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- PDB-3c1v: The 1.5 A Crystal structure of Ca2+-bound S100A4 -

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Basic information

Entry
Database: PDB / ID: 3c1v
TitleThe 1.5 A Crystal structure of Ca2+-bound S100A4
ComponentsProtein S100-A4
KeywordsCALCIUM BINDING PROTEIN / S100A4 / Ca2+-bound / calcium-bound
Function / homology
Function and homology information


RAGE receptor binding / chemoattractant activity / transition metal ion binding / epithelial to mesenchymal transition / calcium-dependent protein binding / actin binding / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / calcium ion binding / perinuclear region of cytoplasm ...RAGE receptor binding / chemoattractant activity / transition metal ion binding / epithelial to mesenchymal transition / calcium-dependent protein binding / actin binding / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / calcium ion binding / perinuclear region of cytoplasm / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / 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, calcium binding motif / EF-Hand 1, calcium-binding site ...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, calcium binding motif / 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGingras, A.R. / Barsukov, I.L.
CitationJournal: Febs Lett. / Year: 2008
Title: Crystal structure of the Ca(2+)-form and Ca(2+)-binding kinetics of metastasis-associated protein, S100A4
Authors: Gingras, A.R. / Basran, J. / Prescott, A. / Kriajevska, M. / Bagshaw, C.R. / Barsukov, I.L.
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
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_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-A4
B: Protein S100-A4
C: Protein S100-A4
D: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,92512
Polymers52,6044
Non-polymers3218
Water9,944552
1
A: Protein S100-A4
B: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4626
Polymers26,3022
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-86 kcal/mol
Surface area10430 Å2
MethodPISA
2
C: Protein S100-A4
D: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4626
Polymers26,3022
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-86.2 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.320, 52.320, 139.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Protein S100-A4 / S100 calcium-binding protein A4 / Metastasin / Protein Mts1 / Placental calcium-binding protein / Calvasculin


Mass: 13151.065 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A4 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26447
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 40% PEG600, 0.1M CHES, pH9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 68764 / Num. obs: 68427 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.75 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.46
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.14 / Num. unique all: 11006 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MHO

1mho


Resolution: 1.5→45.31 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.099 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21796 3409 5 %RANDOM
Rwork0.19511 ---
obs0.19627 64569 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.508 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 8 552 3814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223357
X-RAY DIFFRACTIONr_angle_refined_deg0.9651.9874551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0145464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42425.472159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38615694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.5691512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022536
X-RAY DIFFRACTIONr_nbd_refined0.1850.21872
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22338
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0710.2466
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.2140
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.279
X-RAY DIFFRACTIONr_mcbond_it0.4921.52093
X-RAY DIFFRACTIONr_mcangle_it0.78323308
X-RAY DIFFRACTIONr_scbond_it1.41331394
X-RAY DIFFRACTIONr_scangle_it1.754.51198
X-RAY DIFFRACTIONr_rigid_bond_restr1.42733487
X-RAY DIFFRACTIONr_sphericity_free0.9593562
X-RAY DIFFRACTIONr_sphericity_bonded0.79433254
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 244 -
Rwork0.239 4806 -
obs-4806 99.92 %

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