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- PDB-4odp: Structure of SlyD delta-IF from Thermus thermophilus in complex w... -

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Basic information

Entry
Database: PDB / ID: 4odp
TitleStructure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide
Components
  • 30S ribosomal protein S2
  • Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimera
KeywordsISOMERASE / CHAPERONE / FKBP domain / peptidyl-prolyl isomerase / PPIase
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding / regulation of amyloid precursor protein catabolic process / signaling receptor inhibitor activity / terminal cisterna / ryanodine receptor complex / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / protein maturation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / protein folding / regulation of protein localization / protein refolding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / cytoplasmic translation / positive regulation of canonical NF-kappaB signal transduction / structural constituent of ribosome / zinc ion binding / metal ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. ...Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Roll / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Small ribosomal subunit protein uS2 / Peptidyl-prolyl cis-trans isomerase FKBP1A / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Homo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.747 Å
AuthorsQuistgaard, E.M. / Low, C. / Nordlund, P.
CitationJournal: BMC Biol. / Year: 2016
Title: Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD.
Authors: Quistgaard, E.M. / Weininger, U. / Ural-Blimke, Y. / Modig, K. / Nordlund, P. / Akke, M. / Low, C.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification
Revision 1.2Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimera
B: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1768
Polymers13,9222
Non-polymers2546
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-51 kcal/mol
Surface area6700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.690, 93.690, 93.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

21A-351-

HOH

31A-388-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimera / TtSlyD / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506- ...TtSlyD / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 12179.549 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria), (gene. exp.) Homo sapiens (human)
Gene: TTHA0346, FKBP1, FKBP12, FKBP1A / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SLE7, UniProt: P62942, peptidylprolyl isomerase
#2: Protein/peptide 30S ribosomal protein S2


Mass: 1742.095 Da / Num. of mol.: 1 / Fragment: S2-W23 peptide (UNP residues 20-34) / Mutation: W23A / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P0A7V0

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Non-polymers , 4 types, 107 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN
Sequence detailsPROTEIN SLYD DELTA-IF IS A CHIMERA IN WHICH THE IF DOMAIN OF SYLD (UNP RESIDUES 65-125) HAS BEEN ...PROTEIN SLYD DELTA-IF IS A CHIMERA IN WHICH THE IF DOMAIN OF SYLD (UNP RESIDUES 65-125) HAS BEEN REPLACED BY THE FLAP LOOP OF FKBP12 (UNP RESIDUES 85-97).

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG400, 0.1 M HEPES, pH 7.5, 0.2 M calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.4 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 1.747→29.627 Å / Num. all: 14823 / Num. obs: 14816 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17.6 % / Biso Wilson estimate: 29.88 Å2 / Rsym value: 0.044 / Net I/σ(I): 35.85
Reflection shellResolution: 1.747→1.79 Å / Redundancy: 16.4 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1993 / Rsym value: 0.872 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXAutoSolmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.747→29.627 Å / SU ML: 0.21 / σ(F): 1.37 / Phase error: 19.5 / Stereochemistry target values: ML / Details: PDB ENTRY 3LUO
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 468 3.13 %RANDOM
Rwork0.1844 ---
obs0.1849 14816 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.747→29.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 6 101 950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016912
X-RAY DIFFRACTIONf_angle_d1.2581247
X-RAY DIFFRACTIONf_dihedral_angle_d15.012325
X-RAY DIFFRACTIONf_chiral_restr0.087128
X-RAY DIFFRACTIONf_plane_restr0.007160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.747-1.85680.28041390.24184352X-RAY DIFFRACTION100
1.8568-2.00010.18711460.18464354X-RAY DIFFRACTION100
2.0001-2.20130.22721580.17994313X-RAY DIFFRACTION100
2.2013-2.51970.21321320.18984361X-RAY DIFFRACTION100
2.5197-3.1740.22731530.20014341X-RAY DIFFRACTION100
3.174-29.63160.17191160.17244390X-RAY DIFFRACTION100
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)
10.7404-0.05650.07132.01030.13420.41270.0191-0.22540.01920.00190.0225-0.1402-0.0409-0.07090.00020.2296-0.0441-0.0060.26240.02020.189538.288262.184732.0635
20.00680.0060.0005-0.00090.00710.00410.1726-0.0801-0.0670.16970.1299-0.2852-0.02150.062-00.4709-0.1108-0.0660.68550.01010.814645.973557.724333.2884
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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