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- PDB-4odo: Structure of SlyD from Thermus thermophilus in complex with FK506 -

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Basic information

Entry
Database: PDB / ID: 4odo
TitleStructure of SlyD from Thermus thermophilus in complex with FK506
ComponentsPeptidyl-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 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 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 1.2Feb 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_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_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,11815
Polymers52,2013
Non-polymers2,91712
Water11,331629
1
A: Peptidyl-prolyl cis-trans isomerase SlyD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3136
Polymers17,4001
Non-polymers9125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase SlyD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4494
Polymers17,4001
Non-polymers1,0493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidyl-prolyl cis-trans isomerase SlyD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3565
Polymers17,4001
Non-polymers9564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.710, 50.210, 57.670
Angle α, β, γ (deg.)85.74, 68.92, 80.12
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 17400.234 Da / Num. of mol.: 3
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

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Non-polymers , 6 types, 641 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M magnesium 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 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.599→27.81 Å / Num. all: 63368 / Num. obs: 63368 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 20.93 Å2 / Rsym value: 0.052 / Net I/σ(I): 14.46
Reflection shellResolution: 1.599→1.64 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.47 / Rsym value: 0.568 / % possible all: 87.4

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.599→27.81 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 24.2 / Stereochemistry target values: ML / Details: PDB ENTRY 3LUO
RfactorNum. reflection% reflection
Rfree0.2041 1931 3.05 %
Rwork0.18 --
obs0.1808 63367 95.46 %
all-63367 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.599→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 198 629 4358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053869
X-RAY DIFFRACTIONf_angle_d0.8995261
X-RAY DIFFRACTIONf_dihedral_angle_d17.6631443
X-RAY DIFFRACTIONf_chiral_restr0.036583
X-RAY DIFFRACTIONf_plane_restr0.004694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5992-1.63910.381170.30164016X-RAY DIFFRACTION87
1.6391-1.68350.33291370.28144330X-RAY DIFFRACTION94
1.6835-1.7330.29411330.24894325X-RAY DIFFRACTION94
1.733-1.78890.24031330.2224340X-RAY DIFFRACTION94
1.7889-1.85280.25871350.20594370X-RAY DIFFRACTION95
1.8528-1.9270.22621360.20334373X-RAY DIFFRACTION95
1.927-2.01470.23031350.19624394X-RAY DIFFRACTION96
2.0147-2.12090.22131290.18164481X-RAY DIFFRACTION97
2.1209-2.25370.26031350.18464442X-RAY DIFFRACTION97
2.2537-2.42760.21111450.18854483X-RAY DIFFRACTION97
2.4276-2.67170.23291500.19094468X-RAY DIFFRACTION98
2.6717-3.05790.20421420.18154506X-RAY DIFFRACTION97
3.0579-3.8510.16141530.15274459X-RAY DIFFRACTION97
3.851-27.81390.15941510.15374449X-RAY DIFFRACTION97
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)
11.5875-0.1726-0.6940.38790.12030.3252-0.05250.02380.00380.05880.02190.00440.03770.02330.02120.1535-0.0048-0.02240.13080.01690.13131.168749.372752.1009
20.14460.01750.32570.64360.13422.06270.07-0.07920.02610.01480.0174-0.01820.06480.0065-0.08810.1061-0.01270.00990.1448-0.00180.153446.250228.484914.7
3-0.15690.1122-0.22442.24552.70882.73240.1051-0.0849-0.0264-0.2718-0.5120.2694-0.4026-0.58640.26290.28730.0795-0.05370.3933-0.05940.243727.530646.657926.8359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'

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