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- PDB-5v8t: Crystal structure of SMT fusion Peptidyl-prolyl cis-trans isomera... -

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Basic information

Entry
Database: PDB / ID: 5v8t
TitleCrystal structure of SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with SF354
ComponentsUbiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Burkholderia / Peptidyl / Proline
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) / SUMOylation of SUMOylation proteins / 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 ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / 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 RNA binding proteins / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / peptidylprolyl isomerase / condensed nuclear chromosome / peptidyl-prolyl cis-trans isomerase activity / protein tag activity / identical protein binding / nucleus
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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain ...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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-8ZV / FORMIC ACID / Peptidyl-prolyl cis-trans isomerase / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Burkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLorimer, D.D. / Dranow, D.M. / Seufert, F. / Abendroth, J. / Holzgrabe, U.
CitationJournal: to be published
Title: Crystal structure of SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with SF354
Authors: Lorimer, D.D. / Dranow, D.M. / Seufert, F. / Abendroth, J. / Holzgrabe, U.
History
DepositionMar 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)46,9696
Polymers45,7412
Non-polymers1,2284
Water4,810267
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A: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4953
Polymers22,8711
Non-polymers6252
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)23,4743
Polymers22,8711
Non-polymers6032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.640, 32.500, 99.350
Angle α, β, γ (deg.)90.000, 96.730, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -76 through -65 or (resid -64...
21(chain B and (resid -76 through -40 or (resid -39...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRSERSER(chain A and (resid -76 through -65 or (resid -64...AA-76 - -6519 - 30
12GLUGLUGLUGLU(chain A and (resid -76 through -65 or (resid -64...AA-6431
13GLUGLUVALVAL(chain A and (resid -76 through -65 or (resid -64...AA-77 - 11318 - 208
14GLUGLUVALVAL(chain A and (resid -76 through -65 or (resid -64...AA-77 - 11318 - 208
15GLUGLUVALVAL(chain A and (resid -76 through -65 or (resid -64...AA-77 - 11318 - 208
16GLUGLUVALVAL(chain A and (resid -76 through -65 or (resid -64...AA-77 - 11318 - 208
21THRTHRLYSLYS(chain B and (resid -76 through -40 or (resid -39...BB-76 - -4019 - 55
22GLUGLUASPASP(chain B and (resid -76 through -40 or (resid -39...BB-39 - -3756 - 58
23GLUGLUVALVAL(chain B and (resid -76 through -40 or (resid -39...BB-77 - 11318 - 208
24GLUGLUVALVAL(chain B and (resid -76 through -40 or (resid -39...BB-77 - 11318 - 208
25GLUGLUVALVAL(chain B and (resid -76 through -40 or (resid -39...BB-77 - 11318 - 208
26GLUGLUVALVAL(chain B and (resid -76 through -40 or (resid -39...BB-77 - 11318 - 208

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Components

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


Mass: 22870.633 Da / Num. of mol.: 2 / Fragment: unp residues 13-97; unp residues 2-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Burkholderia pseudomallei (bacteria)
Strain: ATCC 204508 / S288c
Gene: SMT3, YDR510W, D9719.15, fbp_2, DP46_4351, DP49_3058, ERS012314_03208, SY87_03945
Plasmid: pET28-HisSMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q12306, UniProt: A0A069BB90, peptidylprolyl isomerase
#2: Chemical ChemComp-8ZV / 2-{[3,5-bis(2-methoxyethoxy)benzene-1-carbonyl]amino}ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate


