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- PDB-3bwl: Crystal structure of PAS domain of HTR-like protein from Haloarcu... -

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Basic information

Entry
Database: PDB / ID: 3bwl
TitleCrystal structure of PAS domain of HTR-like protein from Haloarcula marismortui
ComponentsSensor protein
KeywordsTRANSFERASE / structural genomics / APC87707.1 / PAS domain / HTR-like protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Kinase / Phosphoprotein
Function / homology
Function and homology information


phosphorelay sensor kinase activity
Similarity search - Function
PAS fold-4 / PAS fold / PAS domain / 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 / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) ...PAS fold-4 / PAS fold / PAS domain / 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 / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / 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
1H-INDOLE-3-CARBALDEHYDE / HTR-like protein
Similarity search - Component
Biological speciesHaloarcula marismortui ATCC 43049 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.73 Å
AuthorsOsipiuk, J. / Zhou, M. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of PAS domain of HTR-like protein from Haloarcula marismortui.
Authors: Osipiuk, J. / Zhou, M. / Freeman, L. / Joachimiak, A.
History
DepositionJan 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,05413
Polymers59,3524
Non-polymers7029
Water8,467470
1
A: Sensor protein
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0156
Polymers29,6762
Non-polymers3394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
MethodPISA
2
C: Sensor protein
D: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0397
Polymers29,6762
Non-polymers3635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.811, 68.533, 105.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein
Sensor protein


Mass: 14837.896 Da / Num. of mol.: 4 / Fragment: PAS domain: Residues 387-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula marismortui ATCC 43049 (Halophile)
Species: Haloarcula marismortui / Strain: DSM 3752 / JCM 8966 / Gene: htlD, rrnAC0075 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5V5P7, histidine kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-I3A / 1H-INDOLE-3-CARBALDEHYDE


Mass: 145.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H7NO / Comment: agonist*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium chloride, 0.1 M Hepes buffer, 25% PEG 3350, pH 7.5, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.73→35.6 Å / Num. all: 51106 / Num. obs: 51106 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.104 / Χ2: 1.893 / Net I/σ(I): 10.7
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.01 / Num. unique all: 2998 / Χ2: 0.933 / % possible all: 81.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.73→35.6 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.274 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ELECTRON DENSITY INDICATES THAT AN INDOLE DERIVATIVE, MODELED AS INDOLE-3-CARBOXALDEHYDE (I3A), IS LOCATED IN PUTATIVE ACTIVE SITE OF ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ELECTRON DENSITY INDICATES THAT AN INDOLE DERIVATIVE, MODELED AS INDOLE-3-CARBOXALDEHYDE (I3A), IS LOCATED IN PUTATIVE ACTIVE SITE OF EACH MONOMER. HOWEVER, AUTHORS DO NOT EXCLUDE POSSIBILITY THAT ANOTHER LIGAND IS PRESENT IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2589 5.1 %RANDOM
