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- PDB-2y5i: S100Z from zebrafish in complex with calcium -

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Basic information

Entry
Database: PDB / ID: 2y5i
TitleS100Z from zebrafish in complex with calcium
ComponentsS100 CALCIUM BINDING PROTEIN Z
KeywordsMETAL BINDING PROTEIN / METAL-BINDING PROTEIN / EF-HAND / CALCIUM REGULATION / OLIGOMERISATION / NEURONAL DEVELOPMENT / SPINE2 / STRUCTURAL PROTEOMICS IN EUROPE 2
Function / homology
Function and homology information


calcium-dependent protein binding / calcium ion binding
Similarity search - Function
Protein S100-Z / 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 / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...Protein S100-Z / 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 / 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
ISOPROPYL ALCOHOL / Protein S100-Z
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsMoroz, O.V. / Bronstein, I.B. / Wilson, K.S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structure of Zebrafish S100Z: Implications for Calcium-Promoted S100 Protein Oligomerisation.
Authors: Moroz, O.V. / Bronstein, I.B. / Wilson, K.S.
History
DepositionJan 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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_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_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_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: S100 CALCIUM BINDING PROTEIN Z
B: S100 CALCIUM BINDING PROTEIN Z
C: S100 CALCIUM BINDING PROTEIN Z
D: S100 CALCIUM BINDING PROTEIN Z
E: S100 CALCIUM BINDING PROTEIN Z
F: S100 CALCIUM BINDING PROTEIN Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,35224
Polymers67,5116
Non-polymers84218
Water9,170509
1
A: S100 CALCIUM BINDING PROTEIN Z
B: S100 CALCIUM BINDING PROTEIN Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7247
Polymers22,5042
Non-polymers2205
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-72.6 kcal/mol
Surface area10840 Å2
MethodPISA
2
C: S100 CALCIUM BINDING PROTEIN Z
D: S100 CALCIUM BINDING PROTEIN Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7848
Polymers22,5042
Non-polymers2816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-78.7 kcal/mol
Surface area10990 Å2
MethodPISA
3
E: S100 CALCIUM BINDING PROTEIN Z
F: S100 CALCIUM BINDING PROTEIN Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8449
Polymers22,5042
Non-polymers3417
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-76.4 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.611, 132.250, 58.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-2023-

HOH

21E-2034-

HOH

31F-2021-

HOH

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Components

#1: Protein
S100 CALCIUM BINDING PROTEIN Z / S100Z


Mass: 11251.779 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q503K9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.155 Å3/Da / Density % sol: 42.93 % / Description: NONE
Crystal growpH: 5
Details: 0.1M SODIUM ACETATE; 10% PEG 1.5K; 0.2M CACL2, 20% ISOPROPANOL., pH 5.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.03→66.1 Å / Num. obs: 38644 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.3
Reflection shellHighest resolution: 2.03 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.8 / % possible all: 85.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0086refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CGA

3cga


Resolution: 2.03→66.13 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.656 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22677 1909 5 %RANDOM
Rwork0.17092 ---
obs0.1737 36265 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--1.5 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.03→66.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 36 509 5093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224790
X-RAY DIFFRACTIONr_bond_other_d0.0010.023176
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9726468
X-RAY DIFFRACTIONr_angle_other_deg0.9837837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5535620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02427.178241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78215884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.418157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02878
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.028→2.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 101 -
Rwork0.183 2298 -
obs--85.07 %
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)
13.378-0.8027-0.97911.06550.1521.9696-0.0573-0.44650.03640.10920.1312-0.00420.00850.0766-0.0740.02360.01850.00560.0740.00970.015937.308526.31669.6343
23.3501-0.0054-0.93071.31910.26872.0632-0.0170.31180.0688-0.0810.01080.1193-0.0013-0.19050.00630.0051-0.0029-0.00770.03550.00740.012239.494625.9468-9.6326
31.50252.0471-1.07075.7203-2.03180.8901-0.12980.227-0.0573-0.65730.14010.14850.2053-0.1059-0.01030.13160.039-0.01920.0796-0.02780.048116.700514.0986-28.6308
43.44672.8-1.51913.9487-1.94980.97820.2533-0.54060.06410.5116-0.25060.0186-0.23560.1662-0.00280.11830.0039-0.01680.12280.00960.051515.512311.9263-10.5141
51.7254-0.8390.6842.5733-0.62981.6952-0.0709-0.10540.12680.20920.04570.1003-0.1527-0.04380.02520.02840.00590.00590.0077-0.00770.026616.0934-14.1853-29.7734
62.1336-1.44750.54422.4401-0.71991.6460.24270.29670.0109-0.3119-0.20520.0354-0.0124-0.0012-0.03750.07740.06020.03020.06610.02770.038414.7556-11.9921-48.5417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2B1 - 105
3X-RAY DIFFRACTION3C1 - 105
4X-RAY DIFFRACTION4D1 - 105
5X-RAY DIFFRACTION5E1 - 105
6X-RAY DIFFRACTION6F1 - 105

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