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- PDB-4biz: Crystal structure of CpxAHDC (orthorhombic form 2) -

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Basic information

Entry
Database: PDB / ID: 4biz
TitleCrystal structure of CpxAHDC (orthorhombic form 2)
ComponentsSENSOR PROTEIN CPXA
KeywordsTRANSFERASE / SIGNAL TRANSDUCTION / TWO-COMPONENTS SYSTEMS / HISTIDINE KINASES
Function / homology
Function and homology information


cell adhesion involved in biofilm formation / cellular response to cell envelope stress / histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase 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 / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) 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 / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) 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, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Sensor histidine kinase CpxA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsMechaly, A.E. / Sassoon, N. / Betton, J.M. / Alzari, P.M.
CitationJournal: To be Published
Title: Crystal Structures of Cpxahdc
Authors: Mechaly, A.E. / Sassoon, N. / Betton, J.M. / Alzari, P.M.
History
DepositionApr 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: SENSOR PROTEIN CPXA
B: SENSOR PROTEIN CPXA
C: SENSOR PROTEIN CPXA
D: SENSOR PROTEIN CPXA
E: SENSOR PROTEIN CPXA
F: SENSOR PROTEIN CPXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,31016
Polymers200,0256
Non-polymers2,28510
Water3,927218
1
E: SENSOR PROTEIN CPXA
F: SENSOR PROTEIN CPXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7216
Polymers66,6752
Non-polymers1,0474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-66.7 kcal/mol
Surface area22390 Å2
MethodPISA
2
C: SENSOR PROTEIN CPXA
D: SENSOR PROTEIN CPXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2945
Polymers66,6752
Non-polymers6193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-67.6 kcal/mol
Surface area23240 Å2
MethodPISA
3
A: SENSOR PROTEIN CPXA
B: SENSOR PROTEIN CPXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2945
Polymers66,6752
Non-polymers6193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-65.1 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.448, 125.108, 159.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
SENSOR PROTEIN CPXA


Mass: 33337.453 Da / Num. of mol.: 6 / Fragment: CYTOPLASMIC REGION, RESIDUES 188-457 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLI5 / References: UniProt: P0AE82, histidine kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.01 Å3/Da / Density % sol: 59.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.65→49.25 Å / Num. obs: 70801 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 88.81 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.6
Reflection shellResolution: 2.65→2.71 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.65→49.01 Å / Cor.coef. Fo:Fc: 0.9431 / Cor.coef. Fo:Fc free: 0.9277 / SU R Cruickshank DPI: 0.354 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.348 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.247
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 3571 5.05 %RANDOM
Rwork0.2056 ---
obs0.2071 70756 99.99 %-
Displacement parametersBiso mean: 91.33 Å2
Baniso -1Baniso -2Baniso -3
1--3.9955 Å20 Å20 Å2
2---3.6696 Å20 Å2
3---7.6651 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10772 0 138 218 11128
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00911085HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0815032HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5276SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes329HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1617HARMONIC5
X-RAY DIFFRACTIONt_it11085HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1444SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12475SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2445 254 4.92 %
Rwork0.2282 4908 -
all0.229 5162 -
obs--99.99 %
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)
11.6813-0.02991.54970.34110.91831.5197-0.1606-0.28590.2336-0.0036-0.05250.1192-0.0629-0.29920.2131-0.1727-0.06080.0294-0.07360.0396-0.129519.8678.639844.7537
21.28441.6596-0.93452.5827-0.19430.0412-0.31890.4620.3752-0.74550.34070.5511-0.09030.0162-0.0218-0.0119-0.1759-0.1565-0.12010.217-0.262824.748712.010615.1515
30.7715-0.62140.33981.1624-0.74110.95720.0891-0.0232-0.07220.0137-0.1416-0.37360.18390.2140.0525-0.1576-0.03030.0308-0.10040.0402-0.081437.0403-20.259136.7418
40.859-0.15420.64471.61250.7871.47380.1670.1992-0.1312-0.6758-0.2408-0.2854-0.18260.27010.07380.00120.12850.1452-0.23620.0221-0.293325.3867-11.02597.7686
51.0262-0.14970.65651.4069-0.98541.2779-0.2054-0.16090.37240.01780.0365-0.3542-0.18270.18090.1689-0.23940.0488-0.0296-0.0885-0.1552-0.116559.541317.126572.5872
60.4298-1.2395-2.30331.21991.31861.4658-0.224-0.39930.41320.34290.4047-0.4220.2580.6565-0.1807-0.19680.2054-0.13220.1384-0.1645-0.114557.227913.0101101.529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

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