[English] 日本語
Yorodumi
- PDB-4o8t: Structure of sortase A C207A mutant from Streptococcus pneumoniae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o8t
TitleStructure of sortase A C207A mutant from Streptococcus pneumoniae
ComponentsSortase
KeywordsHYDROLASE / 8-stranded beta barrel / sortase-fold / cysteine transpeptidase
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis
Similarity search - Function
Sortase A / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsMisra, A. / Biswas, T. / Das, S. / Marathe, U. / Roy, R.P. / Ramakumar, S.
CitationJournal: To be Published
Title: Structure of sortase A C207A mutant from Streptococcus pneumoniae
Authors: Misra, A. / Biswas, T. / Das, S. / Marathe, U. / Roy, R.P. / Ramakumar, S.
History
DepositionDec 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sortase
B: Sortase
C: Sortase
D: Sortase
E: Sortase
F: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5597
Polymers126,4676
Non-polymers921
Water4,216234
1
A: Sortase
B: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2483
Polymers42,1562
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-66 kcal/mol
Surface area15370 Å2
MethodPISA
2
C: Sortase
D: Sortase


Theoretical massNumber of molelcules
Total (without water)42,1562
Polymers42,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11270 Å2
ΔGint-61 kcal/mol
Surface area16110 Å2
MethodPISA
3
E: Sortase
F: Sortase


Theoretical massNumber of molelcules
Total (without water)42,1562
Polymers42,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-64 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.570, 113.330, 81.340
Angle α, β, γ (deg.)90.000, 90.800, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a dimer. There are 3 such biological units (dimers) in the asymmetric unit (One dimer is formed by chains A & B, the second one by chains C & D and the third dimer by chains E & F).

-
Components

#1: Protein
Sortase


Mass: 21077.781 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, UNP residues 82-247 / Mutation: C207A, T176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-255 / R6 / Gene: sortase A, spr1098, srtA / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8DPM3, sortase A
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.83 Å3/Da / Density % sol: 56.61 % / Mosaicity: 0.93 °
Crystal growTemperature: 293 K / Method: microbatch, under oil / pH: 7
Details: 0.2M tri-ammonium citrate pH 7.0, 20%(w/v) PEG3350, 1.0M Guanidine hydrochloride, Microbatch, Under oil, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9772 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 2.48→91.598 Å / Num. all: 50010 / Num. obs: 50010 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rsym value: 0.092 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.48-2.614.10.5471.42947372450.3110.5472.599.7
2.61-2.774.20.38922865368880.2180.3893.6100
2.77-2.964.20.262.92704264750.1460.265.1100
2.96-3.24.20.1574.72530360420.0880.1577.8100
3.2-3.514.20.0967.62322355420.0540.09611.8100
3.51-3.924.20.06111.12117750440.0340.06116.9100
3.92-4.534.20.04713.11869544600.0260.04720.9100
4.53-5.554.20.05211.41568837450.0290.05221.3100
5.55-7.844.10.06681204629360.0370.06618.8100
7.84-47.15140.03811.4660116330.0220.03823.399.6

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FN5

3fn5


Resolution: 2.48→46.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2115 / WRfactor Rwork: 0.1724 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8392 / SU B: 16.306 / SU ML: 0.179 / SU R Cruickshank DPI: 0.3481 / SU Rfree: 0.2357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.348 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 2535 5.1 %RANDOM
Rwork0.1824 ---
obs0.1846 49987 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.71 Å2 / Biso mean: 44.8676 Å2 / Biso min: 13.05 Å2
Baniso -1Baniso -2Baniso -3
1--3.94 Å20 Å2-1.05 Å2
2--1.45 Å20 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.48→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8012 0 6 234 8252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198161
X-RAY DIFFRACTIONr_bond_other_d0.0010.027730
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.96711052
X-RAY DIFFRACTIONr_angle_other_deg0.869317805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87551021
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14425.707382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.746151425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0671530
X-RAY DIFFRACTIONr_chiral_restr0.0710.21243
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021760
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 204 -
Rwork0.284 3473 -
all-3677 -
obs--99.41 %
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)
12.2728-1.327-1.40621.21540.56152.2585-0.0476-0.15220.053-0.14730.0119-0.09770.0924-0.07910.03570.4777-0.05110.08610.2577-0.01980.02188.8877-42.132424.142
21.82970.12220.68130.8050.8641.9405-0.0641-0.089-0.21630.0556-0.0060.04660.0278-0.10510.07010.39550.01990.05870.2665-0.03860.0537-23.1744-41.075912.0686
32.52250.4703-0.07951.17790.64011.6793-0.1493-0.0126-0.20080.0246-0.04280.04190.07930.03430.1920.46130.0360.08610.2691-0.02380.0504-19.5292-41.411711.5948
42.4023-0.3769-1.21420.67560.00871.87840.0216-0.3667-0.027-0.0270.1292-0.0769-0.0116-0.0184-0.15070.41680.00650.03650.3201-0.02620.05359.8428-40.395428.3747
50.457-1.0333-0.21932.7673-0.11071.1720.1317-0.08110.0692-0.19850.1338-0.0896-0.1782-0.05-0.26550.4489-0.05710.11560.22750.05690.1405-53.2064-10.431714.4681
60.8702-0.66880.18911.82070.19780.8598-0.07490.082-0.0310.25030.24420.22370.05730.1396-0.16930.44440.0490.07180.2049-0.02970.1324-21.4476-13.964827.9912
70.27080.26980.00392.96550.72641.1068-0.01120.08770.04680.1890.14870.21990.03670.104-0.13750.42090.0440.11480.2095-0.02510.1007-23.2412-9.884227.1792
82.5305-0.01250.08311.88260.23830.39550.2099-0.1389-0.2106-0.2224-0.00920.022-0.12970.0187-0.20070.4563-0.02670.08070.18670.00270.1273-55.3819-14.764313.3344
91.82040.89830.0141.2847-0.73210.9720.03920.21110.12020.1544-0.00650.19060.00230.1863-0.03270.42440.01980.10380.2547-0.03490.0705-9.1414.930117.2794
101.84-0.57051.03350.59480.14111.7972-0.00030.13020.02270.0687-0.18120.0295-0.11270.21440.18150.3571-0.0680.08580.30750.14350.132523.695813.59825.2792
111.2668-0.45910.75241.3288-1.0461.5217-0.0017-0.0941-0.04470.0062-0.11330.03280.08320.04170.11510.40250.00110.11380.27720.10580.107220.423811.020627.6192
123.40150.11120.60941.3158-0.21261.0941-0.05230.44870.06580.040.1120.16240.02650.1119-0.05970.3556-0.04780.06720.31420.00670.0349-10.184716.307213.3466
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 188
2X-RAY DIFFRACTION2A189 - 247
3X-RAY DIFFRACTION3B91 - 189
4X-RAY DIFFRACTION4B190 - 247
5X-RAY DIFFRACTION5C73 - 189
6X-RAY DIFFRACTION6C190 - 247
7X-RAY DIFFRACTION7D74 - 188
8X-RAY DIFFRACTION8D189 - 247
9X-RAY DIFFRACTION9E74 - 185
10X-RAY DIFFRACTION10E186 - 247
11X-RAY DIFFRACTION11F74 - 192
12X-RAY DIFFRACTION12F193 - 247

+
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