Rwork0.159 ---
all0.161 51009 --
obs0.161 51009 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.822 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.73→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 49 470 4466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224351
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9755909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0215572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.96623.948271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68215827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6281558
X-RAY DIFFRACTIONr_chiral_restr0.1440.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023470
X-RAY DIFFRACTIONr_nbd_refined0.2150.21935
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22947
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2369
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.244
X-RAY DIFFRACTIONr_mcbond_it1.0061.52667
X-RAY DIFFRACTIONr_mcangle_it1.44224135
X-RAY DIFFRACTIONr_scbond_it2.39731916
X-RAY DIFFRACTIONr_scangle_it3.7884.51727
LS refinement shellResolution: 1.73→1.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 144 -
Rwork0.237 2830 -
all-2974 -
obs-2974 78.12 %
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)
15.30314.4288-1.469314.6034-3.849514.0159-0.01140.2780.2249-0.3465-0.03380.0211-0.30490.19290.0453-0.00570.0013-0.00890.00110.0076-0.009927.126-4.711-10.672
211.1029-0.4448-14.27791.59815.941750.59890.24230.13810.2345-0.0139-0.1562-0.0343-0.993-0.5605-0.0860.03240.0053-0.0016-0.0396-0.0091-0.080222.703-2.311-0.39
37.71624.5346-1.23172.6812-1.225515.55240.18750.3654-0.47520.20730.0961-0.06730.01170.1106-0.28360.0098-0.00950.01280.0193-0.0443-0.043718.104-0.3569.137
41.5327-0.54540.03622.27683.78146.91330.0302-0.0110.1547-0.08740.0148-0.0359-0.1138-0.0692-0.0450.0133-0.00350.01280.0168-0.0009-0.020415.0453.77118.86
54.0044-1.02290.74371.99482.06564.485-0.03130.1944-0.1277-0.37210.1783-0.2055-0.21890.4452-0.147-0.0061-0.08210.04680.0708-0.042-0.021526.27813.60322.723
62.8656-0.8-1.04940.79911.83224.49940.07360.1378-0.0491-0.10230.01170.0117-0.4306-0.1464-0.08530.0358-0.0136-0.00770.00830.0022-0.016412.7719.68519.789
716.52695.4014-7.10752.4819-1.859310.3304-0.01360.40120.754-0.26510.1290.2994-0.2455-0.1518-0.11540.05930.0112-0.0395-0.06710.0425-0.0413.48318.00719.312
82.0677-0.9874-1.43112.5844-1.361715.0940.021-0.02130.0468-0.05170.0974-0.1294-0.3876-0.0718-0.11840.025-0.03830.01850.025-0.004-0.050721.86519.22925.454
91.74920.0167-0.89770.89961.52773.0845-0.06090.094-0.01940.12290.18620.0613-0.19170.1134-0.12540.0446-0.02620.01880.0118-0.0153-0.029920.82817.2134.449
1012.9405-10.45850.649910.83763.68757.47370.0808-0.23920.17060.16420.1137-0.4042-0.1643-0.0495-0.1946-0.0421-0.05360.01120.0673-0.0695-0.01530.21512.68734.174
117.63763.45283.89818.75892.93045.8542-0.0122-0.0554-0.0470.18460.1333-0.30320.39450.6234-0.1211-0.07810.0421-0.0260.1014-0.0532-0.03132.2821.62229.991
