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- PDB-3nsl: Crystal Structure of S100A3 C30A+C68A double mutant expressed in ... -

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Basic information

Entry
Database: PDB / ID: 3nsl
TitleCrystal Structure of S100A3 C30A+C68A double mutant 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: 1.5 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A3
F: Protein S100-A3
C: Protein S100-A3
B: Protein S100-A3
E: Protein S100-A3
D: Protein S100-A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5218
Polymers69,3376
Non-polymers1842
Water10,593588
1
A: Protein S100-A3
B: Protein S100-A3


Theoretical massNumber of molelcules
Total (without water)23,1122
Polymers23,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-36 kcal/mol
Surface area9550 Å2
MethodPISA
2
F: Protein S100-A3
E: Protein S100-A3


Theoretical massNumber of molelcules
Total (without water)23,1122
Polymers23,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-34 kcal/mol
Surface area9470 Å2
MethodPISA
3
C: Protein S100-A3
D: Protein S100-A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2964
Polymers23,1122
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-35 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.357, 101.357, 45.209
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: 11556.129 Da / Num. of mol.: 6 / Mutation: C30A, C68A
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 1.93 Å3/Da / Density % sol: 36.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, 0.1M HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 28, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 83262 / Num. obs: 83178 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.53 Å / % possible all: 99.9

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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: 1.5→24.35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.586 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19655 4163 5 %RANDOM
Rwork0.16 ---
all0.16182 83178 --
obs0.16182 78936 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 0 12 588 5123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224933
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.971.9756732
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2515642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.88324.637248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48615900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9791525
X-RAY DIFFRACTIONr_chiral_restr0.1220.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213786
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_it1.2221.52936
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18424771
X-RAY DIFFRACTIONr_scbond_it3.34331997
X-RAY DIFFRACTIONr_scangle_it5.2334.51916
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 291 -
Rwork0.204 5837 -
obs--99.92 %
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)
10.61120.2353-0.1110.92390.09810.34460.0362-0.0857-0.0150.13010.0183-0.08150.03980.1232-0.05440.04610.0006-0.02650.0521-0.02120.110934.63840.9274.439
20.34080.28380.06711.56620.21430.3696-0.0110.0339-0.0037-0.13170.0486-0.0490.06190.0561-0.03760.04330.0023-0.00940.0148-0.01360.098130.67434.698-11.394
30.74310.0127-0.21630.2894-0.10580.3187-0.03740.07380.0173-0.04150.0316-0.0004-0.0307-0.03180.00580.0377-0.00820.01110.036-0.00180.10294.2738.7124.505
41.1103-0.0628-0.040.46780.01490.1011-0.0292-0.07030.00680.04830.019-0.0025-0.0286-0.01950.01020.02580.00870.0180.0265-0.00490.1075-3.55938.28920.157
50.498-0.36830.17771.298-0.36310.4582-0.0012-0.025-0.06260.15960.01930.05590.0149-0.0478-0.01810.0566-0.0065-0.01240.00860.01610.10319.4275.23134.546
61.078-0.6026-0.07171.3397-0.15960.0550.08860.1572-0.0681-0.0905-0.11110.07480.0017-0.02050.02250.04040.0243-0.01570.0522-0.00260.11816.22512.6219.03
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 94
2X-RAY DIFFRACTION2B3 - 94
3X-RAY DIFFRACTION3C1 - 94
4X-RAY DIFFRACTION4D3 - 94
5X-RAY DIFFRACTION5E2 - 94
6X-RAY DIFFRACTION6F1 - 94

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