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- PDB-4biu: Crystal structure of CpxAHDC (orthorhombic form 1) -

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Basic information

Entry
Database: PDB / ID: 4biu
TitleCrystal structure of CpxAHDC (orthorhombic form 1)
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 / phosphorelay sensor kinase activity / 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 / 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: 3.65 Å
AuthorsMechaly, A.E. / Sassoon, N. / Betton, J.M. / Alzari, P.M.
CitationJournal: Plos Biol. / Year: 2014
Title: Segmental Helical Motions and Dynamical Asymmetry Modulate Histidine Kinase Autophosphorylation.
Authors: Mechaly, A.E. / Sassoon, N. / Betton, J.M. / Alzari, P.M.
History
DepositionApr 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)201,64912
Polymers200,0796
Non-polymers1,5706
Water0
1
C: SENSOR PROTEIN CPXA
D: SENSOR PROTEIN CPXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3125
Polymers66,6932
Non-polymers6193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-85.6 kcal/mol
Surface area24650 Å2
MethodPISA
2
A: SENSOR PROTEIN CPXA
B: SENSOR PROTEIN CPXA


Theoretical massNumber of molelcules
Total (without water)66,6932
Polymers66,6932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-53 kcal/mol
Surface area24470 Å2
MethodPISA
3
E: SENSOR PROTEIN CPXA
F: SENSOR PROTEIN CPXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6435
Polymers66,6932
Non-polymers9503
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-70.6 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.274, 191.697, 205.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
SENSOR PROTEIN CPXA / / CPXA


Mass: 33346.484 Da / Num. of mol.: 6 / Fragment: CYTOPLASMIC REGION, RESIDUES 188-457
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 / Adenosine diphosphate


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 4.17 Å3/Da / Density % sol: 70.52 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 3.65→47.92 Å / Num. obs: 31735 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 127.47 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.7
Reflection shellResolution: 3.65→3.85 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.9 / % 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: 3.65→47.92 Å / Cor.coef. Fo:Fc: 0.9394 / Cor.coef. Fo:Fc free: 0.9393 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.494
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1599 5.04 %RANDOM
Rwork0.2106 ---
obs0.2115 31708 100 %-
Displacement parametersBiso mean: 188.25 Å2
Baniso -1Baniso -2Baniso -3
1-8.4027 Å20 Å20 Å2
2--20.8356 Å20 Å2
3----29.2383 Å2
Refinement stepCycle: LAST / Resolution: 3.65→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11897 0 96 0 11993
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812195HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9616515HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5805SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes363HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1768HARMONIC5
X-RAY DIFFRACTIONt_it12195HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion2.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1573SEMIHARMONIC5
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_contact13997SEMIHARMONIC4
LS refinement shellResolution: 3.65→3.77 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2878 140 4.87 %
Rwork0.2597 2732 -
all0.2611 2872 -
obs--100 %

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