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- PDB-3vaw: Crystal structure of a smt fusion peptidyl-prolyl cis-trans isome... -

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Basic information

Entry
Database: PDB / ID: 3vaw
TitleCrystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase with surface mutation v3i from burkholderia pseudomallei complexed with fk506
ComponentsUbiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
KeywordsIsomerase / PROTEIN BINDING/INHIBITOR / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / PROTEIN BINDING / PROTEIN BINDING-INHIBITOR complex
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 / Resolution: 1.55 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
DepositionDec 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Other
Revision 1.3May 31, 2017Group: Structure summary
Revision 1.4Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.5Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.940, 31.380, 81.260
Angle α, β, γ (deg.)90.000, 95.030, 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 13-99, Q3JK38 RESIDUES 2-113 / Mutation: V3I,V3I
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Burkholderia pseudomallei (bacteria)
Strain: ATCC 204508 / S288c, 1710b / Gene: SMT3, YDR510W, D9719.15, BURPS1710b_A0907 / 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.: 154 / 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: 1.71 Å3/Da / Density % sol: 27.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Internal tracking number 226593. PACT well H3. 0.2M Sodium Iodide, 0.1M Bis-Tris Propane, pH 8.5, 20.0% w/v PEG3350, 30% PEG400 Cryo. BupsA.00130.a.D24 PD00194 19.6mg/ml., vapor diffusion, ...Details: Internal tracking number 226593. PACT well H3. 0.2M Sodium Iodide, 0.1M Bis-Tris Propane, pH 8.5, 20.0% w/v PEG3350, 30% PEG400 Cryo. BupsA.00130.a.D24 PD00194 19.6mg/ml., 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 QUANTUM 315r / Detector: CCD / Date: Nov 17, 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: 1.55→40.47 Å / Num. all: 22924 / Num. obs: 22306 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.88 % / Biso Wilson estimate: 19.899 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 24.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.55-1.590.1514.82169117070.5
1.59-1.630.167.15329162396.4
1.63-1.680.1369.461581548100
1.68-1.730.11411.26406156699.9
1.73-1.790.09313.76114148199.9
1.79-1.850.07915.86028146699.9
1.85-1.920.06419.157211394100
1.92-20.05235608135999.9
2-2.090.04525.85366130899.9
2.09-2.190.0428.95066123199.9
2.19-2.310.03730.24819117199.7
2.31-2.450.03333.44595112499.6
2.45-2.620.03135.64277105599.5
2.62-2.830.02938.4394797399.6
2.83-3.10.02940.8371091799.6
3.1-3.470.02744.7323182199.6
3.47-40.02547.1283672699.6
4-4.90.02349238662499
4.9-6.930.02448.4187348199.4
6.930.02348.496726891.2

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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
RefinementMethod to determine structure: molecular replacement
Starting model: pdb entry 3uqa

3uqa


Resolution: 1.55→40.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.519 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.088 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1148 5.1 %RANDOM
Rwork0.164 ---
all0.166 22924 --
obs0.166 22298 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.153 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-0.15 Å2
2---0.08 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 57 154 1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191530
X-RAY DIFFRACTIONr_bond_other_d0.0010.021041
X-RAY DIFFRACTIONr_angle_refined_deg1.582.0092082
X-RAY DIFFRACTIONr_angle_other_deg0.87132547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1152465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29115249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3181511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02307
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 71 -
Rwork0.23 1076 -
all-1147 -
obs--70.07 %
Refinement TLS params.Method: refined / Origin x: 1.5402 Å / Origin y: 0.7207 Å / Origin z: 20.748 Å
111213212223313233
T0.0116 Å20.0009 Å20.0053 Å2-0.0194 Å2-0.0017 Å2--0.0164 Å2
L0.0168 °2-0.0894 °20.0108 °2-0.5275 °2-0.1283 °2--0.236 °2
S0.0096 Å °-0.0008 Å °0.0025 Å °-0.0633 Å °-0.0087 Å °-0.0284 Å °-0.0045 Å °-0.014 Å °-0.001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-77 - 1
2X-RAY DIFFRACTION1A2 - 113

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