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- PDB-1qiw: Calmodulin complexed with N-(3,3,-diphenylpropyl)-N'-[1-R-(3,4-bi... -

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Basic information

Entry
Database: PDB / ID: 1qiw
TitleCalmodulin complexed with N-(3,3,-diphenylpropyl)-N'-[1-R-(3,4-bis-butoxyphenyl)-ethyl]-propylenediamine (DPD)
ComponentsCALMODULIN
KeywordsCALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / : / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / : / : ...regulation of store-operated calcium channel activity / : / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / : / : / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / positive regulation of DNA binding / negative regulation of high voltage-gated calcium channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / nitric-oxide synthase binding / regulation of synaptic vesicle exocytosis / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / detection of calcium ion / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / catalytic complex / activation of adenylate cyclase activity / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / positive regulation of nitric-oxide synthase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / titin binding / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / regulation of heart rate / response to amphetamine / adenylate cyclase activator activity / sarcomere / nitric-oxide synthase regulator activity / regulation of cytokinesis / spindle microtubule / calcium channel regulator activity / calcium-mediated signaling / response to calcium ion / G2/M transition of mitotic cell cycle / spindle pole / disordered domain specific binding / calcium-dependent protein binding / myelin sheath / protein autophosphorylation / growth cone / vesicle / transmembrane transporter binding / neuron projection / positive regulation of apoptotic process / protein domain specific binding / calcium ion binding / centrosome / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DPD / Calmodulin-1 / Calmodulin
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHarmat, V. / Bocskei, Z.S. / Vertessy, B.G. / Ovadi, J. / Naray-Szabo, G.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: A New Potent Calmodulin Antagonist with Arylalkylamine Structure: Crystallographic, Spectroscopic and Functional Studies
Authors: Harmat, V. / Bocskei, Z.S. / Naray-Szabo, G. / Bata, I. / Csutor, A.S. / Hermecz, I. / Aranyi, P. / Szabo, B. / Liliom, K. / Vertessy, B.G. / Ovadi, J.
#1: Journal: Proteins: Struct.,Funct., Genet. / Year: 1997
Title: Crystallization and Preliminary Diffraction Analysis of Ca(2+)-Calmodulin-Drug and Apocalmodulin-Drug Complexes.
Authors: Vertessy, B.G. / Bocskei, Z.S. / Harmath, V. / Naray-Szabo, G. / Ovadi, J.
#2: Journal: Nat.Struct.Biol. / Year: 1994
Title: Trifluoperazine-Induced Conformational Change in Ca (2+)-Calmodulin
Authors: Vandonselaar, M. / Hickie, R.A. / Quail, J.W. / Delbaere, L.T.J.
#3: Journal: Biochemistry / Year: 1994
Title: Drug Binding by Calmodulin: Crystal Structure of a Calmodulin-Trifluoperazine Complex
Authors: Cook, W.J. / Walter, L.J. / Walter, M.R.
History
DepositionJun 17, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 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 / pdbx_struct_conn_angle / software / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: CALMODULIN
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,31413
Polymers33,4432
Non-polymers1,87111
Water00
1
A: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9157
Polymers16,7211
Non-polymers1,1946
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3986
Polymers16,7211
Non-polymers6775
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.960, 56.200, 35.270
Angle α, β, γ (deg.)99.52, 114.47, 96.86
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.638671, 0.193606, -0.744725), (0.194159, -0.895966, -0.399434), (-0.744581, -0.399702, 0.534637)
Vector: 25.519, 72.2145, 31.1185)

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Components

#1: Protein CALMODULIN


Mass: 16721.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Cellular location: CYTOPLASM / Organ: BRAIN / References: UniProt: P02593, UniProt: P62157*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DPD / N-(3,3,-DIPHENYLPROPYL)-N'-[1-R-(2 3,4-BIS-BUTOXYPHENYL)-ETHYL]-PROPYLENEDIAMINE


Mass: 516.757 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H48N2O2

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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: 2.185 Å3/Da / Density % sol: 44 %
Description: THE TWO DOMAINS OF 1LIN WERE USED SEPARATEDLY AS MODELS
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP TECHNIQUE. 50 MM PH=6.0 SODIUM CACODYLATE/HCL BUFFER, 10 MM MGCL2, 10 MM CACL2, 2MM DPD AND 30% PEG 8000 THE CRYSTAL COULD NOT BE REPRODUCED., pH 6.00
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
21 mMHEPES1drop
35 mM1dropCaCl2
42 mMAAA1drop
550 mMsodium cacodylate1reservoir
610 mM1reservoirCaCl2
710 mM1reservoirMgCl2
825-30 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 15, 1996 / Details: NORMAL FOCUS
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→54.23 Å / Num. obs: 8711 / % possible obs: 69.2 % / Observed criterion σ(I): 3 / Redundancy: 1.7 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.093 / Net I/σ(I): 2.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.513 / % possible all: 25.3

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
bioteXdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIN

1lin


Resolution: 2.3→54.23 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED SIDE CHAIN ATOMS OF RESIDUES A2, A7, A47, A78, A79, A86, A114, A123, B6, B13, B69, B77, B82, B84, B123, B127 AND 146 AS WELL AS TRIMETHYL-LYSINES A115, B115 ARE NOT PRESENT IN THE ...Details: DISORDERED SIDE CHAIN ATOMS OF RESIDUES A2, A7, A47, A78, A79, A86, A114, A123, B6, B13, B69, B77, B82, B84, B123, B127 AND 146 AS WELL AS TRIMETHYL-LYSINES A115, B115 ARE NOT PRESENT IN THE STRUCTURE TEMPERATURE FACTORS FOR THE ATOMS IN THE CENTRAL REGIONS (A73-A80, B75- B82),ATOMS AT THE ENDS OF THE POLIPEPTIDE CHAINS (A144-A146, B4-B7, B144) AS WELL AS FOR SOME SURFACE RESIDUES (A45, A84, A107, A112, B107, B119, B126) ARE UNUSUALLY HIGH, INDICATING FLEXIBILITY IN THESE PARTS OF THE STRUCTURE. THE C-TERMINAL RESIDUES FOR BOTH CHAINS A AND B WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.317 483 5.5 %RANDOM
Rwork0.232 ---
obs0.232 8711 69.24 %-
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.008 Å2-0.196 Å2-1.001 Å2
2---12.279 Å2-2.453 Å2
3----14.919 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.423 Å0.263 Å
Luzzati d res low-2.7 Å
Luzzati sigma a0.41 Å0.0962 Å
Refinement stepCycle: LAST / Resolution: 2.3→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 112 0 2324
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.232
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.506
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSRms dev Biso : 5.019 Å2 / Rms dev position: 0.078 Å / Weight Biso : 10 / Weight position: 50
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.28 13 3.39 %
Rwork0.105 370 -
obs--24.39 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2CA.PARCA.TOP
X-RAY DIFFRACTION3AAA.PARAAA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.506
LS refinement shell
*PLUS
Rfactor Rfree: 0.28

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