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- PDB-4duq: The Structure of Ca2+-loaded S100A2 at 1.3A resolution -

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Basic information

Entry
Database: PDB / ID: 4duq
TitleThe Structure of Ca2+-loaded S100A2 at 1.3A resolution
ComponentsProtein S100-A2
KeywordsMETAL BINDING PROTEIN / EF-hand / Calcium-binding / Zinc-binding / tumor supressor
Function / homology
Function and homology information


transition metal ion binding / endothelial cell migration / calcium-dependent protein binding / calcium ion binding / identical protein binding
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 1, calcium-binding site / EF-hand calcium-binding domain. ...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 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 / SAD / Resolution: 1.3 Å
AuthorsKoch, M. / Fritz, G.
CitationJournal: Febs J. / Year: 2012
Title: The structure of Ca2+-loaded S100A2 at 1.3- angstrom resolution.
Authors: Koch, M. / Fritz, G.
History
DepositionFeb 22, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMar 7, 2012ID: 3N22
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A2
B: Protein S100-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3818
Polymers22,1612
Non-polymers3,2206
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-73 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.670, 84.670, 58.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein S100-A2 / CAN19 / Protein S-100L / S100 calcium-binding protein A2


Mass: 11080.557 Da / Num. of mol.: 2 / Mutation: C2S, C21S, C86S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A2, S100L / Plasmid: pGEMEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29034
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 mM Na+ acetate, 40% PEG 400, pH 4.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→45.63 Å / Num. obs: 59436 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.286 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 30.22
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.3-1.42.121171481172399.9
1.4-1.54.7391461880699.9
1.5-1.68.48733716794100
1.6-1.9181415271278999.9
1.9-229.3634247271099.8
2-2.549.39183737800499.9
2.5-388.241482883566100
3-4122.061138262873100
4-6139.23543371504100
6-10137.631717651599.8
10141.12382515293.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→45.63 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.2594 / WRfactor Rwork: 0.2095 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9104 / SU B: 1.556 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0369 / SU Rfree: 0.0388 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.168 2972 5 %RANDOM
Rwork0.136 ---
obs0.1376 59434 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.21 Å2 / Biso mean: 35.576 Å2 / Biso min: 15.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.2 Å20 Å2
2--0.39 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 17 173 1600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191589
X-RAY DIFFRACTIONr_bond_other_d0.0020.021085
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9832158
X-RAY DIFFRACTIONr_angle_other_deg1.0932722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7185217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09527.02774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09215323
X-RAY DIFFRACTIONr_chiral_restr0.1260.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021777
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02291
X-RAY DIFFRACTIONr_rigid_bond_restr6.35832672
X-RAY DIFFRACTIONr_sphericity_free44.904547
X-RAY DIFFRACTIONr_sphericity_bonded30.74852760
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 217 -
Rwork0.251 4130 -
all-4347 -
obs--99.86 %

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