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- PDB-2rgi: Crystal structure of Ca2+-free S100A2 at 1.6 A resolution -

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Basic information

Entry
Database: PDB / ID: 2rgi
TitleCrystal structure of Ca2+-free S100A2 at 1.6 A resolution
ComponentsProtein S100-A2
KeywordsMETAL BINDING PROTEIN / alpha helical / EF-hand
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
ISOPROPYL ALCOHOL / Protein S100-A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsKoch, M. / Diez, J. / Fritz, G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of Ca2+ -free S100A2 at 1.6-A resolution.
Authors: Koch, M. / Diez, J. / Fritz, G.
History
DepositionOct 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,2586
Polymers22,1292
Non-polymers1294
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.516, 57.820, 59.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 11064.491 Da / Num. of mol.: 2 / Mutation: C2S, C21S, C86S, C93S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A2, S100L / Plasmid: pMW162 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29034
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.69965 Å3/Da / Density % sol: 27.632162 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 0.1 M sodium acetate, 10% isopropanol, 35-40% PEG 4000, pH 7.4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97927 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 20053 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.443 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.59
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.80.563.740070572395.4
1.8-20.315727744379298.3
2-2.20.15812.318656256099
2.2-2.50.0918.618120248698.9
2.5-30.07124.116303226199.2
3-40.0532.612986184099.2
4-50.03638.3452766799.3
5-60.0337204630399
6-100.02938.6216433397.9
100.02337.14748879.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.56 Å
Translation2.5 Å41.56 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL based S100A3 pdb code 1KSO

1kso


Resolution: 1.6→19.28 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.598 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1003 5 %RANDOM
Rwork0.186 ---
all0.188 20053 --
obs0.188 20053 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.88 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 3 175 1654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221503
X-RAY DIFFRACTIONr_bond_other_d0.0010.021021
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9782011
X-RAY DIFFRACTIONr_angle_other_deg1.39332530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8585188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02726.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94615298
X-RAY DIFFRACTIONr_chiral_restr0.0870.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021650
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02278
X-RAY DIFFRACTIONr_nbd_refined0.2470.2424
X-RAY DIFFRACTIONr_nbd_other0.1750.21059
X-RAY DIFFRACTIONr_nbtor_refined0.190.2743
X-RAY DIFFRACTIONr_nbtor_other0.0930.2799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2139
X-RAY DIFFRACTIONr_metal_ion_refined0.1350.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.231
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_mcbond_it0.8321.5924
X-RAY DIFFRACTIONr_mcbond_other0.2331.5381
X-RAY DIFFRACTIONr_mcangle_it1.45421479
X-RAY DIFFRACTIONr_scbond_it2.3143583
X-RAY DIFFRACTIONr_scangle_it3.8014.5530
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 65 -
Rwork0.265 1236 -
all-1301 -
obs--100 %

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