122.8856-1.55241.23321.6985-0.02341.0819-0.0866-0.01010.00720.13970.057-0.0413-0.0459-0.0230.0296-0.00480.00470.01270.0162-0.0199-0.021113.39811.5431.874
134.09810.4207-1.54370.6034-0.00282.1109-0.03170.18530.06860.00290.1261-0.00960.05030.1425-0.0944-0.00950.00140.01080.0489-0.0254-0.017925.6315.14425.115
1423.5583-5.53252.342710.4701-4.727314.0486-0.5790.29860.5119-0.2498-0.1753-0.52680.7050.97650.75430.38660.1840.152-0.00020.0449-0.015631.2087.017-5.504
153.81110.7581-5.65377.2286-8.769516.64450.289-0.17460.4525-0.4119-0.1775-0.11560.16640.1452-0.11150.05810.00630.041-0.0069-0.0086-0.014727.0592.3699.686
162.77851.33041.79780.99560.71121.7880.01380.0310.13030.1506-0.05390.12980.12990.09060.04020.02190.0075-0.0020.0262-0.0161-0.019217.671-7.24419.41
1711.9346.64472.14086.60182.17962.5267-0.12660.08240.2622-0.10770.08690.15250.25540.08020.03970.00580.0142-0.0032-0.0053-0.027-0.033613.664-14.43413.327
182.4429-2.37271.50413.6912-0.9271.1315-0.0017-0.0508-0.0261-0.01030.00970.05720.14820.3385-0.0080.02730.02780.0070.0685-0.0142-0.041724.364-10.86222.313
1914.66812.2025.08520.34881.07567.09070.28130.081-0.3866-0.0232-0.1410.13780.51970.3825-0.14030.03610.0717-0.03130.0123-0.0072-0.025423.076-18.43916.568
201.1984-0.75141.01120.472-0.58953.41770.1309-0.0630.00170.0849-0.00970.06660.4298-0.086-0.12120.0758-0.04220.02780.0042-0.0034-0.03989.997-19.82723.747
2113.0956-1.0925-0.176811.9469-6.06323.11830.0402-0.0521-0.1464-0.55270.00990.33820.0579-0.0622-0.0501-0.0263-0.05370.01340.0189-0.0245-0.00472.659-14.75519.976
224.8141.32083.37411.65533.62798.0126-0.0166-0.11490.06190.0879-0.21770.2231-0.2636-0.350.2343-0.03040.00620.02110.02160.00170.01132.136-2.98118.578
235.3946-3.43851.04613.5789-0.97670.71260.0253-0.0483-0.0830.1882-0.05280.07790.1587-0.00080.02760.05080.0111-0.0024-0.00830.0011-0.057216.144-15.02129.136
241.1217-0.2356-0.33811.3137-0.85230.7762-0.1269-0.0590.10170.151-0.05340.08260.0777-0.02620.18020.05560.00410.011-0.0017-0.0256-0.030510.733-6.49523.62
253.52430.05294.66733.2257-0.49988.8024-0.01620.27560.036-0.11250.0513-0.0878-0.14490.3075-0.0350.0020.00350.03260.0261-0.0077-0.03699.526-6.31210.421
262.3119-2.6907-0.63163.78780.9590.2489-0.2072-0.1075-0.0040.06640.519-0.1187-0.2795-0.0266-0.31170.05450.0125-0.01290.03920.0019-0.038217.062-5.66829.87
2711.8762-1.8283-3.721325.51297.875815.46410.40510.6972-0.0724-2.04330.0357-0.3955-0.3507-0.131-0.44080.205-0.01090.0555-0.04890.006-0.0381-15.297-0.298-12.849
284.38711.74281.04721.31070.42381.55-0.04080.1744-0.0219-0.06180.0109-0.0923-0.1301-0.07190.02990.0612-0.0165-0.0006-0.02370.0118-0.0257-11.8876.098-0.466
2912.83444.688411.1313.15123.63959.8712-0.34570.55650.2793-0.17710.27360.0082-0.5560.39210.07210.0696-0.09760.0081-0.02680.0288-0.0514-5.9213.661-1.427
304.3369-3.0511.01122.41940.07982.52980.06310.0274-0.062-0.0647-0.13320.2788-0.361-0.18090.070.0847-0.0014-0.0179-0.02870.019-0.0257-19.0988.7460.204
3121.04519.454-11.95667.4467-2.30210.82230.39420.1690.7375-0.1766-0.16670.385-0.8507-0.017-0.22740.15680.0572-0.0532-0.10740.03-0.0783-16.90317.212-1.08
