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- PDB-3co2: Mlotik1 ion channel cyclic-nucleotide binding domain mutant -

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Basic information

Entry
Database: PDB / ID: 3co2
TitleMlotik1 ion channel cyclic-nucleotide binding domain mutant
ComponentsMlotik1 ion channel protein
KeywordsMEMBRANE PROTEIN / Mlotik1 cyclic-nucleotide binding domain mutant3 R307W / unliganded
Function / homology
Function and homology information


potassium channel activity / cAMP binding / identical protein binding / plasma membrane
Similarity search - Function
Cyclic nucleotide-regulated ion channel, N-terminal / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls ...Cyclic nucleotide-regulated ion channel, N-terminal / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cyclic nucleotide-gated potassium channel mll3241
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsClayton, G.M. / Alteiri, S.L. / Thomas, L.R. / Morais-Cabral, J.H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural and Energetic Analysis of Activation by a Cyclic Nucleotide Binding Domain.
Authors: Altieri, S.L. / Clayton, G.M. / Silverman, W.R. / Olivares, A.O. / De La Cruz, E.M. / Thomas, L.R. / Morais-Cabral, J.H.
History
DepositionMar 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 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
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mlotik1 ion channel protein
B: Mlotik1 ion channel protein
C: Mlotik1 ion channel protein
D: Mlotik1 ion channel protein


Theoretical massNumber of molelcules
Total (without water)59,4724
Polymers59,4724
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-49.1 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.473, 132.349, 39.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Mlotik1 ion channel protein


Mass: 14868.108 Da / Num. of mol.: 4
Fragment: cyclic-nucleotide binding domain (UNP residues 216-355)
Mutation: R307W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q98GN8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growMethod: vapor diffusion, hanging drop
Details: ammoinium sulfate, Nacitrate, NaCl, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9 Å
DetectorDate: Apr 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 19637 / % possible obs: 97.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.079
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.612 / % possible all: 89.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 2.9→41.03 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.854 / SU B: 45.938 / SU ML: 0.405 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30605 694 5.1 %RANDOM
Rwork0.26078 ---
obs0.26313 12958 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å20 Å2
2---3.76 Å20 Å2
3---1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.9→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 0 9 3519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223582
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9531.9624913
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7035498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92522.692104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48515459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0581517
