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

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Basic information

Entry
Database: PDB / ID: 4giv
TitleCrystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation D44G from Burkholderia pseudomallei complexed with CJ183
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 / SUMOylation of DNA replication proteins ...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 / 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 / identical protein binding / nucleus / metal ion binding
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 / 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 domain / FKBP-type peptidyl-prolyl cis-trans isomerase / 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-4GI / 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: 2.45 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
DepositionAug 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 2.0Jul 12, 2017Group: Advisory / Non-polymer description / Structure summary
Category: entity / pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Revision 2.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 2.2Feb 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
B: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8476
Polymers45,8882
Non-polymers9594
Water1,51384
1
A: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4694
Polymers22,9441
Non-polymers5263
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)23,3772
Polymers22,9441
Non-polymers4331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.420, 32.500, 151.380
Angle α, β, γ (deg.)90.000, 97.520, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-362-

HOH

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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-4GI / 3-(pyridin-3-yl)propyl (2S)-1-[(3-nitrophenyl)sulfonyl]piperidine-2-carboxylate


Mass: 433.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N3O6S
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Internal tracking number 232625a12. Puck IBH5-9, JCSG_A8 optimization screen. 50mM Ammonium Formate, 30% PEG3,350, 25% ethylene glycol cryo-protected. BupsA.00130.a.D214, 20.00 mg/ml, CJ183 ...Details: Internal tracking number 232625a12. Puck IBH5-9, JCSG_A8 optimization screen. 50mM Ammonium Formate, 30% PEG3,350, 25% ethylene glycol cryo-protected. BupsA.00130.a.D214, 20.00 mg/ml, CJ183 (EBSI2864), 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: 5.0.3 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2012
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 16468 / Num. obs: 16480 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 42.263 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.460.541480801209100
2.46-2.530.5024.38083118099.9
2.53-2.60.4345.17671110199.6
2.6-2.680.3985.679911148100
2.68-2.770.3226.874791049100
2.77-2.870.2727.97466104599.9
2.87-2.980.21110.173341011100
2.98-3.10.17311.66862949100
3.1-3.240.128157039967100
3.24-3.390.10417.5630586599.9
3.39-3.580.08321.76179856100
3.58-3.80.07124.5594481499.9
3.8-4.060.06127.25453759100
4.06-4.380.05331483668399.4
4.38-4.80.04534463066299.8
4.8-5.370.04633.1423261399.8
5.37-6.20.05729.23722520100
6.2-7.590.05131.23287465100
7.59-10.730.03838.12486369100
10.730.03838.2125120398.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.85 Å
Translation2.5 Å41.85 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: molecular replacement / Resolution: 2.45→41.85 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.904 / SU B: 15.569 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.496 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 790 5.1 %RANDOM
Rwork0.216 ---
all0.218 16468 --
obs0.218 15513 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.559 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å2-2.98 Å2
2---0.9 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.45→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 0 49 84 2838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192805
X-RAY DIFFRACTIONr_bond_other_d0.0010.021831
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9823802
X-RAY DIFFRACTIONr_angle_other_deg1.39234456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5825373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.90624.037109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26815401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4761516
X-RAY DIFFRACTIONr_chiral_restr0.080.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02578
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 56 -
Rwork0.296 1025 -
all-1081 -
obs--100 %
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)
12.6582-1.64321.22087.0022-3.09875.0708-0.05810.1353-0.0047-0.21780.09920.17720.093-0.0899-0.04110.0226-0.03180.00480.1665-0.05040.18720.9838-7.651268.5582
22.74655.20212.177810.31844.97796.447-0.45910.31420.1475-0.80650.3166-0.00560.09490.57470.14240.32620.00620.07310.5640.14030.46427.73271.167460.5331
32.79611.8879-0.29825.1659-0.68531.6558-0.03650.02060.26780.18360.07060.0303-0.1085-0.1676-0.03410.02040.01820.01730.1798-0.0070.24264.05340.963572.7934
41.3542-1.1382-0.21641.2676-0.16932.77140.16040.2180.0864-0.3888-0.18090.07570.07380.12180.02050.27570.0047-0.04760.24690.00820.2598-2.113215.421849.0893
52.56830.916-0.04982.3789-0.46112.6525-0.02030.11690.0016-0.35940.02280.05960.1638-0.1308-0.00260.23980.015-0.04430.207100.1981-7.061114.587750.7848
62.6836-1.28941.71974.0107-3.00182.55750.255-0.22020.35930.1567-0.15150.23220.0638-0.1109-0.10350.5904-0.0957-0.13710.334-0.01260.1997-24.875729.150712.9096
76.22250.5131-2.96491.8780.12641.48920.1235-0.4452-0.57560.2975-0.3158-0.34810.01430.17740.19220.73920.056-0.19810.35960.00450.2218-14.383221.856113.6296
80.25690.77-0.21722.6128-0.54120.4444-0.0212-0.00330.0153-0.3499-0.10.27510.2168-0.00840.12120.5937-0.0063-0.16160.2948-0.02710.1883-24.588718.4018.4803
93.17541.3009-0.40493.1247-0.73752.3473-0.23730.09020.2364-0.23040.0278-0.28440.12390.05310.20950.4613-0.0063-0.03730.17740.00970.0892-9.88956.615728.1966
104.6038-0.871-2.32282.41870.36784.3385-0.2908-0.0241-0.1684-0.15850.08160.32590.1657-0.22850.20920.3912-0.0096-0.07490.14990.00310.0598-15.31545.399831.4658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-78 - -44
2X-RAY DIFFRACTION2A-43 - -34
3X-RAY DIFFRACTION3A-33 - 0
4X-RAY DIFFRACTION4A1 - 71
5X-RAY DIFFRACTION5A72 - 113
6X-RAY DIFFRACTION6B-76 - -50
7X-RAY DIFFRACTION7B-49 - -37
8X-RAY DIFFRACTION8B-36 - 6
9X-RAY DIFFRACTION9B7 - 58
10X-RAY DIFFRACTION10B59 - 113

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