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- PDB-6o4a: CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERA... -

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Entry
Database: PDB / ID: 6o4a
TitleCRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355
ComponentsUbiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / PROTEIN BINDING / SSGCID / PEPTIDYL / PROLINE / SF355 / 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 / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring ...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 / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 / PML body / protein tag activity / protein folding / chromatin / identical protein binding / nucleus / metal ion binding
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 ...Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-LLD / 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: 2.1 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 SF355
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.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.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_conn.ptnr2_label_seq_id
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
C: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
D: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,81310
Polymers92,0074
Non-polymers1,8066
Water9,044502
1
A: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4733
Polymers23,0021
Non-polymers4722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4332
Polymers23,0021
Non-polymers4321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4733
Polymers23,0021
Non-polymers4722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4332
Polymers23,0021
Non-polymers4321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.820, 32.650, 178.190
Angle α, β, γ (deg.)90.000, 90.010, 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.: 4
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-LLD / 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate


Mass: 431.505 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H25N3O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
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 SF355 (BSI5667). 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 SF355 (BSI5667). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing HamptonResearch PACT screen (B4): 25% PEG 1500, 100m MIB pH 7.0. The sample was cryoprotected with 15% ethylene glycol: Crystal tray ID 290655b4, puck ID PWP0-3

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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 PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2016
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→44.55 Å / Num. obs: 42810 / % possible obs: 98.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.062 / Χ2: 1.02 / Net I/σ(I): 16.63 / Num. measured all: 136959
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 5 / Num. unique obs: 555 / CC1/2: 0.999 / Rrim(I) all: 0.025 / % possible all: 93.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.12RC0_2798: ???)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BE4 model, 2 domains

Resolution: 2.1→44.55 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.26
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2031 4.75 %0
Rwork0.157 ---
obs0.159 42789 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.36 Å2 / Biso mean: 31.01 Å2 / Biso min: 8.34 Å2
Refinement stepCycle: final / Resolution: 2.1→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5625 0 122 508 6255
Biso mean--19.19 33.23 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075873
X-RAY DIFFRACTIONf_angle_d0.9257952
X-RAY DIFFRACTIONf_dihedral_angle_d16.933446
X-RAY DIFFRACTIONf_chiral_restr0.056878
X-RAY DIFFRACTIONf_plane_restr0.0061044
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2664 127 -
Rwork0.1885 2523 -
all-2650 -
obs--93 %
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)
13.1443-0.0567-1.70197.7088-0.74793.95950.13260.34070.0957-0.8542-0.1552-0.29140.00630.11030.05970.395-0.0111-0.02790.27680.00320.2091-61.6402-20.1494194.5173
22.4109-0.06120.47531.35420.09491.5467-0.00760.09060.0213-0.09770.0252-0.05230.08210.0444-0.01760.107-0.00190.01410.09620.01110.1214-62.0734-38.6766214.4643
31.69860.67640.46026.04870.7291.39370.0513-0.11940.10330.2177-0.18960.0386-0.1665-0.27670.16510.3660.0333-0.01750.3771-0.03590.154-68.2826-47.2644258.3539
42.70610.01010.76461.36720.10521.7164-0.0554-0.21180.03320.097-0.0343-0.01820.0004-0.03660.08670.1137-0.00010.00970.12110.01070.1079-63.6829-28.6065237.1703
54.6387-0.34341.64626.5286-0.81145.77530.0821-0.4432-0.00560.8021-0.1347-0.3515-0.0550.16220.06120.37590.00610.00060.2615-0.00640.1887-30.3806-70.3633251.0417
62.77060.0168-0.29881.33150.11461.5632-0.0051-0.09150.01710.10190.004-0.055-0.06710.0136-0.00420.1102-0.00290.00710.10320.01160.138-30.7435-52.1165230.943
74.1272-0.4673-0.5386.89310.39825.03750.07590.1666-0.0814-0.2069-0.31040.03610.4166-0.36640.19340.3316-0.02760.02770.3214-0.04260.1251-37.2625-41.6645186.8786
82.4931-0.1758-0.38771.75160.27561.8711-0.05820.2206-0.0204-0.1308-0.02-0.068-0.0396-0.0380.07730.1164-0.009-0.00010.13620.01610.1052-32.1145-61.9005207.3278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -77 through -6 )
2X-RAY DIFFRACTION2chain 'A' and (resid -5 through 113 )
3X-RAY DIFFRACTION3chain 'B' and (resid -77 through 2 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 113 )
5X-RAY DIFFRACTION5chain 'C' and (resid -77 through -6 )
6X-RAY DIFFRACTION6chain 'C' and (resid -5 through 113 )
7X-RAY DIFFRACTION7chain 'D' and (resid -77 through -5 )
8X-RAY DIFFRACTION8chain 'D' and (resid -4 through 113 )

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