X-RAY DIFFRACTIONr_chiral_restr0.0550.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022692
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.21558
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22528
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.151.52532
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.17723957
X-RAY DIFFRACTIONr_scbond_it0.40131178
X-RAY DIFFRACTIONr_scangle_it0.6134.5956
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 44 -
Rwork0.353 952 -
obs--99.5 %
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)
115.54262.317515.239817.9822.507914.946-0.6588-0.903-2.0321-0.97860.35791.21830.49950.07350.30090.26280.01610.0150.01410.14560.8181-32.698216.8632-17.6007
212.4592-5.8769-1.28042.7720.6040.13160.1518-1.2353-0.3140.5598-0.15650.2418-0.14970.14330.00460.3518-0.1058-0.04330.36880.05840.6462-36.959927.204-10.7659
316.18023.7896-9.27383.4563-3.1259.1933-0.40270.9317-0.1851-0.30020.17070.6939-0.335-1.3550.2320.3564-0.0266-0.10190.0623-0.02280.5165-38.141722.863-21.3351
410.7338-7.0869-4.884711.18994.3552.4190.07820.27411.3559-1.31570.4340.50030.3301-0.3783-0.51230.6571-0.0275-0.10080.40870.07350.5561-32.272237.8201-31.6641
55.70230.9253-6.81760.1502-1.10638.1510.2158-0.50060.6087-0.41750.87080.07190.4-1.4793-1.08660.3303-0.017-0.08670.11770.05170.3816-33.034130.1609-23.2421
69.74196.43953.512210.094314.715227.57820.9556-0.5095-0.2565-1.8514-1.70040.9811-1.68051.41280.74480.19540.05320.12210.2845-0.11830.4495-22.943334.6998-26.0387
710.7744-0.7784-1.360723.66691.54456.6866-1.19511.04140.8412-1.14570.789-1.1317-1.19730.51140.40610.3618-0.0997-0.16080.3708-0.03780.3216-23.991136.9903-21.6636
88.043812.6313-0.801719.835-1.2590.07990.4881.36010.65891.24651.00352.5392-1.70621.2588-1.49160.4958-0.02490.1440.75910.2081.3815-40.309439.7408-20.2304
927.8449-7.1834.765330.6845-14.30866.7489-1.60641.1132-0.24681.02040.6681.8173-0.1272-0.32690.93830.3868-0.1570.05690.2222-0.08630.3847-28.908639.4176-28.0614
109.09422.0592-3.6230.4663-0.83314.63861.94440.79340.7274-0.9757-0.93240.1538-0.7577-0.4799-1.0120.4090.0914-0.00220.0580.04770.5074-33.130628.233-26.2535
1112.5355-11.8038-1.449127.5425-6.07263.53450.72480.66881.5195-0.0236-0.2314-0.09050.6535-3.6806-0.49340.1334-0.01690.04540.62250.02140.641-48.618628.9354-18.527
129.5136-8.6451-2.849212.1874-5.864417.3514-0.5253-1.67380.00741.144-0.3002-0.4422-0.6510.97960.82560.2470.0329-0.18860.36450.11920.7864-48.322734.8355-11.1633
1340.859520.618120.264110.489310.174410.0805-0.728-0.99060.8670.8059-2.03070.43480.3751-0.59432.75870.88540.0893-0.01540.3990.17620.6044-33.535415.3777-5.0463
145.0573-0.5708-1.89192.2927-2.61384.29530.1791-0.08070.5593-0.0413-0.1918-0.3412-0.17180.08910.01270.2066-0.0561-0.04830.15840.04940.2405-36.8165.5055-12.1527
1512.3324-4.47563.121820.1414-0.65696.17760.27740.21280.796-1.57610.33051.127-1.29310.2218-0.60790.22760.0057-0.11920.11880.09140.5-43.44639.0705-13.8152
164.6187-5.92845.28588.4234-7.63178.5966-0.2579-0.70850.61320.50730.1501-0.099-0.1549-0.7260.10780.37440.04430.01890.181-0.07480.1535-35.55673.39474.152
172.7925-0.40041.61366.4681-0.70121.75170.3313-0.25580.06110.3419-0.25280.29860.05760.0921-0.07850.3202-0.00730.05550.18270.02740.0373-36.9676-4.35530.8995
