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- PDB-2q91: Structure of the Ca2+-Bound Activated Form of the S100A4 Metastas... -

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Basic information

Entry
Database: PDB / ID: 2q91
TitleStructure of the Ca2+-Bound Activated Form of the S100A4 Metastasis Factor
ComponentsS100A4 Metastasis Factor
KeywordsMETAL BINDING PROTEIN / S100A4 / myosin / calcium / metastatic tumors / EF-hand
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 / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / 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 / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / 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 / SAD / Resolution: 1.63 Å
AuthorsMalashkevich, V.N. / Knight, D. / Ramagopal, U.A. / Almo, S.C. / Bresnick, A.R.
CitationJournal: Biochemistry / Year: 2008
Title: Structure of Ca(2+)-Bound S100A4 and Its Interaction with Peptides Derived from Nonmuscle Myosin-IIA.
Authors: Malashkevich, V.N. / Varney, K.M. / Garrett, S.C. / Wilder, P.T. / Knight, D. / Charpentier, T.H. / Ramagopal, U.A. / Almo, S.C. / Weber, D.J. / Bresnick, A.R.
History
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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

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Assembly

Deposited unit
A: S100A4 Metastasis Factor
B: S100A4 Metastasis Factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6516
Polymers23,4912
Non-polymers1604
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.424, 52.424, 140.419
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein S100A4 Metastasis Factor / S100 calcium-binding protein A4 / Metastasin / Protein Mts1 / Placental calcium-binding protein / Calvasculin


Mass: 11745.538 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A4, CAPL, MTS1 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL(DE3) / References: UniProt: P26447
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M ammonium sulfate, 0.05M Bis-Tris, 27.5% pentaethythritol-pthoxylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.7 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 21, 2006 / Details: X6A
RadiationMonochromator: X6A / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionRedundancy: 11.5 % / Av σ(I) over netI: 25.9 / Number: 120612 / Rmerge(I) obs: 0.079 / Χ2: 4.69 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 10515 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.03509910.0462.73611.1
4.796.0399.410.0572.68911.6
4.184.7999.610.0663.8311.6
3.84.1899.310.0754.70111.6
3.533.899.210.0845.66311.5
3.323.5399.110.0945.85211.5
3.153.3298.510.1025.02811.5
3.023.1598.610.1125.55311.5
2.93.0298.710.125.50611.4
2.82.998.210.1275.30411.5
ReflectionResolution: 1.63→50 Å / Num. obs: 28584 / % possible obs: 99 % / Redundancy: 10.1 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.096 / Χ2: 4.686 / Net I/σ(I): 10.5
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2784 / Rsym value: 0.58 / Χ2: 5.304 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.63→19.16 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.665 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1440 5.1 %RANDOM
Rwork0.185 ---
obs0.187 28501 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.232 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.63→19.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 4 236 1809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221601
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9792145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2165198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24125.55681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3215316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.182156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021204
X-RAY DIFFRACTIONr_nbd_refined0.2310.2788
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21123
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.2153
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.244
X-RAY DIFFRACTIONr_mcbond_it1.8741.51005
X-RAY DIFFRACTIONr_mcangle_it3.725201557
X-RAY DIFFRACTIONr_scbond_it6.69220665
X-RAY DIFFRACTIONr_scangle_it5.74.5584
LS refinement shellResolution: 1.634→1.676 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 93 -
Rwork0.237 1911 -
obs-2004 98.57 %

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