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- PDB-2a0b: HISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN OF ARCB FROM ESCHERIC... -

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Basic information

Entry
Database: PDB / ID: 2a0b
TitleHISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN OF ARCB FROM ESCHERICHIA COLI
ComponentsHPT DOMAIN
KeywordsSENSORY TRANSDUCTION / HISTIDINE KINASE / PHOSPHOTRANSFER / TWO-COMPONENT SYSTEM / FOUR-HELIX BUNDLE
Function / homology
Function and homology information


peptidyl-histidine phosphorylation / plasma membrane => GO:0005886 / response to oxygen levels / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / protein autophosphorylation / regulation of DNA-templated transcription / signal transduction / ATP binding ...peptidyl-histidine phosphorylation / plasma membrane => GO:0005886 / response to oxygen levels / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / protein autophosphorylation / regulation of DNA-templated transcription / signal transduction / ATP binding / plasma membrane / cytosol
Similarity search - Function
Signal transduction histidine kinase, hybrid-type, aerobic respiration control ArcB / Aerobic respiration control sensor protein ArcB, transmembrane domain superfamily / Histidine kinase receptor ArcB, transmembrane domain / Histidine kinase receptor ArcB trans-membrane domain / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily ...Signal transduction histidine kinase, hybrid-type, aerobic respiration control ArcB / Aerobic respiration control sensor protein ArcB, transmembrane domain superfamily / Histidine kinase receptor ArcB, transmembrane domain / Histidine kinase receptor ArcB trans-membrane domain / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / PAS-associated, C-terminal / PAC domain profile. / 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/HSP90-like ATPase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Aerobic respiration control sensor protein ArcB / Aerobic respiration control sensor protein ArcB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.57 Å
AuthorsKato, M. / Mizuno, T. / Shimizu, T. / Hakoshima, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Refined structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor kinase ArcB from Escherichia coli at 1.57 A resolution.
Authors: Kato, M. / Mizuno, T. / Shimizu, T. / Hakoshima, T.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Insights Into Multistep Phosphorelay from the Crystal Structure of the C-Terminal Hpt Domain of Arcb
Authors: Kato, M. / Mizuno, T. / Shimizu, T. / Hakoshima, T.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary X-Ray Analysis of a Histidine Kinase Domain of the Anaerobic Sensor Protein Arcb from Escherichia Coli
Authors: Kato, M. / Ishige, K. / Mizuno, T. / Shimizu, T. / Hakoshima, T.
History
DepositionApr 2, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: HPT DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0792
Polymers14,0141
Non-polymers651
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.456, 34.924, 110.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HPT DOMAIN


Mass: 14013.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PSU2DH / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): DZ225
References: UniProt: P22763, UniProt: P0AEC3*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.1 Å3/Da / Density % sol: 41 % / Description: THE FURTHER REFINEMENT OF 1A0B
Crystal growpH: 4.1
Details: PROTEIN WAS CRYSTALLIZED FROM 12.5% PEGMME 550, 5 MM ZNSO4, 50 MM ACETIC ACID/SODIUM ACETATE BUFFER, PH 4.1
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110.6 mg/mlprotein1drop
250 mMacetic acid/sodium acetate1drop
35 mM1dropZnSO4
412.5 %mPEG5501drop
513 %mPEG5501reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.57 Å / Num. obs: 16338 / % possible obs: 94.7 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 66
Reflection shellResolution: 1.57→1.7 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / % possible all: 89
Reflection
*PLUS
% possible obs: 95 % / Num. measured all: 98202
Reflection shell
*PLUS
% possible obs: 89 %

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Processing

Software
NameClassification
N/NAmodel building
REFMACrefinement
PROCESSdata reduction
PROCESSdata scaling
RefinementResolution: 1.57→6 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.245 777 4.8 %RANDOM
Rwork0.19 ---
obs-16033 95 %-
Displacement parametersBiso mean: 29.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.57→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 1 156 1113
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8012
X-RAY DIFFRACTIONp_mcangle_it2.4093
X-RAY DIFFRACTIONp_scbond_it2.6942
X-RAY DIFFRACTIONp_scangle_it4.1753
X-RAY DIFFRACTIONp_plane_restr0.0225
X-RAY DIFFRACTIONp_chiral_restr0.1480.15
X-RAY DIFFRACTIONp_singtor_nbd0.1870.3
X-RAY DIFFRACTIONp_multtor_nbd0.2780.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.180.3
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor1715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor37.120
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 16036
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.57 Å / Lowest resolution: 1.63 Å / Rfactor Rfree: 0.299 / Rfactor Rwork: 0.277

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