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- PDB-4d7t: Structure of the SthK Carboxy-Terminal Region in complex with cAMP -

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Basic information

Entry
Database: PDB / ID: 4d7t
TitleStructure of the SthK Carboxy-Terminal Region in complex with cAMP
ComponentsSTHK_CNBD_CAMP
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


nucleotide binding / membrane
Similarity search - Function
Helix hairpin bin / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Potassium channel domain / Ion channel / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Helix hairpin bin / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Potassium channel domain / Ion channel / 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 / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Cyclic nucleotide-binding domain-containing protein
Similarity search - Component
Biological speciesSPIROCHAETA THERMOPHILA DSM 6192 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.582 Å
AuthorsKesters, D. / Brams, M. / Nys, M. / Wijckmans, E. / Spurny, R. / Voets, T. / Tytgat, J. / Ulens, C.
CitationJournal: Plos One / Year: 2015
Title: Structure of the SthK Carboxy-Terminal Region Reveals a Gating Mechanism for Cyclic Nucleotide-Modulated Ion Channels.
Authors: Kesters, D. / Brams, M. / Nys, M. / Wijckmans, E. / Spurny, R. / Voets, T. / Tytgat, J. / Kusch, J. / Ulens, C.
History
DepositionNov 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Database references / Structure summary
Category: citation / diffrn_detector / struct
Item: _citation.title / _diffrn_detector.type / _struct.title
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: STHK_CNBD_CAMP
B: STHK_CNBD_CAMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0564
Polymers46,3972
Non-polymers6582
Water181
1
A: STHK_CNBD_CAMP
hetero molecules

A: STHK_CNBD_CAMP
hetero molecules

A: STHK_CNBD_CAMP
hetero molecules

A: STHK_CNBD_CAMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1128
Polymers92,7954
Non-polymers1,3174
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445y-1,-x-1,z1
crystal symmetry operation3_465-y-1,x+1,z1
crystal symmetry operation2_355-x-2,-y,z1
Buried area8920 Å2
ΔGint-52.5 kcal/mol
Surface area40340 Å2
MethodPISA
2
B: STHK_CNBD_CAMP
hetero molecules

B: STHK_CNBD_CAMP
hetero molecules

B: STHK_CNBD_CAMP
hetero molecules

B: STHK_CNBD_CAMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1128
Polymers92,7954
Non-polymers1,3174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
Buried area6770 Å2
ΔGint-47 kcal/mol
Surface area39630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.439, 87.439, 79.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein STHK_CNBD_CAMP


Mass: 23198.697 Da / Num. of mol.: 2
Fragment: CYCLIC NUCLEOTIDE BINDING DOMAIN, RESIDUES 226-423
Source method: isolated from a natural source
Source: (natural) SPIROCHAETA THERMOPHILA DSM 6192 (bacteria)
References: UniProt: E0RR11
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.27 Å3/Da / Density % sol: 62.43 % / Description: NONE
Crystal growpH: 5 / Details: PH 5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→48.8 Å / Num. obs: 18751 / % possible obs: 99.1 % / Observed criterion σ(I): 1.6 / Redundancy: 3.4 % / Biso Wilson estimate: 69.83 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.58→2.72 Å / Redundancy: 3.1 % / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U11

