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- PDB-3uqb: Crystal structure of a SMT Fusion PEPTIDYL-PROLYL CIS-TRANS ISOME... -

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Basic information

Entry
Database: PDB / ID: 3uqb
TitleCrystal structure of a SMT Fusion PEPTIDYL-PROLYL CIS-TRANS ISOMERASE with surface mutation D44G from Burkholderia pseudomallei complexed with FK506
ComponentsUbiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
KeywordsIsomerase / protein binding / 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 / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity ...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 / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / 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 / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein tag activity / protein folding / metal ion binding / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / 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: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Antimicrob.Agents Chemother. / Year: 2014
Title: A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins.
Authors: Begley, D.W. / Fox, D. / Jenner, D. / Juli, C. / Pierce, P.G. / Abendroth, J. / Muruthi, M. / Safford, K. / Anderson, V. / Atkins, K. / Barnes, S.R. / Moen, S.O. / Raymond, A.C. / Stacy, R. ...Authors: Begley, D.W. / Fox, D. / Jenner, D. / Juli, C. / Pierce, P.G. / Abendroth, J. / Muruthi, M. / Safford, K. / Anderson, V. / Atkins, K. / Barnes, S.R. / Moen, S.O. / Raymond, A.C. / Stacy, R. / Myler, P.J. / Staker, B.L. / Harmer, N.J. / Norville, I.H. / Holzgrabe, U. / Sarkar-Tyson, M. / Edwards, T.E. / Lorimer, D.D.
History
DepositionNov 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Other
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 13, 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 / 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_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: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7482
Polymers22,9441
Non-polymers8041
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.370, 32.640, 77.000
Angle α, β, γ (deg.)90.000, 90.810, 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: 22943.793 Da / Num. of mol.: 1 / Fragment: Q12306 residues 13-98, Q3JK38 residues 2-113 / Mutation: D44G
Source method: isolated from a genetically manipulated source
Details: Fusion Protein
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Burkholderia pseudomallei (bacteria)
Strain: 1710b, S288c / Gene: BURPS1710b_A0907, SMT3, YDR510W, D9719.15 / Plasmid: pET28-HisSMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q12306, UniProt: Q3JK38, peptidylprolyl isomerase
#2: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 38.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Internal tracking number 226421. PACT well B6. 0.1M MIB Buffer pH 9.0, 25.0% w/v PEG1500, 30% PEG400 Cryo. BUPSA.00130.A.D214 PD00190/6 23.7mg/ml, vapor diffusion, sitting drop, temperature ...Details: Internal tracking number 226421. PACT well B6. 0.1M MIB Buffer pH 9.0, 25.0% w/v PEG1500, 30% PEG400 Cryo. BUPSA.00130.A.D214 PD00190/6 23.7mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2011
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.9→38.5 Å / Num. all: 14561 / Num. obs: 14527 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.02 % / Biso Wilson estimate: 24.794 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.950.4083.44271105399.9
1.95-20.3274.24180102299.9
2-2.060.2815.24122101199.8
2.06-2.120.2286398898299.9
2.12-2.190.1927.33956969100
2.19-2.270.1797.83709920100
2.27-2.360.1479.2359787599.9
2.36-2.450.13110.2353387399.9
2.45-2.560.11112.13307816100
2.56-2.690.09314.13195787100
2.69-2.830.08216.23067758100
2.83-30.06220.42874711100
3-3.210.0524.9265266499.7
3.21-3.470.03731.72497630100
3.47-3.80.03336.7227458199.7
3.8-4.250.02941.4196651299.4
4.25-4.910.02248.21886473100
4.91-6.010.02444.31637409100
6.01-8.50.02242.9123131199.7
8.50.01754.561517089.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 3UF8

3uf8


Resolution: 1.9→19.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.59 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.159 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 726 5 %RANDOM
Rwork0.169 ---
all0.172 14561 --
obs0.172 14518 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.783 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å2-0.57 Å2
2---0.38 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 57 163 1651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021544
X-RAY DIFFRACTIONr_bond_other_d0.0010.021047
X-RAY DIFFRACTIONr_angle_refined_deg1.4952.0052096
X-RAY DIFFRACTIONr_angle_other_deg0.86332566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01624.53164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.239159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 51 -
Rwork0.187 931 -
all-982 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: 22.6918 Å / Origin y: 0.6483 Å / Origin z: 58.096 Å
111213212223313233
T0.0191 Å2-0.0089 Å20.0038 Å2-0.0233 Å2-0.018 Å2--0.0222 Å2
L0.3328 °2-0.1721 °20.1983 °2-0.7155 °2-0.6269 °2--0.9844 °2
S0.0089 Å °0.0128 Å °-0.0085 Å °-0.0382 Å °-0.0376 Å °-0.0196 Å °-0.0284 Å °0.0502 Å °0.0286 Å °

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