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- PDB-5a2h: Crystal Structure of Arabidopsis thaliana Calmodulin-7 -

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Basic information

Entry
Database: PDB / ID: 5a2h
TitleCrystal Structure of Arabidopsis thaliana Calmodulin-7
ComponentsCALMODULIN
KeywordsCALCIUM-BINDING PROTEIN / PROTEIN
Function / homology
Function and homology information


regulation of photomorphogenesis / detection of calcium ion / defense response to fungus / calcium ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
EF-hand domain pair / : / 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
ACETATE ION / EF-hand domain-containing protein / Calmodulin-7
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsKumar, S. / Gourinath, S.
CitationJournal: FEBS Lett. / Year: 2016
Title: Crystal Structure of Arabidopsis Thaliana Calmodulin7 and Insight Into its Mode of DNA Binding.
Authors: Kumar, S. / Mazumder, M. / Gupta, N. / Chattopadhyay, S. / Gourinath, S.
History
DepositionMay 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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 / 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4389
Polymers16,8641
Non-polymers5748
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.455, 67.901, 111.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CALMODULIN


Mass: 16863.635 Da / Num. of mol.: 1 / Fragment: HELIX-LOOP-HELIX
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7LMD4, UniProt: P59220*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.7 Å3/Da / Density % sol: 54.7 % / Description: NONE
Crystal growpH: 4.2 / Details: MPD 60%, SODIUM ACETATE PH 4.2, CACL2 5MM

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.985
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.985 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 8910 / % possible obs: 98.6 % / Observed criterion σ(I): 3.3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.1
Reflection shellResolution: 2.27→6.2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.8 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RFJ

1rfj


Resolution: 2.27→57.96 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.624 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23822 439 5 %RANDOM
Rwork0.19079 ---
obs0.19318 8390 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.513 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2---0.62 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.27→57.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 32 46 1235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191193
X-RAY DIFFRACTIONr_bond_other_d0.0010.021115
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9881602
X-RAY DIFFRACTIONr_angle_other_deg0.85232575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29926.86667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84315221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.51155
X-RAY DIFFRACTIONr_chiral_restr0.0960.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02243
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6863.091588
X-RAY DIFFRACTIONr_mcbond_other2.6163.075586
X-RAY DIFFRACTIONr_mcangle_it4.0014.595732
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6773.594605
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.271→2.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 27 -
Rwork0.209 459 -
obs--72.75 %
Refinement TLS params.Method: refined / Origin x: -9.4207 Å / Origin y: 7.9484 Å / Origin z: -25.0351 Å
111213212223313233
T0.0794 Å2-0.0387 Å2-0.0115 Å2-0.1703 Å2-0.0127 Å2--0.1685 Å2
L1.2312 °2-1.1025 °21.5023 °2-1.0761 °2-1.4371 °2--1.9722 °2
S0.0126 Å °0.0649 Å °0.1787 Å °-0.0099 Å °-0.0982 Å °-0.0501 Å °0.0465 Å °0.0351 Å °0.0856 Å °

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