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- PDB-5klx: Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomera... -

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Basic information

Entry
Database: PDB / ID: 5klx
TitleCrystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110
ComponentsChimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / protein binding / BURKHOLDERIA / PEPTIDYL / PROLINE
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) / SUMOylation of SUMOylation proteins / 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 ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / 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 RNA binding proteins / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / peptidylprolyl isomerase / condensed nuclear chromosome / peptidyl-prolyl cis-trans isomerase activity / protein tag activity / protein folding / identical protein binding / metal ion 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 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-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-6UO / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / 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
AuthorsFox III, D. / Edwards, T.E.
CitationJournal: To Be Published
Title: Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110
Authors: Lorimer, D.D. / Fox III, D. / Seufert, F. / Edwards, T.E. / Holzgrabe, U.
History
DepositionJun 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase
B: Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase
C: Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase
D: Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,03013
Polymers92,0074
Non-polymers2,0239
Water2,504139
1
A: Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6345
Polymers23,0021
Non-polymers6324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4342
Polymers23,0021
Non-polymers4321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4342
Polymers23,0021
Non-polymers4321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5284
Polymers23,0021
Non-polymers5263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.890, 34.110, 119.920
Angle α, β, γ (deg.)90.00, 115.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase /


Mass: 23001.830 Da / Num. of mol.: 4
Fragment: UNP Q12306 residues 13-98,UNP Q3JK38 residues 2-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Burkholderia pseudomallei (strain 1710b) (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

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Non-polymers , 5 types, 148 molecules

#2: Chemical
ChemComp-6UO / 2-[(2~{S})-1-(phenylmethyl)sulfonylpiperidin-2-yl]carbonyloxyethyl pyridine-3-carboxylate


Mass: 432.490 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H24N2O6S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BUPSA.00130.A.D21 (CID4597, SMT TAG ON, BATCH 1264062) AT 10.37MG/ML (IN 25MM TRIS, PH8.0, 200MM NACL, 1% GLYCEROL, 1MM TCEP BUFFER) WAS INCUBATED WITH 2MM SF110_S (BSI5665). CRYSTALS WERE ...Details: BUPSA.00130.A.D21 (CID4597, SMT TAG ON, BATCH 1264062) AT 10.37MG/ML (IN 25MM TRIS, PH8.0, 200MM NACL, 1% GLYCEROL, 1MM TCEP BUFFER) WAS INCUBATED WITH 2MM SF110_S (BSI5665). CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR IFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND COMPLEX AND A SOLUTION CONTAINING 10% W/V PEG20,000, 20% V/V PEG MME 550, 0.03M MGCL2, 0.03M CACL2, 0.1M MES/IMIDAZOLE, PH6.5 (MORPHEUS A1). CRYSTAL TRACKING ID 273103A1, RVA0-10, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2016 / Details: BERYLLIUM LENSES
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 29732 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 47.15 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.99
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.26 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXDEV_2443refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3uf8

3uf8


Resolution: 2.45→37.79 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / Phase error: 28.11
RfactorNum. reflection% reflection
Rfree0.256 1486 5 %
Rwork0.198 --
obs0.201 29705 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.54 Å2
Refinement stepCycle: LAST / Resolution: 2.45→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 139 139 5426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075412
X-RAY DIFFRACTIONf_angle_d0.9167355
X-RAY DIFFRACTIONf_dihedral_angle_d15.5723126
X-RAY DIFFRACTIONf_chiral_restr0.052833
X-RAY DIFFRACTIONf_plane_restr0.005966
LS refinement shellResolution: 2.45→2.53 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.323 131 -
Rwork0.2435 2465 -
all-2596 -
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)
16.6778-3.2741-1.30867.5632.74366.18050.0935-0.41030.42990.1505-0.0282-0.6282-0.06360.595-0.1360.423-0.18010.20580.5684-0.01780.5177-10.0129-2.3164143.4776
29.5421-1.97496.61294.4109-4.81897.54480.59880.55940.1398-1.13320.12941.34370.00970.1717-0.59590.718-0.11730.0570.39120.10510.4513-14.2179-2.2188135.3233
30.26480.5652-0.93474.82710.47865.2834-0.20330.39610.2891-1.5289-0.28150.3288-0.07070.60210.1711.14820.04190.33820.59770.19580.5824-11.98076.8306134.2963
41.5193-0.47350.6446.43881.6784.93090.14850.32450.4797-1.1411-0.0132-1.1996-0.2910.7678-0.04680.6328-0.13450.23920.7920.0450.6903-4.65960.2711137.1415
53.40890.3160.61241.8686-0.13333.5308-0.05180.2912-0.0119-0.17170.0183-0.0486-0.04640.0480.03770.2436-0.0066-0.02140.1067-0.02310.1675-28.010221.0469148.1998
65.28770.06180.03845.3457-2.13873.821-0.4567-0.1579-0.02720.6030.71130.1064-0.4213-1.0536-0.24160.60880.25480.17450.97780.23020.6656-9.913217.2555101.5574
71.12651.49890.46032.9008-0.07860.5142-0.33910.2534-0.47650.35180.628-1.2833-0.3444-0.2154-0.35710.57890.28060.11441.0176-0.09330.8114-5.9219.3227104.8093
82.99160.21060.72172.53020.05662.910.04290.33710.07310.048-0.0647-0.30120.21970.98910.02110.31070.0485-0.01730.65470.08110.3299-25.9002-6.2596112.185
98.08940.24287.13712.3871-0.06169.4195-0.45860.1670.1705-0.00340.3056-0.16190.11450.50730.1130.2521-0.00490.05940.59610.04990.4814-28.8211-3.0377108.4185
107.62213.97620.98275.7587-0.84173.25290.0231-0.656-0.89120.5550.41540.9454-0.1241-0.5288-0.30680.4937-0.13570.25810.87330.12850.9085-67.4042-5.0412165.8352
114.56460.2684-0.55293.0953-1.8954.0787-0.0324-0.2991-0.21920.1403-0.00140.157-0.0892-0.64910.04750.2330.020.01930.3972-0.0850.3126-49.069-24.8687157.9827
123.0339-0.52860.25256.08932.90146.3933-0.0842-0.76760.67031.00660.28350.0707-0.2375-0.4868-0.18930.63950.1888-0.00660.7501-0.18720.4233-62.5824-15.1926133.1568
132.12510.2079-0.53272.12470.17411.8975-0.0003-0.0187-0.0344-0.021-0.05370.1005-0.2871-0.0480.03990.35670.0489-0.06940.314-0.02870.2367-48.88834.1293123.5324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -76 through -58 )A-76 - -58
2X-RAY DIFFRACTION2chain 'A' and (resid -57 through -43 )A-57 - -43
3X-RAY DIFFRACTION3chain 'A' and (resid -42 through -27 )A-42 - -27
4X-RAY DIFFRACTION4chain 'A' and (resid -26 through -6 )A-26 - -6
5X-RAY DIFFRACTION5chain 'A' and (resid -5 through 113 )A-5 - 113
6X-RAY DIFFRACTION6chain 'B' and (resid -76 through -51 )B-76 - -51
7X-RAY DIFFRACTION7chain 'B' and (resid -50 through 4 )B-50 - 4
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 92 )B5 - 92
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 113 )B93 - 113
10X-RAY DIFFRACTION10chain 'C' and (resid -75 through -6 )C-75 - -6
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 113 )C1 - 113
12X-RAY DIFFRACTION12chain 'D' and (resid -76 through -21 )D-76 - -21
13X-RAY DIFFRACTION13chain 'D' and (resid -20 through 113 )D-23 - 113

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