[English] 日本語
Yorodumi
- PDB-6o4a: CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o4a
TitleCRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355
ComponentsUbiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / PROTEIN BINDING / SSGCID / PEPTIDYL / PROLINE / SF355 / 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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of SUMOylation proteins / 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 / Ubiquitin family / Ubiquitin homologues ...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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-LLD / 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: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355
Authors: Iwasaki, J. / Lorimer, D.D. / Vivoli, M. / Harmer, N.J. / Kibble, E.A. / Peacock, C.S. / Abendroth, J. / Mayclin, S.J. / Dranow, D.M. / Pierce, P.G. / Fox III, D. / Lewis, M. / Bzdyl, N. / ...Authors: Iwasaki, J. / Lorimer, D.D. / Vivoli, M. / Harmer, N.J. / Kibble, E.A. / Peacock, C.S. / Abendroth, J. / Mayclin, S.J. / Dranow, D.M. / Pierce, P.G. / Fox III, D. / Lewis, M. / Bzdyl, N. / Kristensen, S. / Schmidberger, J.W. / Bond, C.B. / Seufert, F. / Schmitz, J. / Norville, I.H. / Myler, P.J. / Holzgrabe, U. / Sarkar-Tyson, M.
History
DepositionFeb 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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
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.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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
B: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
C: 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)93,81310
Polymers92,0074
Non-polymers1,8066
Water9,044502
1
A: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4733
Polymers23,0021
Non-polymers4722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4332
Polymers23,0021
Non-polymers4321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4733
Polymers23,0021
Non-polymers4722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4332
Polymers23,0021
Non-polymers4321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.820, 32.650, 178.190
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 23001.830 Da / Num. of mol.: 4
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
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-LLD / 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate


Mass: 431.505 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H25N3O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.2 %
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 SF355 (BSI5667). 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 SF355 (BSI5667). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing HamptonResearch PACT screen (B4): 25% PEG 1500, 100m MIB pH 7.0. The sample was cryoprotected with 15% ethylene glycol: Crystal tray ID 290655b4, puck ID PWP0-3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2016
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→44.55 Å / Num. obs: 42810 / % possible obs: 98.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.062 / Χ2: 1.02 / Net I/σ(I): 16.63 / Num. measured all: 136959
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 5 / Num. unique obs: 555 / CC1/2: 0.999 / Rrim(I) all: 0.025 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.12RC0_2798: ???)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BE4 model, 2 domains

Resolution: 2.1→44.55 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.26
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2031 4.75 %0
Rwork0.157 ---
obs0.159 42789 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.36 Å2 / Biso mean: 31.01 Å2 / Biso min: 8.34 Å2
Refinement stepCycle: final / Resolution: 2.1→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5625 0 122 508 6255
Biso mean--19.19 33.23 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075873
X-RAY DIFFRACTIONf_angle_d0.9257952
X-RAY DIFFRACTIONf_dihedral_angle_d16.933446
X-RAY DIFFRACTIONf_chiral_restr0.056878
X-RAY DIFFRACTIONf_plane_restr0.0061044
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2664 127 -
Rwork0.1885 2523 -
all-2650 -
obs--93 %
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)
13.1443-0.0567-1.70197.7088-0.74793.95950.13260.34070.0957-0.8542-0.1552-0.29140.00630.11030.05970.395-0.0111-0.02790.27680.00320.2091-61.6402-20.1494194.5173
22.4109-0.06120.47531.35420.09491.5467-0.00760.09060.0213-0.09770.0252-0.05230.08210.0444-0.01760.107-0.00190.01410.09620.01110.1214-62.0734-38.6766214.4643
31.69860.67640.46026.04870.7291.39370.0513-0.11940.10330.2177-0.18960.0386-0.1665-0.27670.16510.3660.0333-0.01750.3771-0.03590.154-68.2826-47.2644258.3539
42.70610.01010.76461.36720.10521.7164-0.0554-0.21180.03320.097-0.0343-0.01820.0004-0.03660.08670.1137-0.00010.00970.12110.01070.1079-63.6829-28.6065237.1703
54.6387-0.34341.64626.5286-0.81145.77530.0821-0.4432-0.00560.8021-0.1347-0.3515-0.0550.16220.06120.37590.00610.00060.2615-0.00640.1887-30.3806-70.3633251.0417
62.77060.0168-0.29881.33150.11461.5632-0.0051-0.09150.01710.10190.004-0.055-0.06710.0136-0.00420.1102-0.00290.00710.10320.01160.138-30.7435-52.1165230.943
74.1272-0.4673-0.5386.89310.39825.03750.07590.1666-0.0814-0.2069-0.31040.03610.4166-0.36640.19340.3316-0.02760.02770.3214-0.04260.1251-37.2625-41.6645186.8786
82.4931-0.1758-0.38771.75160.27561.8711-0.05820.2206-0.0204-0.1308-0.02-0.068-0.0396-0.0380.07730.1164-0.009-0.00010.13620.01610.1052-32.1145-61.9005207.3278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -77 through -6 )
2X-RAY DIFFRACTION2chain 'A' and (resid -5 through 113 )
3X-RAY DIFFRACTION3chain 'B' and (resid -77 through 2 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 113 )
5X-RAY DIFFRACTION5chain 'C' and (resid -77 through -6 )
6X-RAY DIFFRACTION6chain 'C' and (resid -5 through 113 )
7X-RAY DIFFRACTION7chain 'D' and (resid -77 through -5 )
8X-RAY DIFFRACTION8chain 'D' and (resid -4 through 113 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more