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- PDB-3o5y: The Crystal Structure of the GAF domain of a two-component sensor... -

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Basic information

Entry
Database: PDB / ID: 3o5y
TitleThe Crystal Structure of the GAF domain of a two-component sensor histidine kinase from Bacillus halodurans to 2.45A
ComponentsSensor protein
Keywordstranscription regulator / GAF domain / sensor / histidine / kinase / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / ATP binding
Similarity search - Function
GAF domain / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / GAF domain ...GAF domain / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Histidine kinase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsStein, A.J. / Mack, J. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of the GAF domain of a two-component sensor histidine kinase from Bacillus halodurans to 2.45A
Authors: Stein, A.J. / Mack, J. / Buck, K. / Joachimiak, A.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4985
Polymers38,3212
Non-polymers1773
Water39622
1
A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2202
Polymers19,1611
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2793
Polymers19,1611
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.961, 96.961, 104.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Sensor protein /


Mass: 19160.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: pMCSG7 / Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C / Gene: cckA, BH0536 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KFE5, histidine kinase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2M Magnesium acetate, 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2010
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 18880 / % possible obs: 99.6 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.066 / Χ2: 1.349 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.45-2.548.10.62618530.893100
2.54-2.648.10.44118430.91599.9
2.64-2.768.10.3318630.92100
2.76-2.98.10.22218550.962100
2.9-3.098.10.14518700.95699.9
3.09-3.328.10.08518660.963100
3.32-3.6680.05718921.003100
3.66-4.197.90.04419081.221100
4.19-5.287.70.05119252.50599.7
5.28-507.10.04720053.30497

