[English] 日本語
Yorodumi
- PDB-3s3u: Crystal Structure of Uncleaved ThnT T282C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s3u
TitleCrystal Structure of Uncleaved ThnT T282C
Componentscysteine transferase
KeywordsTRANSFERASE / autoproteolytic / carbapenem / biosynthesis / DOM-fold / amidohydrolase
Function / homology
Function and homology information


aminopeptidase activity / transferase activity / identical protein binding
Similarity search - Function
Peptidase S58, DmpA / Peptidase family S58 / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative cysteine transferase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsSchildbach, J.F. / Wright, N.T. / Buller, A.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Insights into cis-autoproteolysis reveal a reactive state formed through conformational rearrangement.
Authors: Buller, A.R. / Freeman, M.F. / Wright, N.T. / Schildbach, J.F. / Townsend, C.A.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cysteine transferase
B: cysteine transferase


Theoretical massNumber of molelcules
Total (without water)82,7482
Polymers82,7482
Non-polymers00
Water12,827712
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: cysteine transferase
B: cysteine transferase

A: cysteine transferase
B: cysteine transferase


Theoretical massNumber of molelcules
Total (without water)165,4964
Polymers165,4964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area14320 Å2
ΔGint-46 kcal/mol
Surface area42880 Å2
MethodPISA
3
A: cysteine transferase

A: cysteine transferase


Theoretical massNumber of molelcules
Total (without water)82,7482
Polymers82,7482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3380 Å2
ΔGint-17 kcal/mol
Surface area25460 Å2
MethodPISA
4
B: cysteine transferase

B: cysteine transferase


Theoretical massNumber of molelcules
Total (without water)82,7482
Polymers82,7482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3420 Å2
ΔGint-18 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.534, 68.651, 73.761
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein cysteine transferase


Mass: 41374.117 Da / Num. of mol.: 2 / Mutation: T282C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (bacteria) / Gene: ThnT / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaII(DE3) / References: UniProt: Q83XN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1542.79
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, sitting drop7.512%PEG3350, 0.5M NaAcetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
2982vapor diffusion, sitting drop7.512%PEG3350, 0.5M NaAcetate, 200uM EtHgPhosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.80011,0.7336,1.00961
SYNCHROTRONSSRL BL12-220.7336,1.00961
Detector
TypeIDDetectorDate
RAYONIX MX-3251CCDMay 30, 2009
RAYONIX MX-3252CCDMay 30, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Liquid nitrogen-cooled double crystalSINGLE WAVELENGTHMx-ray1
2Liquid nitrogen-cooled double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.800111
20.73361
31.009611
ReflectionRedundancy: 7.3 % / Av σ(I) over netI: 31.11 / Number: 520220 / Rmerge(I) obs: 0.045 / Χ2: 1.72 / D res high: 1.76 Å / D res low: 50 Å / Num. obs: 70958 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.785098.410.0272.0336.8
3.794.7810010.0281.9657.2
3.313.7910010.0322.0757.3
3.013.3110010.042.347.3
2.793.0110010.0442.1667.4
2.632.7910010.0471.8847.4
2.52.6310010.0521.8257.4
2.392.510010.0591.8267.5
2.32.3910010.0671.887.4
2.222.310010.0771.8117.4
2.152.2210010.0811.6367.4
2.092.1510010.0941.5667.4
2.032.0910010.1061.4947.4
1.982.0310010.1251.4857.4
1.941.9810010.1611.4717.4
1.91.9410010.1841.4417.4
1.861.910010.2151.3947.4
1.821.8610010.2681.3777.4
1.791.8210010.3171.3637.2
1.761.7999.810.351.3516.8
ReflectionResolution: 1.6→50 Å / Num. obs: 89654 / % possible obs: 94.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.058 / Χ2: 1.06 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.653.70.66453070.941,268.3
1.65-1.74.70.57661240.9641,278.7
1.7-1.765.50.50369630.9741,288.6
1.76-1.836.30.42376411.0041,298
1.83-1.917.10.32978271.0541,299.9
1.91-2.027.50.23378811.0941,2100
2.02-2.147.50.15378631.1041,2100
2.14-2.317.50.10978751.11,2100
2.31-2.547.50.08279161.1031,2100
2.54-2.917.50.05679231.0161,2100
2.91-3.667.50.03380211.0631,2100
3.66-507.20.02383131.121,299.7

-
Phasing

PhasingMethod: MAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 72721
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.48-10022.50.643551
6.71-9.4822.90.819904
5.48-6.7124.20.8351158
4.74-5.4823.40.8561339
4.24-4.7421.90.8611507
3.87-4.2422.20.8421643
3.58-3.8721.90.8491801
3.35-3.5822.20.8421907
3.16-3.3524.30.8312030
3-3.16260.8212138
2.86-326.70.8142251
2.74-2.8627.40.8232321
2.63-2.7428.40.8172458
2.53-2.6327.70.832521
2.45-2.5329.50.8242624
2.37-2.4527.90.8222680
2.3-2.3727.30.8282794
2.24-2.327.10.8272872
2.18-2.2428.60.8232942
2.12-2.18270.8283031
2.07-2.1227.50.8163096
2.02-2.0728.10.8193171
1.98-2.0228.50.813223
1.94-1.9829.40.7973313
1.9-1.9429.70.7953380
1.86-1.930.30.7773427
1.83-1.8633.90.7583506
1.79-1.8334.60.7383592
1.75-1.7940.30.7114541

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→39.54 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1808 / WRfactor Rwork: 0.1466 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8859 / SU B: 3.555 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0814 / SU Rfree: 0.0837 / Cross valid method: THROUGHOUT / σ(F): 1.3 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 4524 5.1 %RANDOM
Rwork0.1578 ---
obs0.1595 84968 94.43 %-
all-94877 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.3 Å2 / Biso mean: 24.417 Å2 / Biso min: 3.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--0.73 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4992 0 0 712 5704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215321
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9647323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.575781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14922.103195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11515694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6211557
X-RAY DIFFRACTIONr_chiral_restr0.130.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0214187
X-RAY DIFFRACTIONr_mcbond_it1.5841.53684
X-RAY DIFFRACTIONr_mcangle_it2.49625832
X-RAY DIFFRACTIONr_scbond_it3.43431637
X-RAY DIFFRACTIONr_scangle_it5.2014.51471
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 235 -
Rwork0.336 4407 -
all-4642 -
obs--67.15 %
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)
11.0081-0.14050.16890.4456-0.04910.52710.00440.0119-0.06340.00170.0113-0.01940.05310.0497-0.01570.03770.0010.00220.0688-0.01970.04116.00526.049-3.252
21.142-0.1026-0.24360.27340.03740.8338-0.0566-0.22240.05320.0270.0565-0.0503-0.02950.10880.00010.03890.0347-0.01860.1414-0.03750.017217.63135.85427.406
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 398
2X-RAY DIFFRACTION2B25 - 397

+
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