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- PDB-1fw4: CRYSTAL STRUCTURE OF E. COLI FRAGMENT TR2C FROM CALMODULIN TO 1.7... -

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Basic information

Entry
Database: PDB / ID: 1fw4
TitleCRYSTAL STRUCTURE OF E. COLI FRAGMENT TR2C FROM CALMODULIN TO 1.7 A RESOLUTION
ComponentsCALMODULIN
KeywordsMETAL BINDING PROTEIN / EF-hand / Helix-loop-helix / Fragment / Calcium / TR2C / C-terminal domain / Calmodulin
Function / homology
Function and homology information


positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / spindle pole / protein domain specific binding / calcium ion binding / protein-containing complex / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOlsson, L.-L. / Sjolin, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Escherichia coli fragment TR2C from calmodulin to 1.7 A resolution.
Authors: Olsson, L.L. / Sjolin, L.
History
DepositionSep 21, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionMay 2, 2001ID: 1trc
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 9, 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_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

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Assembly

Deposited unit
A: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2363
Polymers8,1561
Non-polymers802
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.802, 37.802, 99.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein CALMODULIN /


Mass: 8155.828 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (RESIDUES 78-148)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P62157
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, calcium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
188 mg/mlprotein1drop
215 %PEG40001reservoir
340 mMsodium acetate1reservoir
470 mM1reservoirCaCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU11.5418
SYNCHROTRONMAX II I71120.996
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEDec 22, 1998
MARRESEARCH2IMAGE PLATEFeb 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9961
ReflectionResolution: 1.6→35.4 Å / Num. all: 8839 / Num. obs: 8839 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 1.95 / Num. unique all: 621 / % possible all: 65.2
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.367

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cll

1cll


Resolution: 1.7→20 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 363 4.7 %random
Rwork0.218 ---
all-7694 --
obs-7694 99.9 %-
Displacement parametersBiso mean: 45.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms533 0 2 40 575
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_mcbond_it3.81.5
X-RAY DIFFRACTIONc_mcangle_it4.72
X-RAY DIFFRACTIONc_scbond_it5.72
X-RAY DIFFRACTIONc_scangle_it7.42.5
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.434 36 3.7 %
Rwork0.39 928 -
obs--99.3 %

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