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- PDB-1a0b: HISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN OF ARCB FROM ESCHERIC... -

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Basic information

Entry
Database: PDB / ID: 1a0b
TitleHISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN OF ARCB FROM ESCHERICHIA COLI
ComponentsAEROBIC RESPIRATION CONTROL SENSOR PROTEIN ARCB
KeywordsHISTIDINE 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 / phosphorelay sensor kinase activity / histidine kinase / 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 / phosphorelay sensor kinase activity / histidine kinase / 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 / Histidine kinase/HSP90-like ATPase / 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. / 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 / MIR / Resolution: 2.06 Å
AuthorsKato, M. / Mizuno, T. / Shimizu, T. / Hakoshima, T.
Citation
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.
#1: 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
DepositionNov 27, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: AEROBIC RESPIRATION CONTROL SENSOR PROTEIN ARCB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0792
Polymers14,0141
Non-polymers651
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.560, 34.930, 110.780
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 AEROBIC RESPIRATION CONTROL SENSOR PROTEIN ARCB


Mass: 14013.939 Da / Num. of mol.: 1 / Fragment: C-TERMINAL HPT DOMAIN
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.: 121 / 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 %
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
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: Kato, M., (1996) Acta Crystallogr.,Sect.D, 52, 1214.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 %PEG5501reservoir
210.6 mg/mlprotein1drop
350 mMsodium acetate1drop
45 mM1dropZnSO4
512.5 %PEG5501drop

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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: Jan 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.06 Å / Num. obs: 6999 / % possible obs: 87 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 17
Reflection shellResolution: 2.06→2.25 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.11 / % possible all: 83
Reflection
*PLUS
Num. measured all: 25850

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
XTALVIEWrefinement
X-PLOR3.1refinement
PROCESSdata reduction
PROCESSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.06→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.271 742 10.9 %RANDOM
Rwork0.181 ---
obs0.181 6792 87.8 %-
Displacement parametersBiso mean: 28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.22 Å
Luzzati d res low-8 Å
Luzzati sigma a0.23 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.06→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 1 121 1042
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.581.5
X-RAY DIFFRACTIONx_mcangle_it2.452
X-RAY DIFFRACTIONx_scbond_it3.342
X-RAY DIFFRACTIONx_scangle_it5.312.5
LS refinement shellResolution: 2.06→2.15 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.286 92 12.6 %
Rwork0.285 640 -
obs--79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34

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