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Basic information

Entry
Database: PDB / ID: 3e3r
TitleCrystal structure and biochemical characterization of recombinant human calcyphosine delineates a novel EF-hand-containing protein family
ComponentsCalcyphosin
KeywordsCALCIUM BINDING PROTEIN / human calcyphosine / EF-hand / Phosphoprotein
Function / homology
Function and homology information


vesicle / intracellular signal transduction / calcium ion binding / cytoplasm
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsDong, H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal-structure and biochemical characterization of recombinant human calcyphosine delineates a novel EF-hand-containing protein family
Authors: Dong, H. / Li, X. / Lou, Z. / Xu, X. / Su, D. / Zhou, X. / Zhou, W. / Bartlam, M. / Rao, Z.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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_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: Calcyphosin
B: Calcyphosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,32511
Polymers44,9642
Non-polymers3619
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcyphosin
hetero molecules

A: Calcyphosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,32511
Polymers44,9642
Non-polymers3619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x+1/2,-y+1/2,-z-11
Buried area2010 Å2
ΔGint-99 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.593, 130.411, 46.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Calcyphosin / Calcyphosine


Mass: 22482.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q13938
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 20% PEG8000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 12799 / Num. obs: 12719 / % possible obs: 95 % / Observed criterion σ(F): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.103
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.282 / Num. unique all: 931 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.881 / SU B: 28.724 / SU ML: 0.265 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 4.459 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27653 1262 9.9 %RANDOM
Rwork0.22818 ---
obs0.23297 11457 97.88 %-
all-12799 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.05 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å20 Å2
2--2.27 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 9 49 2857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212829
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9583804
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8775352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07223.533150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.70815487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2691533
X-RAY DIFFRACTIONr_chiral_restr0.0870.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022193
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21390
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21949
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2122
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1490.213
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5431.51798
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9522786
X-RAY DIFFRACTIONr_scbond_it1.40231143
X-RAY DIFFRACTIONr_scangle_it2.3724.51018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 95 -
Rwork0.311 711 -
obs--83.26 %
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)
10.415-0.0977-0.25280.2956-0.1220.27480.03940.06160.0833-0.06320.0254-0.0334-0.06180.0447-0.06480.02430-0.03660.0316-0.01030.064457.777944.2284-5.7947
20.58610.3077-0.17250.1763-0.18240.62050.05730.00530.0618-0.011-0.02430.0740.0140.0327-0.03310.02320.02790.01350.0424-0.01310.012186.318232.8032-18.7881
30.58970.0994-0.01030.4637-0.01310.1426-0.0204-0.04430.06830.0428-0.0515-0.1075-0.05450.04050.0719-0.07640.0225-0.0143-0.01430.04620.017476.944940.3181-5.2578
40.7153-0.184-0.35780.08890.14060.23570.03480.03510.11710.07850.0579-0.0562-0.06090.0131-0.09270.04260.0205-0.03240.0119-0.0378-0.014775.482633.2621-8.5961
510.70850.5077-1.17152.4305-8.372628.8731-0.2338-0.51070.2428-0.88930.32-0.31450.7890.3848-0.0862-0.11920.02190.07220.013-0.14310.005775.94527.4713-6.4527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 189
2X-RAY DIFFRACTION2B4 - 189
3X-RAY DIFFRACTION3A192 - 195
4X-RAY DIFFRACTION4A198 - 222
5X-RAY DIFFRACTION4B196 - 219
6X-RAY DIFFRACTION5A-12 - -6

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