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.45→43.99 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 16.94 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.269 962 5.1 %RANDOM
Rwork0.221 ---
obs0.223 18796 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.973 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.45→43.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 12 22 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222344
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9753178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05124.752101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.95915420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3291510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021712
X-RAY DIFFRACTIONr_mcbond_it0.5871.51449
X-RAY DIFFRACTIONr_mcangle_it1.14422330
X-RAY DIFFRACTIONr_scbond_it1.7913895
X-RAY DIFFRACTIONr_scangle_it2.8484.5848
LS refinement shellResolution: 2.452→2.516 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 84 -
Rwork0.277 1264 -
all-1348 -
obs--99.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.73045.3582-3.559525.0759-18.330613.2966-0.1902-0.68370.2405-0.3201-0.0013-0.19340.1376-0.11420.19150.4491-0.0258-0.07560.3015-0.06370.3286-45.80414.4814-22.4549
213.46067.621-17.07269.0762-3.743928.4418-0.34160.0001-0.279-0.2708-0.1886-0.01130.2792-0.20680.53020.24930.023-0.05730.36830.04660.1799-49.14448.3516-16.8829
39.7216-1.14297.45668.569-0.57195.7461-0.0659-0.3863-0.1777-0.19460.25830.1324-0.1454-0.2339-0.19240.279-0.00150.06830.3275-0.03290.1969-49.63994.503-9.252
46.96146.0395-3.32015.8759-4.03153.4662-0.0971-0.1001-0.00220.10340.15020.0093-0.2495-0.344-0.05310.26560.0376-0.01190.2827-0.00860.2412-43.376711.444-7.3175
56.15351.0808-2.32032.59081.0625.07340.06940.70010.4887-0.61820.13150.2028-0.33760.219-0.20090.3735-0.05290.00070.32260.05730.1811-31.251115.8473-20.1341
65.54494.14140.39144.1478-1.1462.01-0.19790.05190.4004-0.15160.15960.3346-0.0374-0.07830.03830.29790.0421-0.03580.24670.01230.2715-41.584617.8506-13.4086
715.60538.03175.25163.99142.66251.73880.2776-1.30821.09620.0589-0.63040.5674-0.0938-0.40820.35280.8423-0.1360.14760.21230.01460.4109-38.965822.9901-8.156
87.5964-0.19490.69063.2552-1.10290.3913-0.06110.00540.1498-0.23630.0028-0.1470.03970.0030.05830.3305-0.03050.00210.2578-0.01650.2265-27.787619.573-13.1086
93.5904-1.32760.8670.4901-0.10073.01960.0550.03390.1148-0.0003-0.0052-0.0676-0.1010.1371-0.04980.2515-0.012-0.02470.2522-0.02750.2947-26.359311.5018-10.4266
1026.34020.90823.95757.83362.6291.24160.07670.1145-0.57090.01660.3361-0.91430.04270.1488-0.41280.33630.0598-0.04550.3556-0.05960.2462-25.58833.8528-15.2082
112.4544-1.99453.42684.0851-2.72184.39180.28090.4022-0.04210.2836-0.19220.09370.42230.5947-0.08870.33280.0995-0.0520.41290.01920.2393-31.32624.1016-4.2952
1221.9854-0.57678.43822.1614-6.3725.48550.3308-0.7524-0.98790.0224-0.6445-0.4722-0.02580.57810.31370.2404-0.0663-0.03550.56280.19520.4367-27.94899.7335.1018
135.81355.6274-3.70956.1877-2.6383.12360.1823-0.2151-0.06270.3065-0.1835-0.12420.02460.15650.00120.2562-0.0333-0.02130.2411-0.02930.2979-27.349115.4858-4.0874
141.10090.1891-0.9574.48932.30372.47310.1086-0.25470.11960.2449-0.1260.2002-0.0602-0.00990.01750.2453-0.0185-0.00670.3178-0.03830.2293-35.526113.0828-3.0463
152.9264-0.10481.56935.67075.15965.51460.03380.17090.1828-0.20710.368-0.5546-0.16090.4183-0.40170.288-0.02970.02140.3550.0070.2508-30.81125.5358-24.4112
162.64560.9619-2.90910.5572-0.29276.11340.1103-0.02930.16370.05040.03530.0381-0.1107-0.1449-0.14560.26250.0249-0.02510.313-0.00320.2312-39.93888.6121-6.0437
172.0739-1.3381-2.21120.84991.75998.8689-0.041-0.0283-0.14530.0166-0.00410.08730.04330.1220.0450.2585-0.0336-0.03070.31140.04910.2406-40.8804-1.6495-3.967
181.40032.38090.11753.7809-0.18210.8687-0.1210.02240.0257-0.19710.12040.0582-0.0217-0.23270.00060.27110.0289-0.04110.3306-0.00210.2137-42.3703-1.1198-15.7512
192.94693.6476-1.09636.04121.08224.2056-0.06720.01140.106-0.04950.03910.1613-0.03090.11330.0280.2528-0.0171-0.02180.30120.02990.2344-39.44063.0131-22.8276
203.41185.0933-12.575912.8247-10.855341.6899-0.32721.20910.2075-1.18871.5492-0.8519-0.2329-3.6217-1.2220.7538-0.1722-0.07440.51170.11440.2446-38.74729.8846-29.3362
219.8439-5.0263-0.38935.90665.42756.9848-0.12070.61490.1676-0.1053-0.01840.0326-0.25770.37410.13910.3941-0.06170.1040.29730.05140.2821-4.68331.1654-26.7175
