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- PDB-6wn7: Homo sapiens S100A5 -

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Basic information

Entry
Database: PDB / ID: 6wn7
TitleHomo sapiens S100A5
ComponentsProtein S100-A5
KeywordsMETAL BINDING PROTEIN / S100 / calcium / HA5 / EF-Hand
Function / homology
Function and homology information


calcium-dependent protein binding / copper ion binding / neuronal cell body / calcium ion binding / protein homodimerization activity / zinc ion binding / nucleus
Similarity search - Function
S-100 / 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, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...S-100 / 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, 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPerkins, A. / Harms, M.J. / Wong, C.E. / Wheeler, L.C.
CitationJournal: Protein Sci. / Year: 2020
Title: Learning peptide recognition rules for a low-specificity protein.
Authors: Wheeler, L.C. / Perkins, A. / Wong, C.E. / Harms, M.J.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A5
B: Protein S100-A5
C: Protein S100-A5
D: Protein S100-A5
F: Protein S100-A5
E: Protein S100-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,71924
Polymers65,9976
Non-polymers72118
Water7,188399
1
A: Protein S100-A5
B: Protein S100-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2809
Polymers21,9992
Non-polymers2817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-115 kcal/mol
Surface area9730 Å2
MethodPISA
2
C: Protein S100-A5
D: Protein S100-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2408
Polymers21,9992
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-97 kcal/mol
Surface area10110 Å2
MethodPISA
3
F: Protein S100-A5
E: Protein S100-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1997
Polymers21,9992
Non-polymers2005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-92 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.280, 76.280, 84.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein
Protein S100-A5 / Protein S-100D / S100 calcium-binding protein A5


Mass: 10999.547 Da / Num. of mol.: 6 / Mutation: C43S, C80S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A5, S100D / Production host: Escherichia coli (E. coli) / References: UniProt: P33763
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 20% w/v PEG8000, cryoprotectant: 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2018
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→51.98 Å / Num. obs: 151437 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 14.87 Å2 / CC1/2: 1 / Net I/σ(I): 16.2
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 8.4 % / Num. unique obs: 4561 / CC1/2: 0.48 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MOSFLM1.16_3549data reduction
PHASERphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DIR

4dir


Resolution: 1.25→26 Å / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 37.2278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Data is twinned, as was refined with a twin law of -k, -h, -l and twin fraction of 0.44.
RfactorNum. reflection% reflection
Rfree0.206 15282 5.05 %
Rwork0.1707 287319 -
obs0.1862 151437 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.55 Å2
Refinement stepCycle: LAST / Resolution: 1.25→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 0 18 399 4586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01194326
X-RAY DIFFRACTIONf_angle_d1.16735828
X-RAY DIFFRACTIONf_chiral_restr0.0695680
X-RAY DIFFRACTIONf_plane_restr0.0054738
X-RAY DIFFRACTIONf_dihedral_angle_d23.13031603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.33848580.319214201X-RAY DIFFRACTION93.72
1.27-1.290.29657660.314814451X-RAY DIFFRACTION94.79
1.29-1.320.29617920.301814294X-RAY DIFFRACTION94.74
1.32-1.350.29117060.283914318X-RAY DIFFRACTION95.3
1.35-1.380.26767820.280714544X-RAY DIFFRACTION94.89
1.38-1.410.27387520.268914352X-RAY DIFFRACTION95.01
1.41-1.440.26897180.250814434X-RAY DIFFRACTION95.26
1.44-1.480.23156920.238814402X-RAY DIFFRACTION95.42
1.48-1.530.22968960.232814326X-RAY DIFFRACTION94.11
1.53-1.570.23487800.225314408X-RAY DIFFRACTION94.86
1.57-1.630.24346880.221414508X-RAY DIFFRACTION95.47
1.63-1.70.23767560.213814468X-RAY DIFFRACTION95.03
1.7-1.770.22739000.209314186X-RAY DIFFRACTION94.03
1.77-1.870.21768040.201914366X-RAY DIFFRACTION94.7
1.87-1.980.20176640.197414468X-RAY DIFFRACTION95.61
1.98-2.140.20476720.184614453X-RAY DIFFRACTION95.49
2.14-2.350.19486440.16914563X-RAY DIFFRACTION95.7
2.35-2.690.20578570.158614249X-RAY DIFFRACTION94.15
2.69-3.380.22247280.153114437X-RAY DIFFRACTION95.18
3.38-15.410.18858170.139713869X-RAY DIFFRACTION91.26
Refinement TLS params.Method: refined / Origin x: 20.4939936122 Å / Origin y: 3.41248205829 Å / Origin z: -7.00332290166 Å
111213212223313233
T0.124877934309 Å20.0027161791863 Å2-0.00225636402241 Å2-0.151560421772 Å20.0109993723527 Å2--0.103495741631 Å2
L0.0892941741256 °2-0.010478706666 °2-0.00403560034829 °2-0.0950186472421 °20.0563953751786 °2--0.0588362772224 °2
S-0.00208070959799 Å °0.00942847731157 Å °0.00811800875719 Å °0.00228499003225 Å °-0.00352044451273 Å °0.0118677835508 Å °-0.00299055946312 Å °-0.0145623239753 Å °0.00494470593065 Å °
Refinement TLS groupSelection details: all

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