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- PDB-2nxq: Crystal structure of calcium binding protein 1 from Entamoeba his... -

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Basic information

Entry
Database: PDB / ID: 2nxq
TitleCrystal structure of calcium binding protein 1 from Entamoeba histolytica: a novel arrangement of EF hand motifs
ComponentsCalcium-binding protein
KeywordsMETAL BINDING PROTEIN / EF hand motifs / calcium binding
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
ACETATE ION / Calcium-binding protein 1
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKumar, S. / Padhan, N. / Alam, N. / Gourinath, S.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of calcium binding protein-1 from Entamoeba histolytica: A novel arrangement of EF hand motifs.
Authors: Kumar, S. / Padhan, N. / Alam, N. / Gourinath, S.
History
DepositionNov 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 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 1.3Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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)30,39711
Polymers29,9422
Non-polymers4569
Water55831
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)45,50715
Polymers44,9133
Non-polymers59512
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 area5270 Å2
ΔGint-114 kcal/mol
Surface area13460 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)45,68418
Polymers44,9133
Non-polymers77215
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 area5020 Å2
ΔGint-112 kcal/mol
Surface area13080 Å2
MethodPISA
3
A: Calcium-binding protein
B: Calcium-binding protein
hetero molecules

A: Calcium-binding protein
B: Calcium-binding protein
hetero molecules

A: Calcium-binding protein
B: Calcium-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,19233
Polymers89,8256
Non-polymers1,36727
Water1086
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 area14090 Å2
ΔGint-250 kcal/mol
Surface area22740 Å2
MethodPISA
4
A: Calcium-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1695
Polymers14,9711
Non-polymers1984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
B: Calcium-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2286
Polymers14,9711
Non-polymers2575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.250, 95.250, 64.996
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: PET-3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P38505
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.9 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 60% MPD, 5mM CaCl2, 50mM sodium acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 23, 2006 / Details: cylindrically bent rhodium-coated silicon mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. all: 12484 / Num. obs: 12484 / % possible obs: 91.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.144 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.37-2.451.70.38610081.165173.9
2.45-2.552.10.26111110.965182.2
2.55-2.672.90.35111581.539185.4
2.67-2.815.50.35113281.211196.7
2.81-2.995.60.22413230.961197.7
2.99-3.225.60.13613211.06196.8
3.22-3.545.70.0913151.183196.8
3.54-4.055.70.0713171.223196.1
4.05-5.15.60.05213211.13196.1
5.1-503.60.04712821.12190

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1CLL: n-terminal domain

1cll


Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1161 8.8 %Random
Rwork0.258 ---
all-12484 --
obs-11409 86.1 %-
Solvent computationBsol: 61.48 Å2
Displacement parametersBiso mean: 66.482 Å2
Baniso -1Baniso -2Baniso -3
1-8.423 Å20.454 Å20 Å2
2--8.423 Å20 Å2
3----16.847 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 24 31 1068
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4641.5
X-RAY DIFFRACTIONc_scbond_it2.3722
X-RAY DIFFRACTIONc_mcangle_it2.5452
X-RAY DIFFRACTIONc_scangle_it3.7632.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.368 146 -
Rwork0.347 --
obs-1305 66.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3act.param
X-RAY DIFFRACTION4mpd.param
X-RAY DIFFRACTION5water.param

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