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- PDB-4rjd: TFP bound in alternate orientations to calcium-saturated Calmodul... -

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Basic information

Entry
Database: PDB / ID: 4rjd
TitleTFP bound in alternate orientations to calcium-saturated Calmodulin C-Domains
ComponentsCalmodulin
KeywordsCalcium-Binding Protein / anti-psychotic / antagonist / Ca2+ binding / central nervous system / Trifluoromethyl / promiscuous binding / TFP-binding
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / regulation of high voltage-gated 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 ...regulation of store-operated calcium channel activity / regulation of high voltage-gated 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 / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / protein phosphatase activator activity / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / positive regulation of DNA binding / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / spindle pole / cellular response to type II interferon / response to calcium ion / calcium-dependent protein binding / disordered domain specific binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / vesicle / transmembrane transporter binding / protein autophosphorylation / neuron projection / positive regulation of apoptotic process / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
OXALATE ION / THIOCYANATE ION / Chem-TFP / Calmodulin-1 / Calmodulin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFeldkamp, M.D. / Gakhar, L. / Pandey, N. / Shea, M.A.
CitationJournal: Proteins / Year: 2015
Title: Opposing orientations of the anti-psychotic drug trifluoperazine selected by alternate conformations of M144 in calmodulin.
Authors: Feldkamp, M.D. / Gakhar, L. / Pandey, N. / Shea, M.A.
History
DepositionOct 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 29, 2020Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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)17,46215
Polymers15,2172
Non-polymers2,24613
Water1,44180
1
A: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8658
Polymers7,6081
Non-polymers1,2577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5977
Polymers7,6081
Non-polymers9896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.606, 85.637, 35.341
Angle α, β, γ (deg.)90.00, 93.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Calmodulin / / CaM


Mass: 7608.289 Da / Num. of mol.: 2 / Fragment: Calmodulin C-Domian, UNP residues 83-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc
Production host: Escherichia coli (E. coli) / Strain (production host): E.Coli BL21 (DE3) / References: UniProt: P62161, UniProt: P0DP29*PLUS

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Non-polymers , 7 types, 93 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-TFP / 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE / Trifluoperazine


Mass: 407.496 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H24F3N3S / Comment: antipsychotic*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#7: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 50 mM HEPES, 100 mM KCl, 1mM MgCl2, 5 mM NTA, 50 uM EGTA, with 500 ul of 200 mM potassium thiocyanate, 20% polyethylene glycol 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 14, 2007 / Details: Mirror
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→27.23 Å / Num. obs: 8955 / % possible obs: 90.45 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 21.02 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 24
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 8.1 / Num. unique all: 1367 / % possible all: 94.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1760)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LIN

1lin


Resolution: 2→27.23 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 426 4.76 %RANDOM
Rwork0.1774 ---
obs0.1809 8955 90.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 143 80 1283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011216
X-RAY DIFFRACTIONf_angle_d1.4521635
X-RAY DIFFRACTIONf_dihedral_angle_d20.088474
X-RAY DIFFRACTIONf_chiral_restr0.049152
X-RAY DIFFRACTIONf_plane_restr0.004208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.28940.28981290.20222421X-RAY DIFFRACTION78
2.2894-2.88390.25111430.19563077X-RAY DIFFRACTION98
2.8839-27.23640.24321540.16293031X-RAY DIFFRACTION95
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)
14.9901-0.6607-0.61183.2178-0.36231.97330.1130.2196-0.0179-0.5054-0.0660.54180.0303-0.2051-0.06090.23150.0006-0.08760.1376-0.0170.148314.635441.543224.9341
25.3271-1.5858-1.18696.4056-0.09043.4374-0.0377-0.12410.5503-0.25530.2252-0.2620.15810.0541-0.15580.1689-0.0235-0.07720.1607-0.00550.175726.503239.469126.1761
37.1121.6561-3.74196.77090.86637.3184-0.25431.0145-0.1409-1.3794-0.1183-0.9110.47460.36690.27240.38290.03970.10890.27210.05850.248521.573649.70519.618
48.4979-0.3382-1.82427.4120.02988.51860.1773-0.0051-0.32010.2028-0.17140.26320.0989-0.34070.00110.1059-0.0312-0.04090.1128-0.03510.13231.012620.13568.484
59.19540.539-0.33973.5175-0.28354.72340.4658-0.24610.67540.4316-0.15240.542-0.7631-0.1812-0.26550.21190.01260.09860.27030.01690.18686.03333.28263.8821
65.91952.5157-1.59877.0987-0.99293.14590.1282-0.063-0.49080.1607-0.0297-0.41880.08220.0636-0.1060.09070.0061-0.04020.1471-0.01540.133713.086821.10448.0415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 147 )
4X-RAY DIFFRACTION4chain 'B' and (resid 82 through 101 )
5X-RAY DIFFRACTION5chain 'B' and (resid 102 through 117 )
6X-RAY DIFFRACTION6chain 'B' and (resid 118 through 147 )

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