1817.3106-1.28334.87040.734-3.856720.4959-0.6273-0.3373-1.84821.3571.351-0.38541.62980.9745-0.72380.20190.02210.03740.35840.0140.1912-26.152-7.4797-0.1665
1926.04050.7333-5.51972.972310.858942.27110.50580.1113-1.9522-1.0260.20980.08593.54161.0506-0.71560.5030.1167-0.08660.68820.10010.4996-22.6756-9.6081-2.953
2032.69361.0862-7.33554.101-5.5158.48161.19430.02710.4080.6671-0.67820.74380.38541.1935-0.51610.3473-0.00270.04970.22620.04970.1403-31.6361-0.7836-5.8337
212.9924-7.22531.633623.1844-7.76923.441-0.44691.0761-0.7637-0.33270.86451.18721.0235-1.4896-0.41760.2603-0.2016-0.04820.43550.00270.4395-42.8139-8.573-5.5244
228.564-1.07490.12572.5848-0.93194.9950.1754-0.06770.14650.2831-0.11470.1684-0.00190.0551-0.06070.249-0.02390.00570.12570.05720.1071-34.4039-1.631.4297
2316.28923.4896.576119.5873-9.87999.4185-0.1319-0.4345-0.13871.5821-0.15290.844-0.2351-2.46670.28490.30310.0904-0.01760.59130.07540.4013-51.17482.9326-6.4503
2419.55045.59492.87219.69284.641611.5404-0.02461.68630.37560.1404-0.1668-0.57240.17910.88080.19140.15730.08720.02510.49010.07220.399-51.94460.3939-15.0049
254.87319.5186-6.777778.1816-27.14829.4271-1.2360.79460.3831-3.0528-0.2225-0.70792.05750.35151.45850.4667-0.04090.02780.45050.05880.6358-18.242616.6526-20.9928
269.18086.656-11.79627.6881-8.686515.1628-0.0326-0.47050.31760.461-0.4875-1.0302-0.48990.62320.52010.19190.00890.01710.22880.00970.5141-18.044311.9555-12.28
2739.791930.11030.152535.5096-3.55399.81580.4252-1.30032.01591.3638-0.3145-0.25931.23790.1593-0.11070.49870.1217-0.1460.41220.09910.6336-10.275410.6392-6.2267
2825.04689.6814-16.08163.7421-6.21610.3254-0.2718-0.53811.51140.5269-0.6878-1.4251.15920.04390.95960.5620.15740.0072-0.15690.14641.0477-8.770112.1722-14.4428
292.0805-1.1618-0.36412.3067-1.97992.9385-0.09231.0863-0.1413-0.54980.4585-0.72260.23440.157-0.36620.2388-0.03540.09470.1157-0.00890.2237-21.44610.0871-22.5243
305.83826.3336-0.166210.8149-0.1360.00520.2042-0.1346-1.3557-0.0937-0.5316-1.8438-0.33340.0290.32740.3698-0.03130.01190.3044-0.09120.6584-15.5769-8.6103-16.0873
315.02582.34610.03751.12070.608913.7313-0.55970.461-0.027-0.48920.8110.28410.1146-0.1599-0.25130.0638-0.00850.03880.1391-0.00060.1584-24.7244-0.4063-14.5621
321.7349-2.0919-2.94888.2617-3.84714.56-0.6336-0.1223-0.519-0.05360.38240.71810.5172-0.37240.25120.16430.01320.0130.26410.02050.1808-26.7078-3.2576-9.4495
3321.86135.7665-3.215434.35755.42499.5639-0.15570.442-1.30790.87210.5607-1.45540.70580.789-0.4050.53180.0689-0.0860.54640.020.6469-11.6566-6.7998-9.8216
341.2886-0.3508-1.95996.48543.07443.99120.2461-0.0079-0.595-0.1745-0.2469-0.93280.0478-0.09310.00090.2902-0.0777-0.05290.1390.09810.2788-21.5745-2.3168-17.4119
3538.446219.49721.957311.181114.289120.2295-1.15990.00520.06140.3569-0.8032-1.9822-3.17090.27041.9630.59710.1818-0.11790.18040.12321.8482-3.07683.5327-15.6495
3627.019816.237723.59319.758214.178420.6015.42791.45814.05942.2952-1.1835-4.8991-4.3129-4.4765-4.24442.46240.6770.17061.37530.50651.97270.07137.0851-7.6192
3746.873114.2647-66.170717.3756-10.6172100.3667-2.7345-1.8420.61163.1942-0.6019-2.97861.2722-0.68073.33640.8427-0.06610.09170.42770.13420.898-16.316322.6893-8.646
3814.80116.2044-3.929813.3168-7.99824.80720.17030.355-0.4164-0.16520.0180.9420.68580.0545-0.18830.1789-0.03340.12580.1078-0.15070.4442-14.229827.7535-20.3422
