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- PDB-4d7s: Structure of the SthK Carboxy-Terminal Region in complex with cGMP -

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Basic information

Entry
Database: PDB / ID: 4d7s
TitleStructure of the SthK Carboxy-Terminal Region in complex with cGMP
ComponentsSTHK_CNBD_CGMP
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


intracellularly cyclic nucleotide-activated monoatomic cation channel activity / nucleotide binding / protein-containing complex 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. ...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
CYCLIC GUANOSINE MONOPHOSPHATE / Cyclic nucleotide-binding domain-containing protein
Similarity search - Component
Biological speciesSPIROCHAETA THERMOPHILA DSM 6192 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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_CGMP
B: STHK_CNBD_CGMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0884
Polymers46,3972
Non-polymers6902
Water19811
1
A: STHK_CNBD_CGMP
hetero molecules

A: STHK_CNBD_CGMP
hetero molecules

A: STHK_CNBD_CGMP
hetero molecules

A: STHK_CNBD_CGMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1768
Polymers92,7954
Non-polymers1,3814
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 area9620 Å2
ΔGint-59.1 kcal/mol
Surface area37050 Å2
MethodPISA
2
B: STHK_CNBD_CGMP
hetero molecules

B: STHK_CNBD_CGMP
hetero molecules

B: STHK_CNBD_CGMP
hetero molecules

B: STHK_CNBD_CGMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1768
Polymers92,7954
Non-polymers1,3814
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 area10010 Å2
ΔGint-53.9 kcal/mol
Surface area37410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.202, 87.202, 142.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein STHK_CNBD_CGMP


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-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.92 Å3/Da / Density % sol: 57.82 % / Description: NONE
Crystal growpH: 7.5 / Details: PH 7.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.55→46.61 Å / Num. obs: 17256 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.6
Reflection shellResolution: 2.55→2.68 Å / Redundancy: 3.1 % / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D7T

4d7t


Resolution: 2.55→46.603 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 920 5.3 %
Rwork0.2028 --
obs0.2049 17255 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→46.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 46 11 3210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053269
X-RAY DIFFRACTIONf_angle_d1.1174429
X-RAY DIFFRACTIONf_dihedral_angle_d14.9251235
X-RAY DIFFRACTIONf_chiral_restr0.042487
X-RAY DIFFRACTIONf_plane_restr0.004567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5502-2.68460.33861560.30062317X-RAY DIFFRACTION100
2.6846-2.85280.32661300.26592326X-RAY DIFFRACTION100
2.8528-3.0730.30631170.24962326X-RAY DIFFRACTION100
3.073-3.38220.30271590.23462315X-RAY DIFFRACTION100
3.3822-3.87140.24651340.19792319X-RAY DIFFRACTION99
3.8714-4.87680.22471020.17752380X-RAY DIFFRACTION100
4.8768-46.61030.18261220.18022352X-RAY DIFFRACTION99
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)
10.12610.2033-0.16530.2484-0.23430.67290.7726-0.2482-0.475-0.1437-0.3357-0.30090.0154-0.48670.03660.737-0.1496-0.23890.9184-0.09860.6651-22.6001-45.647417.5546
2-0.0822-0.1005-0.70310.0340.32430.35820.29230.03520.1343-0.0555-0.1272-0.1421-0.0381-0.04460.0010.47150.0508-0.00450.4522-0.09220.489-29.0533-25.95292.8793
31.4633-0.5241-0.86551.87820.26171.7560.16860.17260.00210.1635-0.0786-0.1522-0.1365-0.03230.00030.30250.0029-0.08310.4005-0.10560.3776-16.8295-35.7436-8.4522
40.3876-0.02330.00150.0545-0.06030.65310.0986-0.19040.6638-0.1307-0.25550.13420.29320.4754-0.01620.6613-0.06820.14570.64350.12310.5187-42.945-21.5065-59.4358
5-0.0047-0.060.03680.06440.18010.00170.27640.1402-0.14960.5192-0.32210.67390.29-0.20390.00110.5662-0.08910.05210.7968-0.1720.5699-25.8415-37.533-51.6233
60.064-0.0437-0.09280.1421-0.0070.13140.38470.48320.6611-0.12260.5611-0.2762-0.27410.69970.0120.7150.12020.14710.6226-0.0030.8228-17.2884-25.6997-40.4716
72.0064-0.1888-0.79771.69270.57952.36280.08320.04490.56510.367-0.0048-0.16640.1353-0.10170.24750.4501-0.00850.09470.3799-0.04760.5412-29.5991-20.5919-35.1436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 226 THROUGH 266 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 267 THROUGH 322 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 323 THROUGH 422 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 232 THROUGH 266 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 267 THROUGH 291 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 292 THROUGH 306 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 307 THROUGH 422 )

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