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- PDB-3nso: Crystal Structure of S100A3 Protein Expressed in Insect Cell -

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Basic information

Entry
Database: PDB / ID: 3nso
TitleCrystal Structure of S100A3 Protein Expressed in Insect Cell
ComponentsProtein S100-A3
KeywordsMETAL BINDING PROTEIN / EF-hand / Ca2+ / Zn2+ binding
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 / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsUnno, M. / Takahara, H. / Kizawa, K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Refined crystal structures of human Ca(2+)/Zn(2+)-binding S100A3 protein characterized by two disulfide bridges
Authors: Unno, M. / Kawasaki, T. / Takahara, H. / Heizmann, C.W. / Kizawa, K.
History
DepositionJul 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 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-A3
B: Protein S100-A3


Theoretical massNumber of molelcules
Total (without water)23,4512
Polymers23,4512
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-37 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.673, 58.673, 45.797
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 Protein S100-A3 / S100 calcium-binding protein A3 / Protein S-100E


Mass: 11725.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A3, S100E / Cell line (production host): IPLB-Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33764
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.94 Å3/Da / Density % sol: 36.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Ammonium Sulfate, 0.1M Bicine , pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 13, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 31271 / Num. obs: 30896 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.45→1.48 Å / % possible all: 87.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NSI

3nsi


Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.973 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 1568 5.1 %RANDOM
Rwork0.19859 ---
all0.1998 30896 --
obs0.1998 29306 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.613 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 0 133 1638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221627
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.972219
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6525209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20724.32181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95715295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4541510
X-RAY DIFFRACTIONr_chiral_restr0.1280.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211252
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1461.5976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01921589
X-RAY DIFFRACTIONr_scbond_it3.4673651
X-RAY DIFFRACTIONr_scangle_it5.4154.5619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 102 -
Rwork0.302 1982 -
obs--89.83 %
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)
10.42250.67610.11883.1037-0.18240.58090.1079-0.060.02170.2676-0.14380.01090.0282-0.07490.03590.0342-0.0254-0.0070.04540.02840.178120.52930.3974.963
20.3957-0.6896-0.10133.1787-0.12890.59190.10910.0586-0.0308-0.2965-0.14570.0293-0.0293-0.0830.03660.03920.02540.00560.04810.02720.179520.24737.465-9.788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 99
2X-RAY DIFFRACTION2B3 - 99

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