3u11


Resolution: 2.582→48.799 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 36.12 / Stereochemistry target values: ML
Details: DUE TO LOW RESOLUTION IN SOME AREAS A NUMBER OF RESIDUES WERE DELETED OR A NUMBER OF SIDE CHAIN WERE DELETED
RfactorNum. reflection% reflection
Rfree0.31 970 5.2 %
Rwork0.2654 --
obs0.2677 18737 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.582→48.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 44 1 2975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053027
X-RAY DIFFRACTIONf_angle_d1.0144092
X-RAY DIFFRACTIONf_dihedral_angle_d13.5041096
X-RAY DIFFRACTIONf_chiral_restr0.036466
X-RAY DIFFRACTIONf_plane_restr0.006512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5825-2.71860.41161430.36392444X-RAY DIFFRACTION96
2.7186-2.88890.37851400.34212539X-RAY DIFFRACTION100
2.8889-3.11190.42761320.34032556X-RAY DIFFRACTION100
3.1119-3.4250.36121590.30722531X-RAY DIFFRACTION100
3.425-3.92050.28471290.26622550X-RAY DIFFRACTION99
3.9205-4.93860.3031460.22752549X-RAY DIFFRACTION99
4.9386-48.80730.26621210.24532598X-RAY DIFFRACTION98
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)
16.718-5.2398-5.39045.35156.49568.79720.5107-0.32410.01241.8675-0.9960.4889-0.2336-0.8140.8940.8473-0.14910.0421.16090.09940.487-70.5075-4.72643.675
25.1772-5.52211.747210.0037-3.08944.7349-0.9096-0.78290.55060.95261.1005-0.9286-0.2605-0.2414-0.1260.5783-0.0372-0.12370.70350.05120.4225-62.1598-2.97-2.7151
38.6811-6.94955.89658.9429-6.43625.6169-0.4334-1.2288-0.4428-0.0310.4794-0.08370.5314-1.86280.09870.7187-0.0033-0.00570.8537-0.08440.5772-77.854816.1284-8.2647
44.11190.60240.71099.02255.37933.24391.29712.45850.4475-1.2199-1.40411.6018-1.5279-2.0810.06020.8420.34770.03050.9194-0.05071.0602-63.149922.4719-18.7129
59.7626-5.27190.48732.9641-0.35047.40390.76951.39790.5369-0.9135-1.4664-0.45150.4375-0.47240.73750.35930.06590.02510.71290.05050.6639-71.365316.8483-19.0907
65.147-0.9253-1.52366.20470.79245.93690.40761.3196-0.314-0.69-0.3501-0.0576-0.7863-0.2931-0.04820.36350.0646-0.04680.71110.04490.4291-59.57838.154-25.3638
74.2739-0.7907-1.54952.84890.05613.5097-0.72180.3324-1.4077-0.3962-0.5366-0.41752.5042-0.58210.01510.9035-0.52450.20621.81180.37350.4867-27.7495-50.489341.9035
89.01966.6533.65789.8960.89146.8459-1.57621.5005-0.1138-0.42042.4606-0.8928-0.83470.5666-0.51230.72140.0309-0.14711.35710.27950.8699-18.1598-49.933836.5346
95.85321.8701-2.44335.57970.32074.0129-0.34161.5747-0.8302-0.0342-0.2132-0.7666-2.1951-0.7473-0.29141.71660.01850.08690.3127-0.30330.5281-29.5706-26.512529.9703
107.8494-2.41590.1666.902-0.08499.021-0.1954-0.16-0.80190.96930.32010.12640.3129-1.43290.1251.1250.03210.18970.73140.05670.5455-18.3022-35.448919.7088
112.1254-0.11551.59058.6842-5.5454.60770.8566-0.3749-0.19610.2153-0.65780.495-2.14520.5737-0.25950.90180.12930.12290.6985-0.03110.5936-7.1874-40.394816.2682
123.69351.007-3.53085.1027-0.2226.67480.1708-0.1346-0.5656-0.964-0.2683-0.1318-0.4435-0.94730.38211.79550.1817-0.16610.5003-0.0840.5869-13.4458-40.023513.7093
137.35943.269-3.29186.2286-2.98731.9701-0.80541.66180.2037-0.63580.24793.1987-0.7294-2.2545-0.66691.50490.6733-0.38861.08030.05351.2032-22.7993-33.032117.0494
145.0732-0.4836-5.82745.60110.65078.40930.35580.74510.3847-1.1673-0.62220.5478-0.9952-0.87940.03371.85050.10160.02121.048-0.03920.6425-11.2116-28.64976.6623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 226 THROUGH 245 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 246 THROUGH 267 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 268 THROUGH 291 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 292 THROUGH 305 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 306 THROUGH 322 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 323 THROUGH 423 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 227 THROUGH 245 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 246 THROUGH 265 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 266 THROUGH 295 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 296 THROUGH 347 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 348 THROUGH 367 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 368 THROUGH 387 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 388 THROUGH 397 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 398 THROUGH 423 )

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