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- PDB-1qx2: X-ray Structure of Calcium-loaded Calbindomodulin (A Calbindin D9... -

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Basic information

Entry
Database: PDB / ID: 1qx2
TitleX-ray Structure of Calcium-loaded Calbindomodulin (A Calbindin D9k Re-engineered to Undergo a Conformational Opening) at 1.44 A Resolution
ComponentsVitamin D-dependent calcium-binding protein, intestinal
KeywordsSIGNALING PROTEIN / EF-Hand (helix-loop-helix) Calcium Binding Protein / Four-helix Domain / Protein Engineering / Calcium-induced Conformational Response / calmodulin / calbindin D9k
Function / homology
Function and homology information


vitamin D binding / calcium-dependent protein binding / basolateral plasma membrane / apical plasma membrane / calcium ion binding / extracellular space / cytoplasm
Similarity search - Function
S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / 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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.44 Å
AuthorsBunick, C.G. / Nelson, M.R. / Mangahas, S. / Mizoue, L.S. / Bunick, G.J. / Chazin, W.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Designing Sequence to Control Protein Function in an EF-Hand Protein
Authors: Bunick, C.G. / Nelson, M.R. / Mangahas, S. / Hunter, M.J. / Sheehan, J.H. / Mizoue, L.S. / Bunick, G.J. / Chazin, W.J.
History
DepositionSep 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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

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Assembly

Deposited unit
A: Vitamin D-dependent calcium-binding protein, intestinal
B: Vitamin D-dependent calcium-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3298
Polymers17,0382
Non-polymers2916
Water3,837213
1
A: Vitamin D-dependent calcium-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5993
Polymers8,5191
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Vitamin D-dependent calcium-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7305
Polymers8,5191
Non-polymers2114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Vitamin D-dependent calcium-binding protein, intestinal
hetero molecules

A: Vitamin D-dependent calcium-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3298
Polymers17,0382
Non-polymers2916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
Buried area1900 Å2
ΔGint-109 kcal/mol
Surface area7910 Å2
MethodPISA
4
B: Vitamin D-dependent calcium-binding protein, intestinal
hetero molecules

A: Vitamin D-dependent calcium-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3298
Polymers17,0382
Non-polymers2916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z+1/21
Buried area1160 Å2
ΔGint-89 kcal/mol
Surface area8660 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-89 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.540, 62.174, 69.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1014-

HOH

21B-1070-

HOH

DetailsThe biological unit is the four-helix domain containing a pair of EF-hands. There are two biological units in the asymmetric unit.

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Components

#1: Protein Vitamin D-dependent calcium-binding protein, intestinal / CABP / Calbindin D9K


Mass: 8518.773 Da / Num. of mol.: 2
Mutation: L6I, I9A, K12V, Y13F, L23I, L31V, L32M, E35L, F36G, L49M, F50I, L53V, Q67L, L69M, V70M, P43M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CALB3 OR S100D / Plasmid: pSV271 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02633
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.89 Å3/Da / Density % sol: 34.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 550 MME, MES, zinc sulfate, Tris-HCl, sodium chloride, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0000, 1.2818, 1.2823, 1.2703
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 17, 2003
RadiationMonochromator: Si 220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.28181
31.28231
41.27031
ReflectionResolution: 1.44→50 Å / Num. all: 22435 / Num. obs: 22435 / % possible obs: 94.7 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.075 / Net I/σ(I): 20.2
Reflection shellResolution: 1.44→1.49 Å / Mean I/σ(I) obs: 6.1 / Num. unique all: 1349 / Rsym value: 0.164 / % possible all: 58.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.44→28.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 0.84 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.075
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.19358 1164 5.2 %RANDOM
Rwork0.15635 ---
all0.15825 21245 --
obs0.15825 21245 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.795 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.44→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 6 213 1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221240
X-RAY DIFFRACTIONr_bond_other_d0.0020.021161
X-RAY DIFFRACTIONr_angle_refined_deg1.4652.0281647
X-RAY DIFFRACTIONr_angle_other_deg1.44332778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7035149
X-RAY DIFFRACTIONr_chiral_restr0.0710.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021305
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02191
X-RAY DIFFRACTIONr_nbd_refined0.2370.2347
X-RAY DIFFRACTIONr_nbd_other0.2210.21373
X-RAY DIFFRACTIONr_nbtor_other0.0940.2706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2162
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.238
X-RAY DIFFRACTIONr_mcbond_it0.8321.5758
X-RAY DIFFRACTIONr_mcangle_it1.45621233
X-RAY DIFFRACTIONr_scbond_it2.1873482
X-RAY DIFFRACTIONr_scangle_it3.6654.5414
X-RAY DIFFRACTIONr_rigid_bond_restr1.10821240
X-RAY DIFFRACTIONr_sphericity_free2.3882219
X-RAY DIFFRACTIONr_sphericity_bonded1.45421228
LS refinement shellResolution: 1.444→1.481 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.206 59
Rwork0.173 899
obs-958

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