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- PDB-3tqf: Structure of the Hpr(Ser) kinase/phosphatase from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3tqf
TitleStructure of the Hpr(Ser) kinase/phosphatase from Coxiella burnetii
ComponentsHpr(Ser) kinase
KeywordsTRANSFERASE / HYDROLASE
Function / homology
Function and homology information


regulation of carbohydrate metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphorelay sensor kinase activity / hydrolase activity / ATP binding
Similarity search - Function
HPr kinase/phosphorylase, C-terminal / HPr Serine kinase C-terminal domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hpr(Ser) kinase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsFranklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Hpr(Ser) kinase
B: Hpr(Ser) kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1984
Polymers41,0082
Non-polymers1902
Water28816
1
A: Hpr(Ser) kinase
hetero molecules

A: Hpr(Ser) kinase
hetero molecules

A: Hpr(Ser) kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7986
Polymers61,5133
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5900 Å2
ΔGint-52 kcal/mol
Surface area24180 Å2
MethodPISA
2
B: Hpr(Ser) kinase
hetero molecules

B: Hpr(Ser) kinase
hetero molecules

B: Hpr(Ser) kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7986
Polymers61,5133
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
Buried area4960 Å2
ΔGint-52 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.451, 149.451, 149.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 169
2114B1 - 169

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Components

#1: Protein Hpr(Ser) kinase / Hpr(Ser) kinase/phosphatase


Mass: 20504.211 Da / Num. of mol.: 2 / Fragment: UNP residues 15-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_0744 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q820W5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M sodium chloride, 0.1 M Na/K phosphate, pH 6.2, 20% PEG1000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 28, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→105.68 Å / Num. all: 14624 / Num. obs: 14561 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 23 % / Rsym value: 0.076 / Net I/σ(I): 47.4
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 17.6 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 713 / Rsym value: 0.744 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→41.45 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.904 / SU B: 28.922 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.58 / ESU R Free: 0.323
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26509 730 5 %RANDOM
Rwork0.2497 ---
obs0.25046 14473 99.28 %-
all-14578 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.604 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 10 16 2492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222523
X-RAY DIFFRACTIONr_bond_other_d0.0010.021675
X-RAY DIFFRACTIONr_angle_refined_deg0.9321.9883428
X-RAY DIFFRACTIONr_angle_other_deg0.7634153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2185311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68425.385104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65615457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.903159
X-RAY DIFFRACTIONr_chiral_restr0.0570.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
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_it0.2041.51567
X-RAY DIFFRACTIONr_mcbond_other0.0281.5632
X-RAY DIFFRACTIONr_mcangle_it0.39222556
X-RAY DIFFRACTIONr_scbond_it0.4953956
X-RAY DIFFRACTIONr_scangle_it0.8594.5872
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1960 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.50.5
medium thermal0.162
LS refinement shellResolution: 2.8→2.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 60 -
Rwork0.372 994 -
obs--99.53 %
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)
13.98240.1998-0.68113.4004-1.13653.168-0.08510.14720.2356-0.16810.0390.1329-0.1868-0.17380.04610.1230.06860.01110.05680.01710.062367.032889.694565.7244
25.3236-0.22874.54632.5757-1.01738.921-0.302-0.19050.2949-0.23290.19820.44430.1926-0.31980.10390.2705-0.0931-0.12660.16630.08370.365645.772294.172945.4618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 179
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B15 - 169
4X-RAY DIFFRACTION2B201

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