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- PDB-3rm1: 1.24 Angstrom X-ray structure of bovine TRTK12-Ca(2+)-S100B D63N -

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Basic information

Entry
Database: PDB / ID: 3rm1
Title1.24 Angstrom X-ray structure of bovine TRTK12-Ca(2+)-S100B D63N
Components
  • F-actin-capping protein subunit alpha-2
  • Protein S100-B
KeywordsMETAL BINDING PROTEIN/PROTEIN BINDING / alpha-helical / EF hand / METAL BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / COPI-mediated anterograde transport / F-actin capping protein complex / adaptive thermogenesis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation ...Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / COPI-mediated anterograde transport / F-actin capping protein complex / adaptive thermogenesis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / Factors involved in megakaryocyte development and platelet production / RAGE receptor binding / negative regulation of monocyte chemotactic protein-1 production / barbed-end actin filament capping / S100 protein binding / axonogenesis / astrocyte activation / tau protein binding / calcium-dependent protein binding / actin filament binding / regulation of translation / actin cytoskeleton organization / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / phosphorylation / calcium ion binding / positive regulation of cell population proliferation / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm
Similarity search - Function
Protein S100-B / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / S-100/ICaBP type calcium binding protein signature. ...Protein S100-B / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / 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 / 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
Protein S100-B / F-actin-capping protein subunit alpha-2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsLiriano, M.A. / Weber, D.J.
CitationJournal: To be Published
Title: The effects of CapZ peptide (TRTK12) on the protein dynamics of S100B and S100B D63N
Authors: Liriano, M.A. / Varney, K.M. / Inman, K.G. / Ishima, R. / Weber, D.J.
History
DepositionApr 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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_ref_seq_dif / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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-B
B: F-actin-capping protein subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8934
Polymers11,8132
Non-polymers802
Water2,180121
1
A: Protein S100-B
B: F-actin-capping protein subunit alpha-2
hetero molecules

A: Protein S100-B
B: F-actin-capping protein subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7878
Polymers23,6274
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)35.007, 89.251, 59.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-262-

HOH

21A-282-

HOH

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Components

#1: Protein Protein S100-B / S-100 protein beta chain / S-100 protein subunit beta / S100 calcium-binding protein B


Mass: 10680.989 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: S100B / Plasmid: PET11B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02638
#2: Protein/peptide F-actin-capping protein subunit alpha-2 / CapZ alpha-2


Mass: 1132.352 Da / Num. of mol.: 1 / Fragment: TRTK12 peptide (UNP residues 267-275) / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: Q5E997
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 6.875
Details: 22% PEG3350, 7.5 mM calcium chloride, 100 mM cacodylate, pH 6.875, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 26591 / % possible obs: 98.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.085 / Χ2: 1.149 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.24-1.286.40.55926310.871199.5
1.28-1.346.90.44526570.9091100
1.34-1.47.10.31426590.9511100
1.4-1.477.10.23126711.0561100
1.47-1.567.20.16126581.155199.9
1.56-1.687.20.13226741.2911100
1.68-1.857.20.11126951.3891100
1.85-2.127.10.10426861.4451100
2.12-2.676.80.08927191.376199.2
2.67-505.90.06125410.961189.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IQQ

3iqq


Resolution: 1.24→44.63 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.334 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1335 5 %RANDOM
Rwork0.2039 ---
obs0.2048 26563 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 44.66 Å2 / Biso mean: 18.7833 Å2 / Biso min: 7.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-0 Å2
2---0.6 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.24→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms771 0 2 121 894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022783
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9361052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.998596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.29726.05338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.63415141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.432151
X-RAY DIFFRACTIONr_chiral_restr0.110.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02576
X-RAY DIFFRACTIONr_mcbond_it0.8961.5484
X-RAY DIFFRACTIONr_mcangle_it1.5672775
X-RAY DIFFRACTIONr_scbond_it2.1213299
X-RAY DIFFRACTIONr_scangle_it3.2884.5277
LS refinement shellResolution: 1.24→1.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 104 -
Rwork0.312 1817 -
all-1921 -
obs--98.51 %
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)
15.809-1.1793-0.43914.1834-2.58084.33620.04740.0558-0.0564-0.13290.18940.7644-0.0412-0.3074-0.23680.02150.00240.00740.03610.00680.0652-3.61456.23432.249
21.8633-2.8738-0.122911.2332-1.54990.4539-0.0476-0.0972-0.00050.31970.09680.1817-0.0520.0167-0.04920.1071-0.00630.00090.058-0.00360.05950.9997-5.97857.0224
32.8776-0.03920.37891.49770.26882.3875-0.0282-0.1782-0.20020.18970.037-0.01880.10020.0202-0.00880.03320.0042-0.01110.01820.01140.03975.6056-16.85414.8514
41.1237-1.0721-0.0081.2345-0.01770.53250.05420.0997-0.0374-0.0917-0.0232-0.07360.00970.0443-0.03090.0804-0.0051-0.00340.0878-0.00960.095110.626-16.9966-5.227
51.7-0.67660.2322.6772-0.94653.4878-0.0205-0.0672-0.03330.16150.1246-0.0554-0.10820.0281-0.10410.0267-0.0008-0.01830.0178-0.01230.063212.8855-8.23873.4996
61.99720.70933.24221.608-1.23919.4787-0.1762-0.06450.0193-0.15760.0077-0.0683-0.1298-0.16490.16860.09890.0052-0.0170.1161-0.03580.08786.5734-1.4271-12.0862
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 16
3X-RAY DIFFRACTION3A17 - 40
4X-RAY DIFFRACTION4A41 - 63
5X-RAY DIFFRACTION5A64 - 78
6X-RAY DIFFRACTION6A79 - 88

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