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- PDB-4odm: Structure of SlyD from Thermus thermophilus in complex with S2-W2... -

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Basic information

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


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein refolding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / zinc ion binding / metal ion binding / cytoplasm
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. / Ribosomal protein S2, conserved site ...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
ACETATE ION / Small ribosomal subunit protein uS2 / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.1Oct 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 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Peptidyl-prolyl cis-trans isomerase SlyD
B: Peptidyl-prolyl cis-trans isomerase SlyD
C: Peptidyl-prolyl cis-trans isomerase SlyD
D: Peptidyl-prolyl cis-trans isomerase SlyD
E: 30S ribosomal protein S2
F: 30S ribosomal protein S2
G: 30S ribosomal protein S2
H: 30S ribosomal protein S2
I: 30S ribosomal protein S2
J: 30S ribosomal protein S2
K: 30S ribosomal protein S2
L: 30S ribosomal protein S2
M: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,13920
Polymers82,75413
Non-polymers3857
Water10,917606
1
B: Peptidyl-prolyl cis-trans isomerase SlyD
G: 30S ribosomal protein S2
H: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2884
Polymers20,2533
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase SlyD
E: 30S ribosomal protein S2
F: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4396
Polymers20,2533
Non-polymers1873
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidyl-prolyl cis-trans isomerase SlyD
I: 30S ribosomal protein S2
J: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2884
Polymers20,2533
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptidyl-prolyl cis-trans isomerase SlyD
K: 30S ribosomal protein S2
L: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3805
Polymers20,2533
Non-polymers1282
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: 30S ribosomal protein S2


  • defined by author
  • 1.74 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,7421
Polymers1,7421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.120, 41.200, 131.520
Angle α, β, γ (deg.)90.00, 123.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 13 molecules ABCDEFGHIJKLM

#1: Protein
Peptidyl-prolyl cis-trans isomerase SlyD / TtSlyD


Mass: 16768.693 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA0346 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLE7, peptidylprolyl isomerase
#2: Protein/peptide
30S ribosomal protein S2


