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- PDB-4hsz: Structure of truncated (delta8C) S100A4 -

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Basic information

Entry
Database: PDB / ID: 4hsz
TitleStructure of truncated (delta8C) S100A4
ComponentsProtein S100-A4
KeywordsMETAL BINDING PROTEIN / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
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 / extracellular space / RNA binding / 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: 2.25 Å
AuthorsRamagopal, U.A. / Dulyaninova, N.G. / Kumar, P.R. / Almo, S.C. / Bresnick, A.R. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Structure of truncated (delta8C) S100A4
Authors: Ramagopal, U.A. / Dulyaninova, N.G. / Kumar, P.R. / Almo, S.C. / Bresnick, A.R.
History
DepositionOct 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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_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)43,37412
Polymers43,0534
Non-polymers3218
Water28816
1
A: Protein S100-A4
B: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6876
Polymers21,5272
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-80 kcal/mol
Surface area10760 Å2
MethodPISA
2
C: Protein S100-A4
D: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6876
Polymers21,5272
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-82 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.802, 34.356, 95.313
Angle α, β, γ (deg.)95.490, 95.290, 114.820
Int Tables number1
Space group name H-MP1
Detailsdimer

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Components

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


Mass: 10763.358 Da / Num. of mol.: 4 / Fragment: UNP residues 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPL, MTS1, S100A4 / 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.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.0, Magnesium chloride, 15% PEG 4000, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2011
RadiationProtocol: SINGLE WAWELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 14935 / Num. obs: 14935 / % possible obs: 96.4 % / Redundancy: 2.1 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.046 / Χ2: 1.832 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.291.90.4227811.287194.1
2.29-2.331.90.3666961.204195.7
2.33-2.3820.3377661.262195.8
2.38-2.422.10.3677511.371196.5
2.42-2.482.10.3537191.457197.2
2.48-2.532.10.2867551.462197
2.53-2.62.10.2577811.53198
2.6-2.672.20.2187571.586196.9
2.67-2.752.10.1856991.617197.2
2.75-2.832.10.158181.701197.5
2.83-2.942.20.1247201.719197.8
2.94-3.052.10.1177541.915197.8
3.05-3.192.10.0957692.301198
3.19-3.362.10.0667522.13197.7
3.36-3.572.10.0547612.439197.3
3.57-3.852.10.0437392.309196
3.85-4.232.10.0397272.606194.4
4.23-4.8520.0357232.411191.4
4.85-6.120.0347152.046196.2
6.1-5020.0297522.246196.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q91

2q91


Resolution: 2.25→46.926 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2709 / WRfactor Rwork: 0.2259 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7544 / SU B: 23.869 / SU ML: 0.258 / SU R Cruickshank DPI: 0.5679 / SU Rfree: 0.2912 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.568 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 751 5 %RANDOM
Rwork0.2281 ---
all0.2307 14934 --
obs0.2307 14934 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.69 Å2 / Biso mean: 56.2085 Å2 / Biso min: 31.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å2-0.56 Å21.6 Å2
2---2.97 Å2-0.95 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.25→46.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 8 16 2914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222938
X-RAY DIFFRACTIONr_angle_refined_deg0.9841.9793924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.465356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90625.479146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64415575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8361511
X-RAY DIFFRACTIONr_chiral_restr0.0630.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022187
X-RAY DIFFRACTIONr_mcbond_it1.0951.51788
X-RAY DIFFRACTIONr_mcangle_it2.19722859
X-RAY DIFFRACTIONr_scbond_it3.73431150
X-RAY DIFFRACTIONr_scangle_it5.8864.51065
LS refinement shellResolution: 2.247→2.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 49 -
Rwork0.277 986 -
all-1035 -
obs--87.86 %
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)
1-0.1489-2.1432-0.38555.24131.72862.5615-0.54650.20830.15920.89540.5923-0.00960.25570.21-0.04580.63720.2128-0.04820.3244-0.01780.28582.518-5.85910.164
20.6669-1.9393-0.34093.2521-0.24632.275-0.06060.12330.03970.14770.06030.0333-0.0640.00580.00030.34260.0325-0.11510.39430.00030.3879-1.825.264-9.238
31.25911.48930.48012.3458-0.39472.7097-0.0513-0.08940.0017-0.21510.0781-0.00150.14930.0536-0.02680.3577-0.0072-0.00380.3885-0.0140.39347.158-12.438-36.777
4-0.70442.5317-0.10914.80410.47543.6341-0.5407-0.2289-0.0262-0.82130.56960.1351-0.22250.2703-0.02890.6194-0.148-0.1050.3442-0.02250.294711.503-1.5-56.25
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 202
2X-RAY DIFFRACTION2B3 - 202
3X-RAY DIFFRACTION3C3 - 202
4X-RAY DIFFRACTION4B203 - 212
5X-RAY DIFFRACTION4D9 - 102

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