Mass: 578.674 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H38N2O9S
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 776103) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF354 (BSI5672). Crystals were ...Details: BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 776103) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF354 (BSI5672). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing 24.55% (w/v) PEG-3350, 50 mM ammonium formate (JCSG_A8 opt screen d7) and cryoprotected with 15% ethylene glycol. Crystal Tracking ID 274545d7, uxe3-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→48.915 Å / Num. obs: 23040 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.099 % / Biso Wilson estimate: 20.77 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.128 / Χ2: 0.991 / Net I/σ(I): 11.51 / Num. measured all: 94438 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.153.7680.5083.186424172117050.7530.59499.1
2.15-2.214.1920.443.816782162016180.8370.50799.9
2.21-2.284.1580.4173.976624159715930.870.4899.7
2.28-2.354.1540.3594.646447155515520.8980.41499.8
2.35-2.424.1930.3264.896248149114900.9070.37599.9
2.42-2.514.1390.2865.626146148514850.9180.33100
2.51-2.64.1960.2446.395833139113900.9450.28199.9
2.6-2.714.1480.2077.555666136513660.9640.239100
2.71-2.834.1840.1868.165380128812860.9660.21499.8
2.83-2.974.1460.14310.345265127012700.980.165100
2.97-3.134.1490.1112.564846117211680.9880.12799.7
3.13-3.324.1320.08415.94661113111280.9920.09799.7
3.32-3.554.1080.06718.824404107110720.9960.077100
3.55-3.834.10.05622.2340759979940.9970.06599.7
3.83-4.24.080.04525.3836929059050.9970.052100
4.2-4.74.0440.03829.1134218508460.9980.04399.5
4.7-5.424.0390.0427.2229817387380.9980.046100
5.42-6.643.9830.04623.3825336376360.9970.05499.8
6.64-9.393.8890.03627.5119334974970.9990.042100
9.39-48.9153.5780.02634.8210773063010.9990.0398.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UF8

3uf8


Resolution: 2.1→48.915 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 1962 8.52 %
Rwork0.184 21070 -
obs0.1872 23032 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.73 Å2 / Biso mean: 26.6088 Å2 / Biso min: 7.8 Å2
Refinement stepCycle: final / Resolution: 2.1→48.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 84 269 3202
Biso mean--31.73 29.11 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022985
X-RAY DIFFRACTIONf_angle_d0.6034032
X-RAY DIFFRACTIONf_chiral_restr0.046440
X-RAY DIFFRACTIONf_plane_restr0.003526
X-RAY DIFFRACTIONf_dihedral_angle_d19.1611751
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1650X-RAY DIFFRACTION8.5TORSIONAL
12B1650X-RAY DIFFRACTION8.5TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15250.28811350.21741498163399
2.1525-2.21070.28711590.209314641623100
2.2107-2.27570.23581430.215214581601100
2.2757-2.34920.23341330.209514971630100
2.3492-2.43310.22281470.210614921639100
2.4331-2.53060.22971370.202314941631100
2.5306-2.64570.24281040.204515211625100
2.6457-2.78520.2361400.212514981638100
2.7852-2.95970.24761400.200115011641100
2.9597-3.18810.25511530.193114931646100
3.1881-3.50890.20961340.174214981632100
3.5089-4.01640.18661690.161515071676100
4.0164-5.05950.18341400.141715241664100
5.0595-48.92840.19831280.172316251753100
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)
12.038-0.362-0.54863.68150.17191.89310.03970.11130.098-0.3097-0.0307-0.34780.03450.0912-0.00930.1870.01660.03590.1871-0.00960.1451-121.0258-13.0319125.1036
21.3971-0.00960.06341.3392-0.04150.8772-0.0196-0.0121-0.0513-0.00180.0221-0.0450.01580.00850.00540.0911-0.00380.01530.07090.00770.1035-123.5168-29.5868145.471
34.85680.783-0.15033.91710.40545.68060.1257-0.21850.18430.5739-0.304-0.2191-0.2539-0.24110.10790.32110.0049-0.01120.2275-0.01470.1709-122.9053-39.0476190.8004
42.3890.157-0.3151.88830.072.0870.0524-0.1503-0.06660.04080.0196-0.01890.0385-0.0119-0.0710.11290.0027-0.00280.09380.01480.1036-123.6998-19.4539170.1206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -77 through 2 )A-77 - 2
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 113 )A3 - 113
3X-RAY DIFFRACTION3chain 'B' and (resid -77 through -5 )B-77 - -5
4X-RAY DIFFRACTION4chain 'B' and (resid -4 through 113 )B-4 - 113

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