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- PDB-4g50: Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isome... -

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Basic information

Entry
Database: PDB / ID: 4g50
TitleCrystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation D44G from Burkholderia pseudomallei complexed with CJ168
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 / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / 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 / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / 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
Chem-861 / FORMIC ACID / 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: 1.75 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
DepositionJul 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 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
B: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,17910
Polymers45,8882
Non-polymers1,2918
Water5,855325
1
A: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5274
Polymers22,9441
Non-polymers5843
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)23,6526
Polymers22,9441
Non-polymers7085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.630, 35.110, 75.150
Angle α, β, γ (deg.)91.540, 99.900, 97.230
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 22943.793 Da / Num. of mol.: 2 / Fragment: Q12306 residues 13-98, Q3JK38 residues 2-113 / Mutation: D44G
Source method: isolated from a genetically manipulated source
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-861 / 3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate


Mass: 491.597 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H33NO7S
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 1.89 Å3/Da / Density % sol: 34.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Internal tracking number 233897a9. Puck VKT6-9, JCSG_A8 optimization. 50mM Ammonium formate, 24.55% PEG 3,350, 10% ethylene glycol. BupsA.00130.a.D214, 20.00 mg/ml, CJ168 (EBSI2861), pH 7.5, ...Details: Internal tracking number 233897a9. Puck VKT6-9, JCSG_A8 optimization. 50mM Ammonium formate, 24.55% PEG 3,350, 10% ethylene glycol. BupsA.00130.a.D214, 20.00 mg/ml, CJ168 (EBSI2861), pH 7.5, vapor diffusion, sitting drop, temperature 295K

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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: May 26, 2012
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: 1.75→37 Å / Num. all: 33838 / Num. obs: 32845 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 25.712 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.44
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.75-1.80.522.577072356195.5
1.8-1.840.432378452380196.2
1.84-1.90.33474602268195.6
1.9-1.960.2315.472822226196.7
1.96-2.020.1916.669712122196.4
2.02-2.090.158.470732149196.9
2.09-2.170.1251065872003196.7
2.17-2.260.10811.563931955197.1
2.26-2.360.09412.861111874197.7
2.36-2.470.07315.658451788197.4
2.47-2.610.06118.155301690197.7
2.61-2.770.0552053271631198.2
2.77-2.960.0432549501525197.6
2.96-3.20.03430.546101428198
3.2-3.50.02836.541941309198.1
3.5-3.910.02641.236551155197.5
3.91-4.520.02345.132251036196.9
4.52-5.530.02147.42913888199.1
5.53-7.830.02144.12249683199
7.83-370.01852.51258379199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 4FN2

4fn2


Resolution: 1.75→37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.108 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1662 5.1 %RANDOM
Rwork0.17 ---
all0.172 33838 --
obs0.172 32845 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å21.03 Å20.87 Å2
2--0.16 Å2-0.09 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 88 325 3265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193025
X-RAY DIFFRACTIONr_bond_other_d0.0070.022833
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9894092
X-RAY DIFFRACTIONr_angle_other_deg1.07136510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12324.394132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51215481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5871520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023495
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02681
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 94 -
Rwork0.242 2261 -
all-2355 -
obs--95.46 %
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)
10.2512-0.26530.01761.65610.13750.1449-0.01660.06590.0021-0.0479-0.0267-0.02130.0489-0.0190.04320.0442-0.0160.0180.026-0.01060.015810.557317.691449.1084
20.74550.0313-0.36360.5410.05380.5601-0.038-0.02090.0353-0.01170.0315-0.05310.02010.02830.00650.0067-0.0027-0.0060.00540.00080.016222.4992-0.8666.8389
30.2479-0.11770.25251.87660.05660.29710.0112-0.01820.02950.0576-0.07390.05580.02210.00630.06270.02360.00990.01550.05550.02250.023821.70592.463430.0901
40.73470.1424-0.09090.4365-0.09190.8904-0.0294-0.04140.04750.01750.03930.0243-0.0252-0.0751-0.00990.00890.0074-0.00210.0150.00140.008616.0443-16.593112.4477
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-77 - 1
2X-RAY DIFFRACTION2A2 - 113
3X-RAY DIFFRACTION3B-76 - 1
4X-RAY DIFFRACTION4B2 - 113

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