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- PDB-5idm: Bifunctional histidine kinase CckA (domain, CA) in complex with c... -

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Basic information

Entry
Database: PDB / ID: 5idm
TitleBifunctional histidine kinase CckA (domain, CA) in complex with c-di-GMP and AMPPNP/Mg2+
ComponentsCell cycle histidine kinase CckA
KeywordsTRANSFERASE / bifunctional / histidine kinase / phosphatase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / membrane / metal ion binding
Similarity search - Function
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. / Response regulator receiver domain / cheY-homologous receiver domain / Histidine kinase-like ATPase, C-terminal 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. / Response regulator receiver domain / cheY-homologous receiver domain / Histidine kinase-like ATPase, C-terminal domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / Heat Shock Protein 90 / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-C2E / histidine kinase
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsDubey, B.N. / Schirmer, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-138414 Switzerland
CitationJournal: Sci Adv / Year: 2016
Title: Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.
Authors: Dubey, B.N. / Lori, C. / Ozaki, S. / Fucile, G. / Plaza-Menacho, I. / Jenal, U. / Schirmer, T.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Advisory / Author supporting evidence
Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 21, 2022Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / citation_author ...chem_comp / citation_author / database_2 / pdbx_refine_tls_group / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID ..._chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell cycle histidine kinase CckA
B: Cell cycle histidine kinase CckA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0807
Polymers39,3292
Non-polymers1,7515
Water7,314406
1
A: Cell cycle histidine kinase CckA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8854
Polymers19,6641
Non-polymers1,2213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell cycle histidine kinase CckA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1953
Polymers19,6641
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.280, 62.110, 103.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A380 - 553
2010B380 - 553

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Components

#1: Protein Cell cycle histidine kinase CckA


Mass: 19664.297 Da / Num. of mol.: 2 / Fragment: UNP residues 378-547
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: cckA / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9X688
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.35 Å3/Da / Density % sol: 47.59 % / Mosaicity: 0.5 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M ammonium sulfate, 28.4% polyethylene glycol 4000 and 0.1 M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 29150 / % possible obs: 99.2 % / Redundancy: 6.4 % / Rsym value: 0.088 / Net I/av σ(I): 7.647 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-26.50.32.5199.3
2-2.1260.2183.5199.3
2.12-2.275.60.1564.8198.2
2.27-2.456.50.1315.8198.7
2.45-2.696.90.1057.1199.6
2.69-36.70.0828.8199.9
3-3.476.60.06610.31100
3.47-4.255.50.05512.1199.6
4.25-6.016.80.04414.4199.1
6.01-29.75470.04314.5197.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.75 Å
Translation2.5 Å29.75 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.1phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.265 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.151
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 1492 5.1 %RANDOM
Rwork0.1935 ---
obs0.1953 27618 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.75 Å2 / Biso mean: 16.367 Å2 / Biso min: 4.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.47 Å2
Refinement stepCycle: final / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 110 406 3251
Biso mean--7.94 24.62 -
Num. residues----350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192860
X-RAY DIFFRACTIONr_bond_other_d0.0050.022692
X-RAY DIFFRACTIONr_angle_refined_deg1.6282.013910
X-RAY DIFFRACTIONr_angle_other_deg1.27636163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6485347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23823.125128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85915434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9931525
X-RAY DIFFRACTIONr_chiral_restr0.0860.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213190
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02657
X-RAY DIFFRACTIONr_mcbond_it0.9481.5231397
X-RAY DIFFRACTIONr_mcbond_other0.9481.5241396
X-RAY DIFFRACTIONr_mcangle_it1.6592.2751741
Refine LS restraints NCS

Ens-ID: 1 / Number: 17980 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 119 -
Rwork0.219 1997 -
all-2116 -
obs--98.79 %
Refinement TLS params.Method: refined / Origin x: 11.862 Å / Origin y: 0.206 Å / Origin z: -8.034 Å
111213212223313233
T0.0205 Å2-0.0189 Å20.0028 Å2-0.018 Å2-0.0013 Å2--0.0088 Å2
L0.325 °2-0.3611 °20.1812 °2-1.1685 °2-0.0509 °2--0.2106 °2
S0.0045 Å °-0.0024 Å °-0.0154 Å °-0.0139 Å °-0.0032 Å °-0.0195 Å °-0.0235 Å °0.0222 Å °-0.0014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A378 - 554
2X-RAY DIFFRACTION1A601 - 603
3X-RAY DIFFRACTION1B380 - 556
4X-RAY DIFFRACTION1B600 - 601

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