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- PDB-5hyd: Crystal structure of calcium-free human S100Z -

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Basic information

Entry
Database: PDB / ID: 5hyd
TitleCrystal structure of calcium-free human S100Z
ComponentsProtein S100-Z
KeywordsPROTEIN BINDING / S100 / calcium-promoted oligomerisation neuronal development
Function / homology
Function and homology information


calcium-dependent protein binding / calcium ion binding / protein homodimerization activity
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 / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCalderone, V. / Fragai, M. / Luchinat, C. / Gallo, G.
Citation
Journal: J. Biol. Inorg. Chem. / Year: 2017
Title: Solving the crystal structure of human calcium-free S100Z: the siege and conquer of one of the last S100 family strongholds.
Authors: Calderone, V. / Fragai, M. / Gallo, G. / Luchinat, C.
#1: Journal: 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
DepositionFeb 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein S100-Z
B: Protein S100-Z
C: Protein S100-Z
D: Protein S100-Z


Theoretical massNumber of molelcules
Total (without water)46,5504
Polymers46,5504
Non-polymers00
Water48627
1
A: Protein S100-Z
B: Protein S100-Z


Theoretical massNumber of molelcules
Total (without water)23,2752
Polymers23,2752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-21 kcal/mol
Surface area11230 Å2
MethodPISA
2
C: Protein S100-Z
D: Protein S100-Z


Theoretical massNumber of molelcules
Total (without water)23,2752
Polymers23,2752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-23 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.326, 96.948, 115.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein S100-Z / S100 calcium-binding protein Z


Mass: 11637.593 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100Z / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXG8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium cacodylate, 0.2 M sodium acetate, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→19.8 Å / Num. obs: 17889 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 3.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2621: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WCE

2wce


Resolution: 2.3→19.799 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 873 5.06 %Random
Rwork0.2105 ---
obs0.2135 17260 96.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 0 27 3160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043173
X-RAY DIFFRACTIONf_angle_d0.6424243
X-RAY DIFFRACTIONf_dihedral_angle_d5.0141987
X-RAY DIFFRACTIONf_chiral_restr0.038485
X-RAY DIFFRACTIONf_plane_restr0.003537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44390.33311340.27592456X-RAY DIFFRACTION89
2.4439-2.63220.3411310.27462595X-RAY DIFFRACTION93
2.6322-2.89630.29761340.25772786X-RAY DIFFRACTION100
2.8963-3.31380.28421510.23952766X-RAY DIFFRACTION99
3.3138-4.16860.24561630.18862824X-RAY DIFFRACTION99
4.1686-19.79970.24641600.17942960X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 35.7202 Å / Origin y: -33.7561 Å / Origin z: -29.3566 Å
111213212223313233
T0.2525 Å20.0505 Å2-0.0132 Å2-0.3272 Å2-0.0425 Å2--0.3902 Å2
L0.5742 °20.3952 °20.7379 °2-0.3715 °20.7837 °2--3.711 °2
S0.0538 Å °0.097 Å °0.0339 Å °-0.0824 Å °0.0351 Å °-0.0599 Å °0.1257 Å °0.1117 Å °-0.0784 Å °
Refinement TLS groupSelection details: all

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