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- PDB-2ptm: Structure and rearrangements in the carboxy-terminal region of Sp... -

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Basic information

Entry
Database: PDB / ID: 2ptm
TitleStructure and rearrangements in the carboxy-terminal region of SpIH channels
ComponentsHyperpolarization-activated (Ih) channel
KeywordsTRANSPORT PROTEIN / ion channel / cyclic nucleotide binding domain / C-linker / cAMP / cGMP / spHCN1 / HCN
Function / homology
Function and homology information


monoatomic ion channel activity / membrane => GO:0016020 / nucleotide binding
Similarity search - Function
Helix hairpin bin / Ion transport N-terminal / Ion transport protein N-terminal / 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 ...Helix hairpin bin / Ion transport N-terminal / Ion transport protein N-terminal / 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 / Voltage-dependent channel domain superfamily / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / COBALT HEXAMMINE(III) / Hyperpolarization-activated (Ih) channel
Similarity search - Component
Biological speciesStrongylocentrotus purpuratus (purple sea urchin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsFlynn, G.E. / Black, K.D. / Islas, L.D. / Sankaran, B. / Zagotta, W.N.
CitationJournal: Structure / Year: 2007
Title: Structure and rearrangements in the carboxy-terminal region of SpIH channels.
Authors: Flynn, G.E. / Black, K.D. / Islas, L.D. / Sankaran, B. / Zagotta, W.N.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 28, 2021Group: Database references / Derived calculations / Refinement description
Category: refine / struct_ref_seq_dif / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details ..._refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hyperpolarization-activated (Ih) channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7833
Polymers23,2931
Non-polymers4902
Water3,675204
1
A: Hyperpolarization-activated (Ih) channel
hetero molecules

A: Hyperpolarization-activated (Ih) channel
hetero molecules

A: Hyperpolarization-activated (Ih) channel
hetero molecules

A: Hyperpolarization-activated (Ih) channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,13212
Polymers93,1704
Non-polymers1,9618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area12000 Å2
ΔGint-47 kcal/mol
Surface area35900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.354, 92.354, 63.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A--

HOH

21A-1-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: Symmetry operation Symm. ID. (Pisa) x,y,z 1_555 -y+1/2,x+1/2,z 3_555 y-1/2,-x+1/2,z 4_455 -x,-y+1,z 2_565

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Components

#1: Protein Hyperpolarization-activated (Ih) channel


Mass: 23292.576 Da / Num. of mol.: 1 / Fragment: C-terminal region (residues 470-665)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Strongylocentrotus purpuratus (purple sea urchin)
Plasmid: pHMalc2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl-21 (DE3) / References: UniProt: O76977
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 % w/v PEG 6000, 0.5 M NaCl, 20 % glycerol, 0.1 M HEPES, 10 mM hexamine cobalt trichloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97935
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2004
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 21275 / Num. obs: 21201 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 30.44 Å2 / Rsym value: 0.074 / Net I/σ(I): 30.5
Reflection shellResolution: 1.93→2 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 7.9 / Num. unique all: 2077 / Rsym value: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1q5o

1q5o


Resolution: 1.93→29.205 Å / FOM work R set: 0.852 / σ(F): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.242 1089 5.14 %
Rwork0.187 --
all-21201 -
obs-21201 99.7 %
Solvent computationBsol: 79.142 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 99.94 Å2 / Biso mean: 41.33 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.473 Å20 Å2-0 Å2
2--1.473 Å20 Å2
3----2.945 Å2
Refinement stepCycle: LAST / Resolution: 1.93→29.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 29 204 1777
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_deg0.6331
X-RAY DIFFRACTIONf_bond_d0.0041
X-RAY DIFFRACTIONfHIRAL0.0511
X-RAY DIFFRACTIONf_dihedral_angle_d9.4741
X-RAY DIFFRACTIONfLANE0.0021
X-RAY DIFFRACTIONfonbonded4.2661

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