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

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Basic information

Entry
Database: PDB / ID: 4ggq
TitleCrystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with CJ40
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) / 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-861 / 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: 1.95 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 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_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
C: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
A: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
B: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
D: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,16011
Polymers92,0074
Non-polymers2,1537
Water7,638424
1
C: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5343
Polymers23,0021
Non-polymers5322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6404
Polymers23,0021
Non-polymers6383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4932
Polymers23,0021
Non-polymers4921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4932
Polymers23,0021
Non-polymers4921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.440, 76.150, 76.350
Angle α, β, γ (deg.)95.070, 90.130, 92.650
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: 23001.830 Da / Num. of mol.: 4 / Fragment: Q12306 residues 13-98, Q3JK38 residues 2-113
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-861 / 3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate


Mass: 491.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H33NO7S
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 424 / 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: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Internal tracking number 235051a1. Puck IBH5-4, Morpheus well A1. 10% PEG 20,000, 20% PEG MME550, 0.03M Divalent Catios (MgCl2, CaCl2), 0.1M MES/Imidazole pH 6.5, Direct Cryo. BupsA.00130.a. ...Details: Internal tracking number 235051a1. Puck IBH5-4, Morpheus well A1. 10% PEG 20,000, 20% PEG MME550, 0.03M Divalent Catios (MgCl2, CaCl2), 0.1M MES/Imidazole pH 6.5, Direct Cryo. BupsA.00130.a.D21, 20.00 mg/ml, CJ40 (EBSI2855), 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: 1.95→38.02 Å / Num. all: 56274 / Num. obs: 54575 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 34.152 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.95-20.5071.994773990195.8
2-2.060.3882.494163925196.2
2.06-2.120.312390413770196.2
2.12-2.180.2653.588673697196
2.18-2.250.2324.186183587196.7
2.25-2.330.1984.883943498196.8
2.33-2.420.1645.979973329196.9
2.42-2.520.1257.277743228197
2.52-2.630.1068.575993157197.3
2.63-2.760.091069832913197.4
2.76-2.910.06813.168912881197.5
2.91-3.080.0517.163572660197.2
3.08-3.30.03821.660422541198.2
3.3-3.560.0326.555482353197.9
3.56-3.90.02529.851092161197.3
3.9-4.360.0223545641950197.5
4.36-5.030.01937.438711716197.1
5.03-6.170.0234.933951453198.5
6.17-8.720.01935.927091156198.6
8.72-38.020.01544.51415610198.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.02 Å
Translation2.5 Å38.02 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: 1.95→38.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.649 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2786 5.1 %RANDOM
Rwork0.187 ---
all0.189 56274 --
obs0.189 54575 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.607 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.16 Å20.03 Å2
2---0.12 Å2-0.12 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 145 424 5967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195672
X-RAY DIFFRACTIONr_bond_other_d0.0070.023687
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9897698
X-RAY DIFFRACTIONr_angle_other_deg1.24139003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.94124.505222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43415830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8681527
X-RAY DIFFRACTIONr_chiral_restr0.090.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216455
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021144
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 177 -
Rwork0.278 3795 -
all-3972 -
obs--95.66 %
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)
13.5191-0.5304-0.09582.6116-0.37054.09560.00460.10860.1247-0.1459-0.0366-0.0222-0.02670.06520.0320.027-0.01160.00810.06340.00440.009-44.4006-27.6052-69.7345
21.4257-0.6013-0.44871.50420.2591.84410.0640.01710.0799-0.0987-0.0336-0.0236-0.1566-0.0286-0.03040.03610.0031-0.00020.06090.02110.0465-23.0383-16.9595-52.2166
36.21721.41810.1024.5835-0.35333.5688-0.06890.5399-0.6767-0.338-0.07020.4730.1737-0.19160.13910.2445-0.0084-0.11420.1589-0.17510.2786-25.6177-68.678-68.047
41.3520.23410.17211.9681-0.13111.94050.00740.09650.03120.02790.01540.05680.08340.0327-0.02280.0677-0.00490.02120.0078-0.00240.0684-47.1702-54.5569-52.6371
53.08430.4466-0.17182.6183-0.24053.33950.0063-0.1434-0.13090.0882-0.0378-0.0385-0.02820.09810.03150.04560.0163-0.01960.07320.010.016-27.0636-28.1061-14.0734
61.27220.35710.12231.3642-0.02081.5482-0.0090.0066-0.06260.0475-0.0328-0.00040.17880.020.04180.05450.00590.00380.0580.01330.0422-5.7289-38.5274-31.4224
75.7863-0.9386-2.17027.46891.85043.8107-0.0987-0.01240.13360.6427-0.16930.1895-0.0684-0.14240.2680.2564-0.00190.06790.0296-0.02490.0734-3.3506-63.151-13.8125
81.0309-0.2718-0.38312.35150.14932.27110.0812-0.04670.02650.0653-0.0364-0.0012-0.1288-0.0138-0.04480.058-0.00420.00390.00420.00560.0723-26.1675-77.1176-30.8799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-77 - -6
2X-RAY DIFFRACTION2A-5 - 113
3X-RAY DIFFRACTION3B-76 - -5
4X-RAY DIFFRACTION4B1 - 113
5X-RAY DIFFRACTION5C-77 - -6
6X-RAY DIFFRACTION6C-5 - 113
7X-RAY DIFFRACTION7D-76 - -7
8X-RAY DIFFRACTION8D-6 - 113

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