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- PDB-3ko0: Structure of the tfp-ca2+-bound activated form of the s100a4 Meta... -

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Basic information

Entry
Database: PDB / ID: 3ko0
TitleStructure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor
ComponentsProtein S100-A4
KeywordsMETAL BINDING PROTEIN / mts1 / s100a4 / tfp / ca2+ / oligomerization / Acetylation / Calcium
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
Chem-TFP / Protein S100-A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsMalashkevich, V.N. / Dulyaninova, N.G. / Knight, D. / Almo, S.C. / Bresnick, A.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Phenothiazines inhibit S100A4 function by inducing protein oligomerization.
Authors: Malashkevich, V.N. / Dulyaninova, N.G. / Ramagopal, U.A. / Liriano, M.A. / Varney, K.M. / Knight, D. / Brenowitz, M. / Weber, D.J. / Almo, S.C. / Bresnick, A.R.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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
K: Protein S100-A4
L: Protein S100-A4
M: Protein S100-A4
N: Protein S100-A4
O: Protein S100-A4
P: Protein S100-A4
Q: Protein S100-A4
R: Protein S100-A4
S: Protein S100-A4
T: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,814100
Polymers234,91120
Non-polymers17,90380
Water16,394910
1
A: Protein S100-A4
B: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28110
Polymers23,4912
Non-polymers1,7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-86 kcal/mol
Surface area11550 Å2
MethodPISA
2
C: Protein S100-A4
D: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28110
Polymers23,4912
Non-polymers1,7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-83 kcal/mol
Surface area11790 Å2
MethodPISA
3
E: Protein S100-A4
F: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28110
Polymers23,4912
Non-polymers1,7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-84 kcal/mol
Surface area11360 Å2
MethodPISA
4
G: Protein S100-A4
H: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28110
Polymers23,4912
Non-polymers1,7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-71 kcal/mol
Surface area11610 Å2
MethodPISA
5
I: Protein S100-A4
J: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28110
Polymers23,4912
Non-polymers1,7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-85 kcal/mol
Surface area11720 Å2
MethodPISA
6
K: Protein S100-A4
L: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28110
Polymers23,4912
Non-polymers1,7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-85 kcal/mol
Surface area11580 Å2
MethodPISA
7
M: Protein S100-A4
N: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28110
Polymers23,4912
Non-polymers1,7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-74 kcal/mol
Surface area11560 Å2
MethodPISA
8
O: Protein S100-A4
P: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28110
Polymers23,4912
Non-polymers1,7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-85 kcal/mol
Surface area11580 Å2
MethodPISA
9
Q: Protein S100-A4
R: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28110
Polymers23,4912
Non-polymers1,7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-83 kcal/mol
Surface area11180 Å2
MethodPISA
10
S: Protein S100-A4
T: Protein S100-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,28110
Polymers23,4912
Non-polymers1,7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-60 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.794, 102.492, 116.629
Angle α, β, γ (deg.)90.000, 92.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11745.538 Da / Num. of mol.: 20
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): BL21(DE3)CODON+RIL / References: UniProt: P26447
#2: Chemical...
ChemComp-TFP / 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE / Trifluoperazine


