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- PDB-3ox5: Crystal Structure of the calcium sensor calcium-binding protein 1... -

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Basic information

Entry
Database: PDB / ID: 3ox5
TitleCrystal Structure of the calcium sensor calcium-binding protein 1 (CaBP1)
ComponentsCalcium-binding protein 1
KeywordsCalcium binding protein / EF-hand / calcium sensor / calcium binding
Function / homology
Function and homology information


nuclear localization sequence binding / Sensory processing of sound by inner hair cells of the cochlea / negative regulation of protein import into nucleus / enzyme inhibitor activity / visual perception / calcium channel regulator activity / calcium-dependent protein binding / cell cortex / cytoskeleton / postsynaptic density ...nuclear localization sequence binding / Sensory processing of sound by inner hair cells of the cochlea / negative regulation of protein import into nucleus / enzyme inhibitor activity / visual perception / calcium channel regulator activity / calcium-dependent protein binding / cell cortex / cytoskeleton / postsynaptic density / Golgi membrane / calcium ion binding / perinuclear region of cytoplasm / extracellular space / plasma membrane / cytoplasm
Similarity search - Function
Calcium binding protein 1/2/4/5 / 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 ...Calcium binding protein 1/2/4/5 / 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
Calcium-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFindeisen, F. / Minor, D.L.
CitationJournal: Structure / Year: 2010
Title: Structural Basis for the Differential Effects of CaBP1 and Calmodulin on Ca(V)1.2 Calcium-Dependent Inactivation.
Authors: Findeisen, F. / Minor, D.L.
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_ref_seq_dif / 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_ref_seq_dif.details / _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 1
B: Calcium-binding protein 1
C: Calcium-binding protein 1
D: Calcium-binding protein 1
E: Calcium-binding protein 1
F: Calcium-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,41918
Polymers106,9386
Non-polymers48112
Water00
1
A: Calcium-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9033
Polymers17,8231
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcium-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9033
Polymers17,8231
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calcium-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9033
Polymers17,8231
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Calcium-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9033
Polymers17,8231
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Calcium-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9033
Polymers17,8231
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Calcium-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9033
Polymers17,8231
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.044, 206.044, 206.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
Calcium-binding protein 1 / CaBP1 / Caldendrin / Calbrain


Mass: 17823.076 Da / Num. of mol.: 6 / Fragment: UNP residues 219-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CABP1 / Plasmid: pEGST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: Q9NZU7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.9M (NH4)2SO4, 2-4% 1,2-propanediol, 0.1M citrate/sodium citrate pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 32321 / Num. obs: 31525 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 99.7 Å2 / Rsym value: 0.095 / Net I/σ(I): 6.4
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 4029 / Rsym value: 0.451 / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 38.177 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25029 1432 5 %RANDOM
Rwork0.2129 ---
obs0.21482 27061 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.125 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7093 0 12 0 7105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0217182
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9749660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01125.422391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.441151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5951551
X-RAY DIFFRACTIONr_chiral_restr0.1080.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025585
X-RAY DIFFRACTIONr_mcbond_it1.89634530
X-RAY DIFFRACTIONr_mcangle_it3.22647187
X-RAY DIFFRACTIONr_scbond_it2.44732652
X-RAY DIFFRACTIONr_scangle_it3.9342473
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 83 -
Rwork0.373 1920 -
obs--85.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5410.5009-0.62391.60181.02732.951-0.03140.40410.2036-0.26170.3083-0.2274-0.3810.1287-0.27680.227-0.11940.16520.134-0.06480.157856.2655-39.187723.3976
23.35910.7590.37013.48422.68034.819-0.06770.1895-0.18240.0923-0.0061-0.10580.4401-0.22970.07380.1718-0.08660.10940.069-0.06550.086647.0245-56.617624.6413
35.39240.0622.54134.3286-0.14495.81170.1992-0.0783-0.7696-0.089-0.2441-0.71840.74010.25770.0450.5653-0.02260.24780.14150.0480.40960.6931-74.437114.8142
46.0318-1.01873.67735.0912-0.46295.50930.22990.5471-0.1855-1.2035-0.281-0.91490.55480.67750.05111.14060.10880.67520.46460.07160.491864.0299-71.081-3.8908
56.64-1.64432.08234.889-0.56297.60670.33510.40571.1469-0.3288-0.10490.1678-1.14380.0063-0.23030.6157-0.11290.32580.49850.04820.465963.2933-34.75240.1306
66.3624-1.27160.45063.571-1.86556.9818-0.5183-0.203-0.6016-0.19290.32590.00220.09890.51070.19240.68280.01210.45790.59870.16170.469474.8156-48.8783-6.7578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 167
2X-RAY DIFFRACTION2B15 - 167
3X-RAY DIFFRACTION3C15 - 167
4X-RAY DIFFRACTION4D15 - 167
5X-RAY DIFFRACTION5E15 - 167
6X-RAY DIFFRACTION6F15 - 167

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