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- PDB-1ij6: CA2+-BOUND STRUCTURE OF MULTIDOMAIN EF-HAND PROTEIN, CBP40, FROM ... -

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Basic information

Entry
Database: PDB / ID: 1ij6
TitleCA2+-BOUND STRUCTURE OF MULTIDOMAIN EF-HAND PROTEIN, CBP40, FROM TRUE SLIME MOLD
ComponentsPLASMODIAL SPECIFIC LAV1-2 PROTEIN
KeywordsMETAL BINDING PROTEIN / FOURTY KDA CALCIUM BINDING PROTEIN / CBP40
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / EF hand / EF-hand / Recoverin; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / EF hand / EF-hand / Recoverin; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Plasmodial-specific protein LAV1-2
Similarity search - Component
Biological speciesPhysarum polycephalum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsIwasaki, W. / Sasaki, H. / Nakamura, A. / Kohama, K. / Tanokura, M.
CitationJournal: Structure / Year: 2003
Title: Metal-Free and Ca(2+)-Bound Structures of a Multidomain EF-Hand Protein, CBP40, from the Lower Eukaryote Physarum polycephalum
Authors: Iwasaki, W. / Sasaki, H. / Nakamura, A. / Kohama, K. / Tanokura, M.
History
DepositionApr 25, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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 / _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: PLASMODIAL SPECIFIC LAV1-2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2985
Polymers37,1381
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.4, 64.4, 209.4
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PLASMODIAL SPECIFIC LAV1-2 PROTEIN


Mass: 37137.617 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / References: UniProt: P14725
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Ammonium Sulfate, Calcium chloride, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / Details: Iwasaki, W., (1999) J.Biochem., 126, 7.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
174 mg/mlprotein1drop
210 mMTris-HCl1droppH7.6
31.4-1.8 Mammonium sulfate1reservoir
41 mMdithiothreitol1reservoir
510 mMEDTA1reservoir
60.02 %1reservoirNaN3
70.1 MHEPES-NaOH1reservoirpH6.4-7.6

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 22, 1997 / Details: focusing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→38.1 Å / Num. all: 13647 / Num. obs: 34014 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.097
Reflection shellResolution: 3.12→3.23 Å / Rmerge(I) obs: 0.342 / % possible all: 99.6
Reflection
*PLUS
Num. obs: 13647 / Num. measured all: 34014

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→10 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.293 465 random
Rwork0.249 --
all-9387 -
obs-9293 -
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 4 0 2384
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.9
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.38

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