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Basic information

Entry
Database: PDB / ID: 3cit
TitleCrystal structure of the GAF domain of a putative sensor histidine kinase from Pseudomonas syringae pv. tomato
ComponentsSensor histidine kinase
KeywordsTRANSFERASE / MEGA: 3.30.450.40 / structural genomics / sensor histidine kinase / Pseudomonas syringae / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phosphorelay sensor kinase activity / protein dimerization activity / membrane
Similarity search - Function
Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / : / Histidine kinase / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Sensor histidine kinase
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Li, H. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the GAF domain of a putative sensor histidine kinase from Pseudomonas syringae pv. tomato
Authors: Cuff, M.E. / Li, H. / Abdullah, J. / Joachimiak, A.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Mar 26, 2025Group: 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_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: Sensor histidine kinase
B: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,04415
Polymers34,9052
Non-polymers1,13913
Water5,837324
1
A: Sensor histidine kinase
B: Sensor histidine kinase
hetero molecules

A: Sensor histidine kinase
B: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,08830
Polymers69,8104
Non-polymers2,27826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area8820 Å2
ΔGint-49 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.471, 107.471, 67.698
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sensor histidine kinase


Mass: 17452.578 Da / Num. of mol.: 2 / Fragment: Domain: Residues 18-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: PSPTO_2131 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q884G2

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Non-polymers , 5 types, 337 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris propane pH 7.0, 1.5M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793, 0.9795
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 7, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
ReflectionRedundancy: 11 % / Av σ(I) over netI: 10.9 / Number: 393091 / Rmerge(I) obs: 0.062 / Χ2: 1.36 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 35808 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.685096.410.042.8310.7
3.724.6899.110.0392.0429.9
3.253.7299.710.0471.92311
2.953.2599.910.0591.66611.2
2.742.9599.810.071.39411.4
2.582.7499.410.0821.24111.3
2.452.5899.510.0951.20611.3
2.342.4599.510.1111.16511.1
2.252.3499.310.1271.11411.1
2.172.2599.510.1481.06511
2.112.1799.310.1751.00211
2.052.1199.610.210.97111
1.992.0599.210.260.97511
1.941.9999.510.3480.9310.9
1.91.9499.410.5070.91510.9
ReflectionResolution: 1.9→50 Å / Num. all: 35808 / Num. obs: 35808 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.361 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 4 / Num. unique all: 2357 / Χ2: 0.915 / % possible all: 99.4

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.9 Å / D res low: 50 Å / FOM : 0.24 / FOM acentric: 0.26 / FOM centric: 0 / Reflection: 35279 / Reflection acentric: 32644 / Reflection centric: 2635
Phasing MAD setR cullis acentric: 1.71 / R cullis centric: 1 / Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 32644 / Reflection centric: 2635
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.01-501.60.20.18546
6.82-12.011.160.20.1520127
4.76-6.821.510.10.11331211
3.66-4.761.090.10.12468284
2.97-3.661.310.10.13980371
2.5-2.972.130.105762450
2.16-2.52.36007985536
1.9-2.162.850010513610
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se28.94595-0.119-0.5-0.0290
2Se23.00053-0.273-0.659-0.2740
3Se42.223180.002-0.5590.1720
4Se76.729910.102-0.579-0.0360
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.01-500.3330.51301318546
6.82-12.010.4520.5620647520127
4.76-6.820.4420.512015421331211
3.66-4.760.3850.429027522468284
2.97-3.660.3810.416043513980371
2.5-2.970.3010.324062125762450
2.16-2.50.1960.209085217985536
1.9-2.160.1080.11501112310513610
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 35279
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.82-10060.90.794514
6.23-7.82580.882513
5.33-6.2359.30.886630
4.73-5.3360.10.908707
4.3-4.7363.40.921768
3.97-4.363.80.906838
3.7-3.9759.10.908922
3.48-3.759.60.899979
3.3-3.4857.80.8991034
3.14-3.360.30.8851062
3.01-3.1460.10.8921145
2.89-3.0162.10.8621155
2.78-2.8961.60.8771240
2.68-2.7864.50.8741240
2.6-2.68610.8731298
2.52-2.664.90.8741320
2.45-2.5263.80.8651353
2.38-2.4564.20.8541434
2.32-2.3864.80.8681443
2.26-2.3265.20.861479
2.21-2.2665.60.8641514
2.16-2.2168.50.8571559
2.11-2.1671.40.8511568
2.07-2.1173.60.8551656
2.03-2.0775.30.8541666
1.99-2.0375.90.8461684
1.96-1.9975.50.8161695
1.9-1.9680.70.7212863

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.9→31.22 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.275 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.112
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1760 5 %RANDOM
Rwork0.165 ---
all0.167 35273 --
obs0.167 35273 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.534 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 68 324 2702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212493
X-RAY DIFFRACTIONr_bond_other_d0.0020.021715
X-RAY DIFFRACTIONr_angle_refined_deg1.4242.0073379
X-RAY DIFFRACTIONr_angle_other_deg0.96434173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2625319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47123.271107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81615420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8611527
X-RAY DIFFRACTIONr_chiral_restr0.0910.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
X-RAY DIFFRACTIONr_nbd_refined0.2090.2498
X-RAY DIFFRACTIONr_nbd_other0.2060.21855
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21146
X-RAY DIFFRACTIONr_nbtor_other0.0860.21395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.30.230
X-RAY DIFFRACTIONr_mcbond_it1.241.51922
X-RAY DIFFRACTIONr_mcbond_other0.2531.5632
X-RAY DIFFRACTIONr_mcangle_it1.54122499
X-RAY DIFFRACTIONr_scbond_it2.4913990
X-RAY DIFFRACTIONr_scangle_it3.6384.5877
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 107 -
Rwork0.202 2438 -
all-2545 -
obs--97.62 %
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)
14.4867-0.19473.14297.1937-7.124210.32840.0218-0.32010.66060.45240.02590.2139-0.5667-0.1233-0.04780.0437-0.03980.0478-0.0167-0.04820.05780.748257.46050.5239
23.07860.6711-0.28130.9138-0.10550.85450.1708-0.1765-0.18330.1973-0.1002-0.05770.0463-0.0149-0.07060.0304-0.0573-0.0124-0.00430.0081-0.040872.835139.90021.6781
311.2961-5.50911.452312.00294.96423.6406-0.5966-1.5805-1.39991.45511.39230.41110.83150.1346-0.79570.28040.137-0.11070.21960.26390.171890.797928.146913.0755
448.5991-2.371712.209872.978214.94086.38050.01462.88692.9981-2.306-0.84410.451-1.06580.43590.82960.21330.0242-0.00090.19940.11050.196387.014769.8427-8.22
52.13050.4680.23161.19150.32611.49970.1253-0.0176-0.250.0818-0.0184-0.12720.21080.0812-0.10690.0630-0.0621-0.0299-0.00210.0094100.263346.9121-3.696
61.96710.83240.18612.00390.24610.24050.2019-0.2036-0.17020.1277-0.0726-0.0980.06420.0579-0.12940.0587-0.029-0.06470.02070.0136-0.0118101.346249.18282.9877
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA16 - 392 - 25
2X-RAY DIFFRACTION2AA40 - 15926 - 145
3X-RAY DIFFRACTION3AA160 - 172146 - 158
4X-RAY DIFFRACTION4BB16 - 202 - 6
5X-RAY DIFFRACTION5BB21 - 997 - 85
6X-RAY DIFFRACTION6BB100 - 16986 - 155

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