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- PDB-3m0w: Structure of S100A4 with PCP -

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Basic information

Entry
Database: PDB / ID: 3m0w
TitleStructure of S100A4 with PCP
ComponentsProtein S100-A4
KeywordsCalcium Binding Protein / MTS1 / S100 CALCIUM-BINDING PROTEIN A4 / S100A4 / METASTASIN
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 / 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 / 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
1,4-DIETHYLENE DIOXIDE / Chem-P77 / Protein S100-A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRamagopal, U.A. / Dulyaninova, N.G. / Almo, S.C. / Bresnick, A.R.
CitationJournal: To be published
Title: Structure of S100A4 with PCP
Authors: Ramagopal, U.A. / Dulyaninova, N.G. / Almo, S.C. / Bresnick, A.R.
History
DepositionMar 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 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 1.3Sep 6, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
E: Protein S100-A4
F: Protein S100-A4
G: Protein S100-A4
H: Protein S100-A4
I: Protein S100-A4
J: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,60944
Polymers116,14310
Non-polymers5,46534
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein S100-A4
B: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,59910
Polymers23,2292
Non-polymers1,3708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-87 kcal/mol
Surface area10760 Å2
MethodPISA
3
C: Protein S100-A4
D: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1378
Polymers23,2292
Non-polymers9086
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-74 kcal/mol
Surface area10270 Å2
MethodPISA
4
E: Protein S100-A4
F: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1378
Polymers23,2292
Non-polymers9086
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-89 kcal/mol
Surface area10600 Å2
MethodPISA
5
G: Protein S100-A4
H: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1378
Polymers23,2292
Non-polymers9086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-90 kcal/mol
Surface area10670 Å2
MethodPISA
6
I: Protein S100-A4
J: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,59910
Polymers23,2292
Non-polymers1,3708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-90 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.577, 102.275, 117.370
Angle α, β, γ (deg.)90.000, 92.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 2 / Auth seq-ID: 3 - 90 / Label seq-ID: 2 - 89

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ

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Components

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


Mass: 11614.342 Da / Num. of mol.: 10
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-P77 / 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine


Mass: 373.943 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H24ClN3S / Comment: medication*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 31659 / % possible obs: 99.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.065 / Χ2: 1.046 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.853.30.5415821.151100
2.85-2.93.30.4615901.2121100
2.9-2.963.30.40315531.1641100
2.96-3.023.30.35316231.1871100
3.02-3.083.30.30315551.1211100
3.08-3.153.30.25815821.18199.9
3.15-3.233.30.20915801.1621100
3.23-3.323.30.17615771.2011100
3.32-3.423.30.13216041.0871100
3.42-3.533.20.10815721.286199.9
3.53-3.653.30.08316011.0261100
3.65-3.83.20.0715521.0991100
3.8-3.973.20.06615911.071199.7
3.97-4.183.20.05415860.891199.9
4.18-4.443.20.05115900.864199.8
4.44-4.783.20.04515670.868199.6
4.78-5.263.20.04515960.81199.8
5.26-6.013.10.04416050.834199.5
6.01-7.533.20.0415920.839199.7
7.53-253.20.03615610.834195.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q91