Mass: 407.496 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C21H24F3N3S / Comment: antipsychotic*YM
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 910 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 110852 / % possible obs: 96.8 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.315 / Num. unique all: 5083 / % possible all: 89.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.01 Å
Translation2.5 Å48.01 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.94 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.198 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.736 / SU B: 14.886 / SU ML: 0.162 / SU R Cruickshank DPI: 0.322 / SU Rfree: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 5579 5 %RANDOM
Rwork0.206 ---
obs0.208 110852 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 79.19 Å2 / Biso mean: 28.439 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.06 Å2
2--0.09 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14735 0 1160 910 16805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02216299
X-RAY DIFFRACTIONr_angle_refined_deg1.7452.0621977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86251844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67825.393751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.737152821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3771553
X-RAY DIFFRACTIONr_chiral_restr0.1680.22313
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112033
X-RAY DIFFRACTIONr_mcbond_it1.2173.59212
X-RAY DIFFRACTIONr_mcangle_it5.1345014723
X-RAY DIFFRACTIONr_scbond_it11.121507087
X-RAY DIFFRACTIONr_scangle_it1.2464.57243
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 381 -
Rwork0.333 7168 -
all-7549 -
obs--91.22 %
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)
12.07090.2965-0.91790.9463-0.29672.231-0.02220.1197-0.1064-0.03070.04590.16440.1221-0.2143-0.02380.0430.0135-0.00750.04740.01510.061733.40251.068545.2393
21.694-0.8733-0.43072.31680.57161.24610.0161-0.04550.08640.0568-0.0391-0.2380.02560.15880.0230.02630.00470.00080.03620.02960.050253.67913.14344.9892
32.13240.9696-0.75742.0193-0.45641.60160.020.05790.1254-0.00230.01580.23490.0252-0.1483-0.03580.001-0.00290.00080.0384-0.02350.05071.011-48.0659-44.9675
41.7963-0.3032-0.75830.9389-0.00342.2022-0.0021-0.0725-0.0093-0.04270.0542-0.12420.09660.242-0.05210.0242-0.01630.010.0753-0.04210.052821.253-50.6935-45.3869
51.64450.0367-1.34591.32880.44452.9903-0.00530.0271-0.1258-0.04190.0438-0.12870.10130.1915-0.03840.0407-0.0202-0.02460.1127-0.03160.066944.56720.234714.0693
62.42070.8548-1.0292.1729-0.62091.76050.00720.28780.1316-0.09460.00580.32930.0895-0.4172-0.0130.0322-0.0272-0.02590.1311-0.00970.067724.13964.659914.3049
71.8613-0.591-0.61681.57810.39151.08840.0609-0.0655-0.09660.053-0.10480.11230.0245-0.05270.04390.0597-0.03810.00940.0393-0.02770.058937.782330.068757.6003
82.3311-0.10040.03572.6899-0.19671.8850.0960.0258-0.02120.0305-0.0789-0.3451-0.1180.2124-0.01710.0493-0.0350.0060.0385-0.0010.055556.698535.45950.2825
91.16590.7417-0.43352.3897-0.25211.5435-0.02330.0486-0.1467-0.1597-0.0675-0.17850.06310.02770.09090.03360.0281-0.00280.06140.0390.117616.8369-21.2385-57.1038
103.06341.0750.32273.02980.01232.30970.1764-0.00240.22680.0167-0.11570.5075-0.1707-0.4349-0.06070.03450.04720.00820.13380.03050.1352-1.6619-15.7435-49.874
112.13540.9594-0.53272.0456-1.00682.17340.03660.1935-0.2186-0.2960.0087-0.21230.00120.0408-0.04530.10290.04610.01650.13020.03130.109742.324329.46270.629
122.73311.01841.00712.35741.02241.2736-0.0084-0.16170.1521-0.3432-0.17260.3728-0.1824-0.22130.1810.120.0738-0.0530.16450.04560.117224.582236.23976.7985
133.3593-0.6349-0.21761.24020.60382.24680.0958-0.0789-0.00490.01940.0438-0.3071-0.00920.3628-0.13960.03860.0317-0.03760.1298-0.03560.106129.5633-48.8348-14.4577
141.8436-0.1407-1.36651.7645-0.3473.60120.005-0.0066-0.21180.0507-0.00790.14520.0733-0.14590.00290.04870.0377-0.03220.10740.01620.08999.1706-52.2609-14.3065
152.3885-0.58920.64391.7349-0.2471.60850.12130.2346-0.00110.1888-0.2071-0.2338-0.16010.28190.08580.1078-0.0932-0.02610.1536-0.00810.073131.1906-17.2247-7.2275
162.9119-1.4438-0.9072.64911.08851.4807-0.0223-0.1047-0.24670.2654-0.04390.1877-0.0296-0.01750.06620.1204-0.0648-0.0040.1177-0.05190.107412.6696-23.516-0.0041
173.0749-0.61751.08381.5908-0.38862.60530.1252-0.38350.22530.273-0.03580.3445-0.3483-0.3573-0.08940.1273-0.00040.10560.0974-0.04380.12926.9567-0.8795-22.6037
183.63680.44111.87091.7483-0.07121.84780.09980.19520.3671-0.0266-0.1477-0.0755-0.20730.19120.04790.1051-0.00640.04260.0330.01520.105623.2348-0.4198-33.5877
193.44780.89651.4661.6340.33312.690.10330.34940.0412-0.00260.0382-0.0881-0.35050.1477-0.14150.12670.04840.03720.06670.01810.067349.433951.388723.7466
203.5144-0.16372.05262.0761-0.15673.22340.0427-0.33820.30810.2424-0.02130.3375-0.4898-0.6724-0.02140.18060.13910.10440.17870.02270.111532.556351.999534.7477
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999
9X-RAY DIFFRACTION9I-10 - 9999
10X-RAY DIFFRACTION10J-10 - 9999
11X-RAY DIFFRACTION11K-10 - 9999
12X-RAY DIFFRACTION12L-10 - 9999
13X-RAY DIFFRACTION13M-10 - 9999
14X-RAY DIFFRACTION14N-10 - 9999
15X-RAY DIFFRACTION15O-10 - 9999
16X-RAY DIFFRACTION16P-10 - 9999
17X-RAY DIFFRACTION17Q-10 - 9999
18X-RAY DIFFRACTION18R-10 - 9999
19X-RAY DIFFRACTION19S-10 - 9999
20X-RAY DIFFRACTION20T-10 - 9999

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