2210.975212.06576.359517.7219-1.092316.3060.0446-0.30480.0211-0.0103-0.1157-0.02980.1045-0.51850.0710.30880.00780.07440.2145-0.00340.2507-2.725433.8609-18.2042
235.27174.1316-3.3484.0653-3.43592.8753-0.08140.0737-0.1234-0.0317-0.1209-0.23180.05470.09820.20230.3073-0.02440.04710.26420.010.2643-0.600135.1869-8.5716
241.39730.1488-0.97861.49110.54823.14290.01850.3232-0.0249-0.2514-0.0121-0.2835-0.5360.2723-0.00640.2839-0.03940.02210.25250.0170.2721-12.155430.4385-15.0484
255.9811-2.5299-0.83993.1226-0.75382.7968-0.07070.6713-0.1977-0.1701-0.02530.0393-0.1327-0.24120.09590.3383-0.01170.01740.2432-0.0070.2249-15.13127.7126-17.4194
2678.9822-16.244737.10752.077-7.976116.31322.2959-0.4495-3.9169-0.51-0.30920.69411.1283-0.0957-1.98670.3258-0.16760.17261.00670.2720.7267-7.996321.2423-9.5655
275.70120.3711-3.04860.03860.10164.6549-0.31270.146-0.4238-0.0647-0.00540.00630.0694-0.07530.31810.3273-0.01010.02820.2409-0.04520.2964-19.905323.259-14.1026
286.1209-2.2558-0.00382.1865-2.34024.71110.16690.32380.13870.0626-0.11550.1676-0.1592-0.3517-0.05140.2698-0.00180.0070.2593-0.07680.2634-24.209230.8076-8.3753
295.409-5.8249-3.10311.58992.62591.44640.15710.65450.5813-0.03410.30741.139-0.0982-0.4432-0.46450.3170.1318-0.0240.40220.25810.7346-23.335940.0861-12.1598
304.1617-2.21635.471114.7647-5.65427.6572-0.1423-0.89430.3174-0.3837-0.3886-0.6775-0.0781-0.99490.53090.2786-0.04260.08280.2951-0.04040.2284-16.691636.3209-1.1034
3115.6098-2.35282.36471.95666.5431.9039-0.8407-0.66470.46610.1949-0.3850.2607-0.3126-1.09441.22570.3121-0.12910.09410.6163-0.11490.2683-21.159529.65295.8834
323.83922.0294-0.5022.0803-0.62275.17830.3095-0.3714-0.06040.0066-0.2015-0.0019-0.0337-0.1906-0.10790.2417-0.04430.00690.225-0.02580.242-18.48724.9127-3.0247
335.77351.85581.047510.140410.072210.46750.1382-0.8212-0.20030.45220.2892-0.62470.49230.6079-0.42750.2786-0.0869-0.01490.31130.08740.3067-9.649726.10031.0788
345.5994-2.5283.66824.5461-0.01033.00610.17460.14620.191-0.0792-0.281-0.09250.0789-0.00190.10640.2695-0.01960.05220.25990.03240.2861-14.557737.1838-9.423
358.89762.4916-0.32413.2849-3.56854.02980.52590.64170.9112-0.19260.20180.89660.2420.002-0.72760.65170.0496-0.12810.31760.19890.4854-20.110440.7432-21.0745
364.12180.72541.49040.87781.04682.03720.11010.03380.02130.0572-0.1076-0.17120.16530.1487-0.00250.2936-0.04530.0360.19180.01480.2882-8.971133.3169-5.0603
374.5671-2.56233.40011.3868-2.04999.91250.0713-0.41240.1237-0.04240.1894-0.0167-0.10290.1252-0.26070.3431-0.0580.04690.2105-0.09870.3793-6.948542.3979-0.71
388.36317.264-6.90987.6033-12.116330.4594-0.46620.19650.428-0.33710.38870.27610.1877-1.0110.07750.31910.03580.00910.22740.02790.334-5.255845.6416-11.207
395.91152.13144.7673.31637.982618.94320.00340.32380.627-0.11040.0533-0.0039-0.24790.1808-0.05670.4535-0.02660.02470.2160.09650.2256-10.144440.2413-22.2652
4042.720344.840825.664745.17826.989913.765-0.4420.2633-0.0176-0.65220.37760.0914-0.31110.140.06441.1155-0.1884-0.37430.49260.11440.1234-12.46333.6429-33.4369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 15
2X-RAY DIFFRACTION2A16 - 20
3X-RAY DIFFRACTION3A21 - 26
4X-RAY DIFFRACTION4A27 - 31
5X-RAY DIFFRACTION5A32 - 40
6X-RAY DIFFRACTION6A41 - 48
7X-RAY DIFFRACTION7A49 - 54
8X-RAY DIFFRACTION8A55 - 62
9X-RAY DIFFRACTION9A63 - 69
10X-RAY DIFFRACTION10A70 - 74
11X-RAY DIFFRACTION11A75 - 79
12X-RAY DIFFRACTION12A80 - 85
13X-RAY DIFFRACTION13A86 - 89
14X-RAY DIFFRACTION14A90 - 105
15X-RAY DIFFRACTION15A106 - 113
16X-RAY DIFFRACTION16A114 - 122
17X-RAY DIFFRACTION17A123 - 131
18X-RAY DIFFRACTION18A132 - 137
19X-RAY DIFFRACTION19A138 - 143
20X-RAY DIFFRACTION20A144 - 149
21X-RAY DIFFRACTION21B7 - 12
22X-RAY DIFFRACTION22B13 - 18
23X-RAY DIFFRACTION23B19 - 29
24X-RAY DIFFRACTION24B30 - 34
25X-RAY DIFFRACTION25B35 - 46
26X-RAY DIFFRACTION26B47 - 53
27X-RAY DIFFRACTION27B54 - 61
28X-RAY DIFFRACTION28B62 - 68
29X-RAY DIFFRACTION29B69 - 74
30X-RAY DIFFRACTION30B75 - 80
31X-RAY DIFFRACTION31B81 - 86
32X-RAY DIFFRACTION32B87 - 94
33X-RAY DIFFRACTION33B95 - 100
34X-RAY DIFFRACTION34B101 - 106
35X-RAY DIFFRACTION35B107 - 113
36X-RAY DIFFRACTION36B114 - 122
37X-RAY DIFFRACTION37B123 - 131
38X-RAY DIFFRACTION38B132 - 136
39X-RAY DIFFRACTION39B137 - 147
40X-RAY DIFFRACTION40B148 - 153

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