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- PDB-1kso: CRYSTAL STRUCTURE OF APO S100A3 -

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Basic information

Entry
Database: PDB / ID: 1kso
TitleCRYSTAL STRUCTURE OF APO S100A3
ComponentsS100 CALCIUM-BINDING PROTEIN A3
KeywordsMETAL BINDING PROTEIN / S100 / EF-hand / Ca2+ binding protein / Zn2+ binding protein
Function / homology
Function and homology information


transition metal ion binding / calcium-dependent protein binding / calcium ion binding / Golgi apparatus / plasma membrane / cytosol
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 / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsMittl, P.R. / Fritz, G. / Sargent, D.F. / Richmond, T.J. / Heizmann, C.W. / Grutter, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Metal-free MIRAS phasing: structure of apo-S100A3.
Authors: Mittl, P.R. / Fritz, G. / Sargent, D.F. / Richmond, T.J. / Heizmann, C.W. / Grutter, M.G.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S100 CALCIUM-BINDING PROTEIN A3
B: S100 CALCIUM-BINDING PROTEIN A3


Theoretical massNumber of molelcules
Total (without water)23,4512
Polymers23,4512
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-36 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.769, 58.769, 45.338
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein S100 CALCIUM-BINDING PROTEIN A3 / S-100E PROTEIN / S-100E PROTEIN


Mass: 11725.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid details: PMALC2 / Plasmid: PMALC2-A3 / Gene (production host): S100A3, S100E / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1 / References: UniProt: P33764
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: tris, ammonium sulfate, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 20K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF BM1410.934
ROTATING ANODEENRAF-NONIUS FR57121.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEMar 20, 2001
MARRESEARCH2IMAGE PLATEOct 15, 2000
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
21.54181
ReflectionResolution: 1.7→20 Å / Num. all: 19298 / Num. obs: 18292 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.2 Å2
Reflection shellResolution: 1.7→1.81 Å / % possible all: 89.1
Reflection
*PLUS
Num. obs: 19298 / Num. measured all: 34465 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Lowest resolution: 1.76 Å / % possible obs: 100 % / Rmerge(I) obs: 0.3

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→19.24 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 594645 / Data cutoff high rms absF: 594645 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1800 9.8 %RANDOM
Rwork0.194 ---
obs0.194 18292 94.9 %-
all-18292 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.3968 Å2 / ksol: 0.351812 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å20.18 Å20 Å2
2---1.96 Å20 Å2
3---3.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 0 199 1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it4.641.5
X-RAY DIFFRACTIONc_mcangle_it5.522
X-RAY DIFFRACTIONc_scbond_it4.512
X-RAY DIFFRACTIONc_scangle_it6.882.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 304 10.5 %
Rwork0.247 2578 -
obs--89.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor obs: 0.194 / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63
LS refinement shell
*PLUS
Rfactor Rfree: 0.279 / Rfactor Rwork: 0.247

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