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- PDB-6o49: CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERA... -

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Entry
Database: PDB / ID: 6o49
TitleCRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF339
ComponentsUbiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / PROTEIN BINDING / PEPTIDYL / PROLINE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein tag activity / protein folding / identical protein binding / nucleus / metal ion binding
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-LL7 / Ubiquitin-like protein SMT3 / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Burkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF339
Authors: Iwasaki, J. / Lorimer, D.D. / Vivoli, M. / Harmer, N.J. / Kibble, E.A. / Peacock, C.S. / Abendroth, J. / Mayclin, S.J. / Dranow, D.M. / Pierce, P.G. / Fox III, D. / Lewis, M. / Bzdyl, N. / ...Authors: Iwasaki, J. / Lorimer, D.D. / Vivoli, M. / Harmer, N.J. / Kibble, E.A. / Peacock, C.S. / Abendroth, J. / Mayclin, S.J. / Dranow, D.M. / Pierce, P.G. / Fox III, D. / Lewis, M. / Bzdyl, N. / Kristensen, S. / Schmidberger, J.W. / Bond, C.B. / Seufert, F. / Schmitz, J. / Norville, I.H. / Myler, P.J. / Holzgrabe, U. / Sarkar-Tyson, M.
History
DepositionFeb 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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
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_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.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_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_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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
B: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3099
Polymers46,0042
Non-polymers1,3067
Water6,467359
1
A: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6244
Polymers23,0021
Non-polymers6223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6865
Polymers23,0021
Non-polymers6844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.860, 33.600, 98.140
Angle α, β, γ (deg.)90.000, 101.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase


Mass: 23001.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: ATCC 204508 / S288c, 1710b / Gene: SMT3, YDR510W, D9719.15, BURPS1710b_A0907 / Plasmid: pET28-HisSMT
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: Q12306, UniProt: Q3JK38, peptidylprolyl isomerase
#2: Chemical ChemComp-LL7 / (2~{S})-~{N}-[3-oxidanylidene-3-[(3,4,5-trimethoxyphenyl)amino]propyl]-1-(phenylmethyl)sulfonyl-piperidine-2-carboxamide


Mass: 519.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H33N3O7S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 1264062) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF339_S (BSI5671). Crystals were ...Details: BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 1264062) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF339_S (BSI5671). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing 100 mM MES pH 6.0, 200 mM Calcium chloride dehydrate, 20% PEG6000 (PACT B11). Crystal Tracking ID 297348b11, izs6-2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2018
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.85→48.13 Å / Num. obs: 31913 / % possible obs: 97.4 % / Redundancy: 3.212 % / Biso Wilson estimate: 25.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.106 / Χ2: 0.967 / Net I/σ(I): 9.91
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2.98 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 405 / CC1/2: 0.995 / Rrim(I) all: 0.054 / % possible all: 80.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BE4 model

Resolution: 1.85→48.13 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.83
RfactorNum. reflection% reflection
Rfree0.211 1959 6.14 %
Rwork0.168 --
obs0.171 31909 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.89 Å2 / Biso mean: 27.18 Å2 / Biso min: 7.62 Å2
Refinement stepCycle: final / Resolution: 1.85→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 122 361 3323
Biso mean--22.24 34.17 -
Num. residues----379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063070
X-RAY DIFFRACTIONf_angle_d0.7664159
X-RAY DIFFRACTIONf_dihedral_angle_d20.6331804
X-RAY DIFFRACTIONf_chiral_restr0.055450
X-RAY DIFFRACTIONf_plane_restr0.005543
LS refinement shellResolution: 1.85→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3554 107 -
Rwork0.2792 1738 -
all-1845 -
obs--80 %
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)
12.5060.3262-0.17431.4045-0.3641.8910.0274-0.1618-0.00530.06920.01870.03690.0131-0.1844-0.04960.0980.0158-0.01430.1230.01480.0977-74.3612-30.1774164.2735
25.1295-1.07841.10223.37260.25934.24640.28130.40130.0887-0.429-0.2944-0.18440.02190.03530.0170.19180.02520.00620.1770.00560.1591-66.1058-21.3724122.0027
31.1946-0.2889-0.02232.5306-0.74951.23510.06830.2820.0261-0.3566-0.1734-0.1969-0.1377-0.12260.04820.21410.05070.00150.2255-0.01590.1106-67.8701-33.4198121.976
43.2904-0.31190.15081.33550.09781.3759-0.04740.07770.09970.0433-0.01270.055-0.0955-0.0320.04710.10230.0026-0.02410.06550.00080.1026-72.6352-40.3809141.1024
53.50780.75282.16965.92461.15142.3930.23440.10060.15750.0393-0.1743-0.1212-0.3932-0.3129-0.03290.34020.070.07460.3766-0.01360.1465-75.0781-50.4601185.6737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid -4 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid -76 through -27 )
3X-RAY DIFFRACTION3chain 'A' and (resid -26 through 16 )
4X-RAY DIFFRACTION4chain 'A' and (resid 17 through 113 )
5X-RAY DIFFRACTION5chain 'B' and (resid -76 through -5 )

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