391.30540.3578-0.25730.08130.09560.2517-0.10650.1476-0.9811-0.3180.27570.57260.1497-0.18950.3598-0.09190.2588-3.476831.7218-8.039
107.01795.91815.95127.64496.84096.2956-1.37110.50871.2974-0.06420.5895-1.1372-1.61650.54850.84430.59870.0255-0.2880.19660.03950.58495.323541.44923.0503
111.9536-0.7873-0.34114.35360.49741.41640.0450.1116-0.0172-0.4924-0.11840.8823-0.0816-0.178-0.03650.28840.1383-0.33990.0057-0.09170.8598-3.91225.22760.6281
126.1319-4.4299-0.51216.4789-4.76278.07850.11290.0791-1.098-0.66350.23821.53720.7172-0.3028-0.35170.6691-0.0188-0.04010.18460.040.58852.97248.36342.3542
133.5583-3.74611.86277.2777-3.32694.3070.30550.1789-0.411-0.9633-0.02810.10470.47420.0787-0.2290.840.13060.21650.05090.10640.39648.304413.14-3.4061
140.08780.0095-0.0630.0528-0.27491.25580.04950.167-0.0307-0.2687-0.23580.0935-0.02090.1222-0.1920.73230.3312-0.19210.08770.2465-0.04149.060124.3855-8.8033
150.4841-0.55450.58231.3197-1.08222.27460.05740.19070.195-0.4627-0.2907-0.72770.1710.36670.40390.11310.29620.16620.27640.35960.633415.023421.671.589
168.68970.6129-2.31126.1722-0.70326.8706-0.1546-0.39780.01720.0212-0.2497-1.3707-0.64680.70930.22660.37660.00330.010.22810.15920.536612.850431.72994.0586
173.40250.34910.46353.3864-0.15262.5309-0.06180.14390.4006-0.6169-0.1237-0.6395-0.28310.05840.07870.35440.09010.1099-0.10080.15330.11537.132830.33191.3661
187.37852.0647-2.09953.1373-1.80724.38860.0720.36030.2725-0.8136-0.12770.0462-0.2180.0539-0.05610.38480.02530.0030.0854-0.00790.12146.333525.65972.0321
190.39140.09080.10420.53790.26050.1681-0.03090.3626-0.1871-0.48930.0261-0.28490.40830.4490.08730.82170.24450.24140.87690.08110.23913.14953.0927-7.1474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 41:71)A41 - 71
2X-RAY DIFFRACTION2chain A and (resseq 72:82)A72 - 82
3X-RAY DIFFRACTION3chain A and (resseq 83:96)A83 - 96
4X-RAY DIFFRACTION4chain A and (resseq 97:109)A97 - 109
5X-RAY DIFFRACTION5chain A and (resseq 110:122)A110 - 122
6X-RAY DIFFRACTION6chain A and (resseq 123:129)A123 - 129
7X-RAY DIFFRACTION7chain A and (resseq 130:141)A130 - 141
8X-RAY DIFFRACTION8chain A and (resseq 142:159)A142 - 159
9X-RAY DIFFRACTION9chain A and (resseq 160:172)A160 - 172
10X-RAY DIFFRACTION10chain B and (resseq 42:48)B42 - 48
11X-RAY DIFFRACTION11chain B and (resseq 49:65)B49 - 65
12X-RAY DIFFRACTION12chain B and (resseq 66:71)B66 - 71
13X-RAY DIFFRACTION13chain B and (resseq 72:82)B72 - 82
14X-RAY DIFFRACTION14chain B and (resseq 83:96)B83 - 96
15X-RAY DIFFRACTION15chain B and (resseq 97:109)B97 - 109
16X-RAY DIFFRACTION16chain B and (resseq 110:129)B110 - 129
17X-RAY DIFFRACTION17chain B and (resseq 130:149)B130 - 149
18X-RAY DIFFRACTION18chain B and (resseq 150:159)B150 - 159
19X-RAY DIFFRACTION19chain B and (resseq 160:172)B160 - 172

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