394.074-2.19053.39868.67621.902129.5824-0.150.96560.80.5072-0.1095-0.49910.46112.06830.25950.4634-0.17510.09980.1452-0.10970.5505-7.448223.6895-20.5695
4024.5825-21.4229-15.385120.08312.366410.3958-0.3746-0.38710.3261-0.0850.6913-1.0867-0.79411.2761-0.31670.37620.07230.04140.29170.03460.3018-10.667733.4274-8.2784
419.0721-7.7529-15.4596.625613.211126.3423-0.91320.4771-0.0725-0.46760.26-0.2989-1.0922-0.15770.65330.2008-0.12650.03320.4244-0.1640.2956-18.488245.9739-7.8456
425.7876-2.6471.60495.91442.93233.30270.0049-0.37760.50080.0129-0.2757-0.9347-0.06470.31560.27090.333-0.01420.10660.094-0.04130.4065-11.942943.007-15.3167
4310.8349-1.0491-4.965911.335711.00112.12770.53340.11171.07291.06950.67241.9787-2.7951-0.897-1.20580.2391-0.1146-0.05430.5115-0.16880.2955-23.706144.0565-15.0943
448.1048-4.64122.26294.26482.07317.6940.24240.92561.2391-1.1084-0.6205-0.2458-0.8265-0.35750.37810.39160.05160.07940.20010.01280.6824-23.047741.4506-18.9295
4513.5671-1.7478-7.04073.212-4.517613.50580.12181.4048-0.6897-1.46480.0728-1.8797-0.28261.1518-0.19460.4448-0.01670.1260.4008-0.03850.5193-7.85642.8137-22.8286
461.6448-3.6296-0.34728.04691.01751.7667-0.26510.09580.08040.04680.0373-0.302-0.0629-0.35350.22780.26-0.0537-0.01620.1845-0.06630.3349-16.166341.1161-12.0547
472.4433-1.6462-3.9328.45146.35568.19871.1845-0.52041.0781-0.9601-0.1813-3.1142-0.76770.2326-1.00330.3915-0.01770.1850.39590.06261.04250.929730.8161-18.5993
486.0994-8.1213-0.002617.09278.203910.70970.12750.9154-1.0318-1.5277-1.23561.2569-0.0133-0.14831.10810.2622-0.16020.06840.4415-0.11470.9592-1.051932.3962-29.3406
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA221 - 2276 - 12
2X-RAY DIFFRACTION2AA228 - 24213 - 27
3X-RAY DIFFRACTION3AA243 - 25628 - 41
4X-RAY DIFFRACTION4AA257 - 27042 - 55
5X-RAY DIFFRACTION5AA271 - 27656 - 61
6X-RAY DIFFRACTION6AA277 - 28362 - 68
7X-RAY DIFFRACTION7AA284 - 29769 - 82
8X-RAY DIFFRACTION8AA298 - 30683 - 91
9X-RAY DIFFRACTION9AA307 - 31492 - 99
10X-RAY DIFFRACTION10AA315 - 325100 - 110
11X-RAY DIFFRACTION11AA326 - 332111 - 117
12X-RAY DIFFRACTION12AA333 - 346118 - 131
13X-RAY DIFFRACTION13BB219 - 2254 - 10
14X-RAY DIFFRACTION14BB226 - 23611 - 21
15X-RAY DIFFRACTION15BB237 - 24722 - 32
16X-RAY DIFFRACTION16BB248 - 26133 - 46
17X-RAY DIFFRACTION17BB262 - 27747 - 62
18X-RAY DIFFRACTION18BB278 - 28463 - 69
19X-RAY DIFFRACTION19BB285 - 29170 - 76
20X-RAY DIFFRACTION20BB292 - 29777 - 82
21X-RAY DIFFRACTION21BB298 - 30783 - 92
22X-RAY DIFFRACTION22BB308 - 32593 - 110
23X-RAY DIFFRACTION23BB326 - 331111 - 116
24X-RAY DIFFRACTION24BB332 - 346117 - 131
25X-RAY DIFFRACTION25CC219 - 2244 - 9
26X-RAY DIFFRACTION26CC225 - 23310 - 18
27X-RAY DIFFRACTION27CC234 - 24219 - 27
28X-RAY DIFFRACTION28CC243 - 24828 - 33
29X-RAY DIFFRACTION29CC249 - 26134 - 46
30X-RAY DIFFRACTION30CC262 - 27247 - 57
31X-RAY DIFFRACTION31CC273 - 28358 - 68
32X-RAY DIFFRACTION32CC284 - 29769 - 82
33X-RAY DIFFRACTION33CC298 - 30783 - 92
34X-RAY DIFFRACTION34CC308 - 32493 - 109
35X-RAY DIFFRACTION35CC325 - 331110 - 116
36X-RAY DIFFRACTION36CC332 - 337117 - 122
37X-RAY DIFFRACTION37DD219 - 2254 - 10
38X-RAY DIFFRACTION38DD226 - 23611 - 21
39X-RAY DIFFRACTION39DD237 - 24722 - 32
40X-RAY DIFFRACTION40DD248 - 25533 - 40
41X-RAY DIFFRACTION41DD256 - 26341 - 48
42X-RAY DIFFRACTION42DD264 - 27649 - 61
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