[English] 日本語
Yorodumi
- PDB-4d70: Structural, biophysical and biochemical analyses of a Clostridium... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d70
TitleStructural, biophysical and biochemical analyses of a Clostridium perfringens Sortase D5 transpeptidase
ComponentsSORTASE FAMILY PROTEIN
KeywordsHYDROLASE
Function / homology
Function and homology information


Sortase D, type 2 / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Sortase family protein / Class D sortase
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSuryadinata, R. / Seabrook, S. / Adams, T.E. / Nuttall, S.D. / Peat, T.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural and Biochemical Analyses of a Clostridium Perfringens Sortase D Transpeptidase
Authors: Suryadinata, R. / Seabrook, S.A. / Adams, T.E. / Nuttall, S.D. / Peat, T.S.
History
DepositionNov 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SORTASE FAMILY PROTEIN
B: SORTASE FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,8832
Polymers41,8832
Non-polymers00
Water1,71195
1
A: SORTASE FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)20,9421
Polymers20,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SORTASE FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)20,9421
Polymers20,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.776, 65.582, 68.057
Angle α, β, γ (deg.)90.00, 93.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A27 - 186
2010B27 - 186

-
Components

#1: Protein SORTASE FAMILY PROTEIN / SORTASE


Mass: 20941.508 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 23-187
Source method: isolated from a genetically manipulated source
Details: THE FIRST 22 AMINO ACIDS WERE REMOVED AND A HIS-TAG WAS ENGINEERED AT THE N-TERMINAL DOMAIN TO AID IN PURIFICATION.
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0TUL5, UniProt: Q8XNW0*PLUS, sortase A
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 22 AMINO ACIDS WERE REMOVED AND REPLACED WITH A N-TERMINAL HIS-TAG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.9 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 5.5
Details: THE PROTEIN CONCENTRATION WAS 20 MG/ML AND THE RESERVOIR CONDITIONS WERE 0.2M AMMONIUM ACETATE, 25% PEG 3350, 0.1M BIS-TRIS CHLORIDE AT PH 5.5 AND INCUBATED AT 8C.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9191
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 1.99→47.2 Å / Num. obs: 23533 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 1.99→2.09 Å / Redundancy: 7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.2 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G66

3g66


Resolution: 1.99→67.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.059 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21335 1214 5.2 %RANDOM
Rwork0.17569 ---
obs0.17769 22304 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.509 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20.4 Å2
2---0.85 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.99→67.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 0 95 2621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192630
X-RAY DIFFRACTIONr_bond_other_d0.0060.022530
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9563556
X-RAY DIFFRACTIONr_angle_other_deg1.22735860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.91726.842133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05315509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.386158
X-RAY DIFFRACTIONr_chiral_restr0.110.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023034
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02554
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5263.8561318
X-RAY DIFFRACTIONr_mcbond_other3.5273.8551317
X-RAY DIFFRACTIONr_mcangle_it4.4746.4551658
X-RAY DIFFRACTIONr_mcangle_other4.4746.4561659
X-RAY DIFFRACTIONr_scbond_it5.164.671312
X-RAY DIFFRACTIONr_scbond_other5.1584.671313
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4377.5061899
X-RAY DIFFRACTIONr_long_range_B_refined8.3316.41611291
X-RAY DIFFRACTIONr_long_range_B_other8.32216.411249
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9552 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.986→2.037 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 83 -
Rwork0.245 1568 -
obs--94.18 %
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)
10.8071-0.06730.35830.678-0.03791.1391-0.04280.20690.0271-0.05820.12660.00240.07080.0043-0.08380.0258-0.0344-0.00580.09180.01520.012715.9715.7717.5421
21.0044-0.31230.28510.7304-0.12330.37090.0442-0.1391-0.02090.0563-0.02940.0418-0.0261-0.0046-0.01480.0192-0.01260.01870.04060.01190.044335.100313.229938.0139
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 186
2X-RAY DIFFRACTION2B27 - 186

+
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