2q91


Resolution: 2.8→24.98 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.028 / SU ML: 0.324 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.503 / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1589 5 %RANDOM
Rwork0.252 ---
obs0.254 31599 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 165.35 Å2 / Biso mean: 48.683 Å2 / Biso min: 15.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20.73 Å2
2--0.66 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 332 9 7351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227476
X-RAY DIFFRACTIONr_angle_refined_deg1.2122.02210035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2665875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80625.783351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.367151297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6671518
X-RAY DIFFRACTIONr_chiral_restr0.0910.21077
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025557
X-RAY DIFFRACTIONr_mcbond_it0.9191.54430
X-RAY DIFFRACTIONr_mcangle_it1.86427056
X-RAY DIFFRACTIONr_scbond_it3.38133046
X-RAY DIFFRACTIONr_scangle_it5.2324.52979
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A332TIGHT POSITIONAL0.070.05
2B332TIGHT POSITIONAL0.090.05
3C332TIGHT POSITIONAL0.050.05
4D332TIGHT POSITIONAL0.050.05
5E332TIGHT POSITIONAL0.060.05
6F332TIGHT POSITIONAL0.060.05
7G332TIGHT POSITIONAL0.090.05
8H332TIGHT POSITIONAL0.080.05
9I332TIGHT POSITIONAL0.10.05
10J332TIGHT POSITIONAL0.110.05
1A269MEDIUM POSITIONAL0.170.5
2B269MEDIUM POSITIONAL0.140.5
3C269MEDIUM POSITIONAL0.090.5
4D269MEDIUM POSITIONAL0.10.5
5E269MEDIUM POSITIONAL0.110.5
6F269MEDIUM POSITIONAL0.110.5
7G269MEDIUM POSITIONAL0.120.5
8H269MEDIUM POSITIONAL0.180.5
9I269MEDIUM POSITIONAL0.220.5
10J269MEDIUM POSITIONAL0.360.5
1A332TIGHT THERMAL0.20.5
2B332TIGHT THERMAL0.330.5
3C332TIGHT THERMAL0.170.5
4D332TIGHT THERMAL0.150.5
5E332TIGHT THERMAL0.150.5
6F332TIGHT THERMAL0.190.5
7G332TIGHT THERMAL0.20.5
8H332TIGHT THERMAL0.250.5
9I332TIGHT THERMAL0.440.5
10J332TIGHT THERMAL0.490.5
1A269MEDIUM THERMAL0.262
2B269MEDIUM THERMAL0.352
3C269MEDIUM THERMAL0.222
4D269MEDIUM THERMAL0.222
5E269MEDIUM THERMAL0.222
6F269MEDIUM THERMAL0.232
7G269MEDIUM THERMAL0.242
8H269MEDIUM THERMAL0.292
9I269MEDIUM THERMAL0.632
10J269MEDIUM THERMAL0.62
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 132 -
Rwork0.315 2155 -
all-2287 -
obs--97.28 %
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)
16.8281-3.5459-0.43337.1616-0.65625.18060.57780.02790.62720.4159-0.4934-1.3339-0.86021.4277-0.08440.2053-0.2478-0.01820.4375-0.12350.436630.28910.35851.156
24.478-5.1249-1.63986.91547.20736.92290.1182-0.079-0.65430.3979-0.4330.8358-0.1493-0.09960.31480.1461-0.20290.12960.0484-0.18890.38949.597.64858.015
312.6775-1.94238.45243.3246-0.41727.10790.6547-0.47312.2507-0.5273-0.52690.1382-2.5887-2.4954-0.12781.63191.27340.82481.32950.52590.98572.97727.89433.502
410.51020.61313.63952.36470.35646.31661.02632.06291.9822-0.3317-0.3411-0.6518-1.90660.6978-0.68521.21370.28850.67310.76510.52670.988323.33127.36724.182
58.94562.24124.76467.00824.10597.29721.28770.17650.2937-1.1257-1.97870.8091-1.1469-2.95820.6910.55431.0373-0.02642.30960.16640.2097-4.8359.916.888
64.31824.5733-1.98985.3293-2.54748.65550.60550.3353-0.7967-1.0695-0.5382-0.9312-1.1211-1.2942-0.06730.53530.84870.28551.33810.70250.473515.3386.7130.177
713.87313.7797-3.52734.6741-3.67423.9596-0.28471.46760.0361-0.25510.58070.71670.6884-1.7809-0.2960.2766-0.3733-0.05811.2465-0.0770.161-2.653-22.20715.439
88.78282.169-6.45972.30161.548312.3955-0.46951.0104-0.9143-0.18140.3008-0.54510.6263-0.49140.16870.0786-0.23020.01830.4173-0.20160.185218.59-23.41112.685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 90
2X-RAY DIFFRACTION2B2 - 90
3X-RAY DIFFRACTION3C2 - 90
4X-RAY DIFFRACTION4D2 - 90
5X-RAY DIFFRACTION5E2 - 90
6X-RAY DIFFRACTION6F2 - 90
7X-RAY DIFFRACTION7G2 - 90
8X-RAY DIFFRACTION8H2 - 90

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