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

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Basic information

Entry
Database: PDB / ID: 3qjk
TitleStructure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Lead
ComponentsCalcium-binding protein
KeywordsMETAL BINDING PROTEIN / EF-hand
Function / homology
Function and homology information


positive regulation of macropinocytosis / regulation of actin filament bundle assembly / regulation of protein kinase activity / pseudopodium / actin monomer binding / phagocytosis / phagocytic cup / positive regulation of phagocytosis / actin filament binding / calcium ion binding / 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 / 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
ACETATE ION / LEAD (II) ION / Calcium-binding protein 1
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.001 Å
AuthorsKumar, S. / Gourinath, S.
CitationJournal: To be Published
Title: Structure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Lead
Authors: Kumar, S. / Gourinath, S.
History
DepositionJan 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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)30,8898
Polymers29,9422
Non-polymers9476
Water30617
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)46,33312
Polymers44,9133
Non-polymers1,4209
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 area5210 Å2
ΔGint-31 kcal/mol
Surface area12780 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)46,33312
Polymers44,9133
Non-polymers1,4209
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 area5260 Å2
ΔGint-35 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.264, 95.264, 64.597
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
Details: cytosol / Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM1:IMSS / Gene: EhCaBP1 / Plasmid: pET-3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P38505
#2: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pb
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 60-65% MPD, 50mM NaOAc, 5mM Pb(NO3)2, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 6777 / Num. obs: 6763 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.054 / Rsym value: 0.0364 / Net I/σ(I): 8.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.054 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.364 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CNSrefinement
AUTOMARdata reduction
PHENIXdev_1011refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NXQ

2nxq


Resolution: 3.001→28.082 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.5 / Isotropic thermal model: RESTRAINED / σ(F): 1.39 / Phase error: 29.01 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.283 685 10.13 %
Rwork0.2518 --
obs0.2549 6763 99.72 %
all-6777 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.955 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso mean: 75.1336 Å2
Baniso -1Baniso -2Baniso -3
1--8.9307 Å20 Å20 Å2
2---8.9307 Å20 Å2
3---17.8614 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3.001→28.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 12 17 1025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151014
X-RAY DIFFRACTIONf_angle_d1.8541353
X-RAY DIFFRACTIONf_dihedral_angle_d16.722373
X-RAY DIFFRACTIONf_chiral_restr0.101144
X-RAY DIFFRACTIONf_plane_restr0.01181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0011-3.23250.36651350.32791210100
3.2325-3.55730.32161340.26111204100
3.5573-4.07070.28981350.23251208100
4.0707-5.12350.25331400.22551220100
5.1235-28.0830.27341410.2631123699

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