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- PDB-3fc7: The crystal structure of a domain of HTR-like protein from Haloar... -

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Basic information

Entry
Database: PDB / ID: 3fc7
TitleThe crystal structure of a domain of HTR-like protein from Haloarcula marismortui ATCC 43049
ComponentsHTR-like protein
KeywordsTRANSFERASE / APC87712.1 / HTR-like protein / Haloarcula marismortui ATCC 43049 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Kinase / Phosphoprotein
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity
Similarity search - Function
PAS fold-4 / PAS fold / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain ...PAS fold-4 / PAS fold / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / 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 / Beta-Lactamase / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsTan, K. / Hatzos, C. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a domain of HTR-like protein from Haloarcula marismortui ATCC 43049
Authors: Tan, K. / Hatzos, C. / Freeman, L. / Joachimiak, A.
History
DepositionNov 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTR-like protein
B: HTR-like protein


Theoretical massNumber of molelcules
Total (without water)27,1752
Polymers27,1752
Non-polymers00
Water1267
1
A: HTR-like protein


Theoretical massNumber of molelcules
Total (without water)13,5881
Polymers13,5881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HTR-like protein


Theoretical massNumber of molelcules
Total (without water)13,5881
Polymers13,5881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.183, 55.183, 249.917
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsExperimentally unknown. The chains A and B are predicted to form a dimer.

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Components

#1: Protein HTR-like protein / Sensor protein


Mass: 13587.576 Da / Num. of mol.: 2 / Fragment: residues 120-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / Gene: Haloarcula marismortui, htlD, rrnAC0487 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5V4P0, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0M Sodium citrate, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937, 0.97951
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2008 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.979511
ReflectionResolution: 2.65→35 Å / Num. all: 7257 / Num. obs: 7257 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 29.66
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 2.4 / Num. unique all: 334 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→34.54 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 29.155 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.685 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27396 340 4.7 %RANDOM
Rwork0.2023 ---
all0.20563 6868 --
obs0.20563 6868 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.12 Å20 Å2
2---0.25 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.65→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 0 7 1481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211494
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.9482029
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0485196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.37524.64871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.6815238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9951512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211158
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0662980
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86731574
X-RAY DIFFRACTIONr_scbond_it1.1842514
X-RAY DIFFRACTIONr_scangle_it1.9013455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.651→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 19 -
Rwork0.287 478 -
obs-497 100 %
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)
15.79322.9797-0.39277.68052.37399.1786-0.11390.24880.28060.1780.24710.227-0.2670.0892-0.13310.2141-0.13010.020.15440.05580.2334-1.91817.7982101.5354
24.85325.1991-1.44488.7047-3.78632.97080.204-0.31630.06280.6456-0.2446-0.3777-0.3690.35450.04070.602-0.0916-0.07180.1885-0.03340.27535.323613.5189120.1457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A142 - 241
2X-RAY DIFFRACTION2B144 - 241

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