Mass: 1742.095 Da / Num. of mol.: 9 / Fragment: S2-W23A 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, 613 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 19% PEG3350, 8% Tacsimate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9199 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 1.75→29.111 Å / Num. all: 83454 / Num. obs: 83454 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 26.98 Å2 / Rsym value: 0.047 / Net I/σ(I): 18.31
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.42 / Num. unique all: 6009 / Rsym value: 0.766 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.111 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 21.8 / Stereochemistry target values: ML / Details: PDB ENTRY 3LUO
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 3312 3.97 %RANDOM
Rwork0.1764 ---
obs0.1777 83451 99.11 %-
all-83451 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→29.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5353 0 20 606 5979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065575
X-RAY DIFFRACTIONf_angle_d1.0947581
X-RAY DIFFRACTIONf_dihedral_angle_d13.5562087
X-RAY DIFFRACTIONf_chiral_restr0.075817
X-RAY DIFFRACTIONf_plane_restr0.0051024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77490.38791290.35423259X-RAY DIFFRACTION98
1.7749-1.80140.36351300.31943269X-RAY DIFFRACTION97
1.8014-1.82960.32641430.27673240X-RAY DIFFRACTION99
1.8296-1.85960.30861390.24513310X-RAY DIFFRACTION99
1.8596-1.89160.26411280.23073297X-RAY DIFFRACTION98
1.8916-1.9260.24291410.2123314X-RAY DIFFRACTION99
1.926-1.9630.23161280.20673337X-RAY DIFFRACTION98
1.963-2.00310.24381420.2023306X-RAY DIFFRACTION100
2.0031-2.04660.2041420.18933330X-RAY DIFFRACTION100
2.0466-2.09420.22481410.1793293X-RAY DIFFRACTION99
2.0942-2.14660.22551330.18053365X-RAY DIFFRACTION100
2.1466-2.20460.22411340.17823315X-RAY DIFFRACTION99
2.2046-2.26950.24431270.18313356X-RAY DIFFRACTION100
2.2695-2.34270.22531450.17963314X-RAY DIFFRACTION99
2.3427-2.42640.24191430.18573361X-RAY DIFFRACTION99
2.4264-2.52350.24161530.18033300X-RAY DIFFRACTION100
2.5235-2.63830.21641530.18493332X-RAY DIFFRACTION99
2.6383-2.77720.22791310.17663410X-RAY DIFFRACTION100
2.7772-2.95110.23281310.18353350X-RAY DIFFRACTION99
2.9511-3.17870.19981440.17333361X-RAY DIFFRACTION99
3.1787-3.49810.18851260.16053380X-RAY DIFFRACTION99
3.4981-4.00320.18111450.15563390X-RAY DIFFRACTION99
4.0032-5.03930.15541360.14023424X-RAY DIFFRACTION99
5.0393-29.11540.17921480.17333526X-RAY DIFFRACTION99
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)
11.18220.5772-0.3661.9567-1.01581.1986-0.03010.01530.0132-0.07410.0560.0679-0.0197-0.1155-0.02120.17490.0471-0.01790.2079-0.03110.189240.56246.341532.209
21.7222-0.60620.09462.47680.89791.1869-0.02150.08540.1074-0.12610.0777-0.0803-0.1120.0333-0.04740.1807-0.0444-0.01260.21870.0030.200517.70593.983927.7106
31.3502-0.31880.07030.82370.57622.3016-0.01380.25740.1742-0.0986-0.0148-0.1162-0.17330.1620.01360.1582-0.02450.01710.16360.04620.1764-23.317-10.180223.2948
42.01850.4507-1.76860.4518-0.32413.1039-0.08960.0851-0.0835-0.0654-0.0135-0.06320.12490.03010.10160.20350.0252-0.01470.1707-0.01030.2428-10.167210.584230.6873
51.02990.9919-1.15193.882-4.15744.4726-0.0253-0.256-0.14891.15750.0730.1703-0.21810.1449-0.18120.61640.03960.08630.35450.01030.395142.16696.772134.4955
64.890.5102-0.72045.4723-1.29862.08320.2326-0.5953-0.230.0986-0.09740.69-0.3686-0.7236-0.21160.22930.0601-0.02780.4461-0.0340.278732.05950.410157.062
78.6508-2.325-6.02660.63531.63534.2242-0.14220.4723-0.53140.31550.1309-0.1478-0.17940.08380.10310.4341-0.01160.0790.3928-0.03520.419620.30746.108327.9185
84.937-2.9173-4.23714.87013.64538.35770.29040.47860.0416-0.27490.4311-0.4754-0.55571.176-0.56390.5742-0.13470.07890.8087-0.06640.325728.5091-0.81113.0516
96.18810.9166-1.43724.9616-0.7537.18310.07590.74260.488-0.71060.04540.162-0.9716-0.1354-0.07380.40130.00030.03180.28540.05740.2703-25.0066-7.7220.8513
101.30282.0612-2.30883.2524-3.6464.08270.05270.03030.2702-0.19160.0494-0.3068-0.35330.8453-0.24570.6907-0.24670.0130.69740.15080.3834-16.41020.6669-2.2187
115.6285-1.2302-0.76281.87890.49711.3731-0.0689-1.3404-0.09270.66740.2236-0.1054-0.22820.3926-0.05110.39110.0133-0.00570.4499-0.01740.348-8.766413.074132.8428
123.5565-0.8864-1.37445.90622.76189.504-0.0399-0.70430.1310.2139-0.07530.4376-0.0082-0.77710.2170.1669-0.0059-0.01810.3014-0.00720.2641-25.020419.943952.8007
132.36230.3051-0.3656.21330.51891.8762-0.33160.02930.23120.0916-0.1957-0.0692-0.0226-0.08650.19950.8634-0.08390.02320.73420.1140.812723.21414.931220.3304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'
7X-RAY DIFFRACTION7chain 'G'
8X-RAY DIFFRACTION8chain 'H'
9X-RAY DIFFRACTION9chain 'I'
10X-RAY DIFFRACTION10chain 'J'
11X-RAY DIFFRACTION11chain 'K'
12X-RAY DIFFRACTION12chain 'L'
13X-RAY DIFFRACTION13chain 'M'

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