324.13373.35543.81018.868210.453312.329-0.2286-0.0676-0.10910.3121-0.3078-0.1904-1.03490.24950.53640.1728-0.0387-0.0369-0.08290.0185-0.0597-7.27118.4774.569
333.5136-0.2187-0.49770.07390.48113.42930.0891-0.16630.177-0.0699-0.02820.0105-0.55460.0494-0.06090.1642-0.0568-0.0152-0.0641-0.0109-0.0447-6.41516.11811.825
343.0581-5.3111-2.424510.46082.66484.7045-0.34570.04750.15380.28580.3186-0.6843-0.2780.18920.0272-0.0045-0.064-0.0562-0.0239-0.00440.02773.5288.0457.635
351.945-1.33481.07791.4248-0.52660.68670.00490.0115-0.01760.25020.2521-0.07430.13510.0915-0.2570.0025-0.0243-0.00190.0188-0.00850.0061-2.7531.0559.496
364.3545-2.05793.15864.03630.70453.867-0.1068-0.22910.1168-0.2666-0.0149-0.1079-0.5017-0.10450.12170.12220.03820.0017-0.0466-0.0225-0.0327-19.00515.37510.363
370.9428-1.5996-2.10512.72573.58634.7186-0.094-0.0542-0.05210.06610.0023-0.0680.09270.04620.09170.04670.00380.0123-0.01660.0081-0.0076-10.0453.9349.088
381.29530.1913-0.54580.59240.05211.8391-0.18450.2465-0.0187-0.13030.06060.0452-0.10160.04140.12390.0549-0.04230.01730.02080.0245-0.0276-4.2064.6840.083
397.0235.1968-10.714717.7424-12.9853115.38820.2220.14810.7633-2.8913-0.7760.31540.72881.00170.5540.44370.23030.02810.08410.17990.0566-8.0295.106-24.678
4011.29044.72970.84659.3312-10.123721.8994-0.15610.48370.1768-0.06230.1035-0.16170.0440.09820.05260.0487-0.02260.0138-0.02710.0072-0.0871-7.7510.382-10.132
413.96921.64741.39621.39470.80570.99670.01310.05420.0471-0.0448-0.01580.0361-0.05270.01490.00270.02290.0046-0.00620.00860.0029-0.0214-13.057-7.864-2.501
422.87833.8183-1.32735.2607-2.68374.96990.01140.0990.0517-0.3002-0.0540.12480.1930.03730.04270.00220.0036-0.00330.0145-0.0244-0.0128-19.114-15.255-7.068
431.4656-1.7330.51092.1122-0.88541.43410.02180.0426-0.0970.11590.02-0.021-0.0310.1645-0.04190.0259-0.01510.00370.0226-0.0044-0.0035-6.81-11.446-0.764
449.9392-0.02869.34340.1492-0.501810.2960.2660.26650.0146-0.0631-0.08620.10.35620.4245-0.17980.01220.0486-0.00860.0267-0.0205-0.0198-8.128-18.774-5.526
451.3928-0.86380.44711.4446-3.858614.25480.0475-0.21690.0947-0.0671-0.0646-0.03940.37490.16170.0170.05010.0084-0.0105-0.015-0.0063-0.0129-17.907-21.427-1.716
462.1477-1.33560.37841.38671.03562.971-0.0025-0.1086-0.04460.10320.03450.11460.119-0.002-0.0320.0152-0.00440.0222-0.01010.03230.0008-21.207-20.3785.987
472.741-2.9681.440912.3731-3.28732.40890.132-0.0328-0.1646-0.1318-0.08670.29320.0837-0.1831-0.0452-0.05870.00060.00240.04390.0065-0.0123-29.4-12.2261.093
482.2299-2.17550.01892.4905-0.74881.4489-0.1234-0.02610.0280.18450.0845-0.0291-0.0028-0.08030.03890.01080.0088-0.0097-0.00750.00380.0057-21.902-8.0996.525
490.5809-0.3471-0.0670.708-0.42280.941-0.1166-0.0593-0.12920.06960.06960.1077-0.09390.03390.04710.00410.003-0.006-0.0023-0.0026-0.0156-15.038-12.4754.002
504.5719-1.64963.75492.7742-0.15763.74180.15860.348-0.081-0.0799-0.0258-0.0786-0.22810.2412-0.13280.04390.00570.00040.04440.0041-0.0503-23.889-7.263-9.405
515.1055-1.22682.87512.04232.45897.88660.01860.0361-0.10130.06080.2081-0.1106-0.09340.1166-0.22670.0173-0.0079-0.0143-0.02030.0163-0.0122-12.516-6.6167.393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA384 - 3911 - 8
2X-RAY DIFFRACTION2AA392 - 3999 - 16
3X-RAY DIFFRACTION3AA400 - 40517 - 22
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