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- PDB-3uf8: Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isome... -

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Basic information

Entry
Database: PDB / ID: 3uf8
TitleCrystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with a G95A surface mutation from Burkholderia pseudomallei complexed with FK506
ComponentsUbiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
KeywordsIsomerase / protein binding / SSGCID / 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 / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / 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, molecular replacement / molecular replacement / Resolution: 1.5 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
DepositionOct 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Other / Structure summary
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Mar 19, 2014Group: Other
Revision 1.4Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)23,8202
Polymers23,0161
Non-polymers8041
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.400, 32.770, 76.990
Angle α, β, γ (deg.)90.000, 90.590, 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: 23015.857 Da / Num. of mol.: 1 / Fragment: Q12306 residues 13-98, Q3JK38 residues 2-113 / Mutation: G95A
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.: 263 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE -95 TO 1 IS PART OF THE SOLUBILITY AND PURIFICATION TAG THAT WAS NOT REMOVED

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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: 38.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Internal tracking number 226425. JCSG well A8. 0.2M Ammonium Formate, 20.0% w/v PEG3500, PEG400 Cryo. BupsA.00130.a.D242 PD00198 21.4mg/ml, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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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 Q315R / 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: 1.5→50 Å / Num. all: 29484 / Num. obs: 29417 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.03 % / Biso Wilson estimate: 19.986 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 23.06
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.540.3014.786422145199.9
1.54-1.580.2375.885592135199.9
1.58-1.630.2026.882112035199.8
1.63-1.680.1757.979701977199.9
1.68-1.730.1419.778151931199.8
1.73-1.790.1121275011852199.9
1.79-1.860.09214.273821812199.9
1.86-1.940.07218.170931752199.9
1.94-2.020.05522.768431679199.9
2.02-2.120.04526.764281578199.9
2.12-2.240.0429.561671517199.9
2.24-2.370.03731.958481439199.9
2.37-2.540.03535.155081358199.9
2.54-2.740.03138.551181268199.7
2.74-30.02843.146741167199.7
3-3.350.02450.241891064199.6
3.35-3.870.0255.33565919199.7
3.87-4.740.01860.23301815199.8
4.74-6.710.01858.22490627199.8
6.71-500.01758.41297347193

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.25 Å
Translation2.5 Å19.25 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: molecular replacement, molecular replacement
Resolution: 1.5→17.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.502 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1495 5.1 %RANDOM
Rwork0.156 ---
all0.158 29484 --
obs0.158 29406 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: 15.238 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-0.28 Å2
2---0.36 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.5→17.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 57 263 1766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021598
X-RAY DIFFRACTIONr_bond_other_d0.0020.021081
X-RAY DIFFRACTIONr_angle_refined_deg1.532.0062180
X-RAY DIFFRACTIONr_angle_other_deg0.87432662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01725.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33315262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.444158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 114 -
Rwork0.187 1927 -
all-2041 -
obs-8642 99.85 %
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)
11.0631-0.16750.03591.4452-0.4451.29580.00110.0230.0189-0.0003-0.0395-0.18140.00020.1580.03840.00640.0007-0.00070.0247-0.00060.026829.3408-6.706566.8824
21.0666-0.5919-0.50451.13630.40951.7443-0.0172-0.06190.07580.01120.0084-0.1023-0.02040.10840.00880.0085-0.00160.00080.0160.00030.029425.4252-3.608769.4633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 92
2X-RAY DIFFRACTION2A93 - 113

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