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- PDB-3px1: Structure of Calcium Binding Protein-1 from Entamoeba histolytica... -

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Basic information

Entry
Database: PDB / ID: 3px1
TitleStructure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Strontium
ComponentsCalcium-binding protein
KeywordsMETAL BINDING PROTEIN / EF hand motif / calcium binding and signalling / kinase / Cytosol and phagocytic cup
Function / homology
Function and homology information


regulation of actin filament bundle assembly / positive regulation of macropinocytosis / regulation of protein kinase activity / pseudopodium / phagocytic cup / actin monomer binding / phagocytosis / positive regulation of phagocytosis / actin filament binding / calcium ion binding ...regulation of actin filament bundle assembly / positive regulation of macropinocytosis / regulation of protein kinase activity / pseudopodium / phagocytic cup / actin monomer binding / phagocytosis / positive regulation of phagocytosis / actin filament binding / calcium ion binding / endoplasmic reticulum / cytoplasm
Similarity search - Function
EF-hand domain / 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 domain / 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
STRONTIUM ION / Calcium-binding protein 1
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKumar, S. / Kumar, S. / Ahmad, E. / Khan, R.H. / Gourinath, S.
CitationJournal: To be Published
Title: Flexibility and plasticity of EF-hand motifs: Structure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Pb2+, Ba2+, and Sr2+.
Authors: Kumar, S. / Kumar, S. / Ahmad, E. / Khan, R.H. / Gourinath, S.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 1, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_seq_id / _struct_conn.ptnr2_label_asym_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: Calcium-binding protein
B: Calcium-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2926
Polymers29,9422
Non-polymers3504
Water48627
1
A: Calcium-binding protein
hetero molecules

A: Calcium-binding protein
hetero molecules

A: Calcium-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4389
Polymers44,9133
Non-polymers5266
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area3110 Å2
ΔGint-25 kcal/mol
Surface area13270 Å2
MethodPISA
2
B: Calcium-binding protein
hetero molecules

B: Calcium-binding protein
hetero molecules

B: Calcium-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4389
Polymers44,9133
Non-polymers5266
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area3070 Å2
ΔGint-25 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.429, 95.429, 63.973
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Calcium-binding protein / / CABP


Mass: 14970.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: hm-1:imss / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38505
#2: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.81 Å3/Da / Density % sol: 56.2 % / Mosaicity: 1.174 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: MPD, Sodium Acetate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 4, 2008 / Details: Monochromator
RadiationMonochromator: Double Crystal Si111 or White Beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→82.64 Å / Num. all: 11558 / Num. obs: 6442 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Χ2: 1.259 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.1140.4546690.978196.8
3.11-3.234.20.3636161.312196.1
3.23-3.384.10.1976671.352196.4
3.38-3.564.10.1486451.469196.4
3.56-3.784.10.1296381.546195.4
3.78-4.074.10.0866471.328196
4.07-4.484.10.0626421.203195
4.48-5.134.10.0556411.157194.5
5.13-6.4640.066441.194193.5
6.46-503.80.0456331.022188.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NXQ

2nxq


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.948 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2814 309 4.8 %RANDOM
Rwork0.2347 ---
all0.2369 11558 --
obs0.2369 6413 94.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 131.61 Å2 / Biso mean: 80.4157 Å2 / Biso min: 49.15 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å2-1.34 Å20 Å2
2---2.68 Å20 Å2
3---4.02 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 4 27 1027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221017
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9571360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5285126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75926.66754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.28615190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.399152
X-RAY DIFFRACTIONr_chiral_restr0.1140.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02772
X-RAY DIFFRACTIONr_mcbond_it0.8881.5629
X-RAY DIFFRACTIONr_mcangle_it1.8332996
X-RAY DIFFRACTIONr_scbond_it2.7913388
X-RAY DIFFRACTIONr_scangle_it5.1554.5364
LS refinement shellResolution: 2.997→3.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 21 -
Rwork0.343 468 -
all-489 -
obs--95.88 %

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