[English] 日本語
Yorodumi
- PDB-5uus: SrtF sortase from Corynebacterium diphtheriae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uus
TitleSrtF sortase from Corynebacterium diphtheriae
ComponentsPossible sortase-like protein
KeywordsHYDROLASE / sortase / structural genomics / IDP58950 / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologySortase E / Sortase family / Sortase domain superfamily / Sortase domain / membrane => GO:0016020 / hydrolase activity / ACETATE ION / FORMIC ACID / Possible sortase-like protein
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsOsipiuk, J. / Gornicki, P. / Ton-That, H. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: to be published
Title: SrtF sortase from Corynebacterium diphtheriae
Authors: Osipiuk, J. / Gornicki, P. / Ton-That, H. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Possible sortase-like protein
B: Possible sortase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,98913
Polymers50,1572
Non-polymers83211
Water2,450136
1
A: Possible sortase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5187
Polymers25,0791
Non-polymers4396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Possible sortase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4726
Polymers25,0791
Non-polymers3935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.990, 69.990, 237.292
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Possible sortase-like protein


Mass: 25078.727 Da / Num. of mol.: 2 / Fragment: UNP residues 48-273 / Mutation: 47 N-termianal residues were deleted
Source method: isolated from a genetically manipulated source
Details: 3 N-terminal residues (SNA) are cloning artifacts
Source: (gene. exp.) Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis) (bacteria)
Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: DIP2272 / Plasmid: pMCSG7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6NEK1

-
Non-polymers , 6 types, 147 molecules

#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Sodium formate; 0.1M Ammonium acetate; 0.1M Sodium citrate tribasic dihydrate; 0.1M Sodium potassium tartrate tetrahydrate; 0.1M Sodium oxamate; 0.1M Tris-BICINE buffer; 12.5% MPD; 12. ...Details: 0.1M Sodium formate; 0.1M Ammonium acetate; 0.1M Sodium citrate tribasic dihydrate; 0.1M Sodium potassium tartrate tetrahydrate; 0.1M Sodium oxamate; 0.1M Tris-BICINE buffer; 12.5% MPD; 12.5% PEG 1000; 12.5% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 13, 2016
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.02→42.396 Å / Num. obs: 45279 / % possible obs: 99.7 % / Redundancy: 9 % / Biso Wilson estimate: 42.44 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.024 / Rrim(I) all: 0.074 / Χ2: 1.178 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.02-2.054.30.5632.110.7040.2880.6370.66496.9
2.05-2.095.80.5180.8290.2280.5690.67398
2.09-2.137.20.5270.830.2070.5680.67699.9
2.13-2.188.40.4440.8930.1610.4730.687100
2.18-2.229.10.3560.9390.1240.3780.72100
2.22-2.278.90.3120.9470.110.3320.751100
2.27-2.339.30.2820.960.0960.2990.76599.9
2.33-2.3910.20.2520.970.0820.2650.779100
2.39-2.4710.20.2210.9780.0720.2330.807100
2.47-2.54100.1850.980.0610.1950.882100
2.54-2.649.80.1530.9890.0510.1620.935100
2.64-2.749.60.1320.9890.0440.1390.943100
2.74-2.879.20.1070.9930.0360.1131.06899.9
2.87-3.0210.30.0960.9940.0310.1011.199100
3.02-3.2110.10.0820.9950.0270.0861.287100
3.21-3.459.90.0680.9960.0230.0721.467100
3.45-3.89.20.0610.9970.0210.0641.78799.9
3.8-4.3510.20.0550.9980.0180.0581.897100
4.35-5.489.30.0520.9980.0180.0552.36999.7
5.48-42.3969.20.0540.9980.0180.0572.2599.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w1k

2w1k


Resolution: 2.02→42.396 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.92
RfactorNum. reflection% reflection
Rfree0.1906 2129 4.71 %
Rwork0.1642 --
obs0.1654 45201 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.49 Å2 / Biso mean: 50.6721 Å2 / Biso min: 27.01 Å2
Refinement stepCycle: final / Resolution: 2.02→42.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 53 136 3377
Biso mean--61.78 50.32 -
Num. residues----413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113320
X-RAY DIFFRACTIONf_angle_d1.2284503
X-RAY DIFFRACTIONf_chiral_restr0.057475
X-RAY DIFFRACTIONf_plane_restr0.007613
X-RAY DIFFRACTIONf_dihedral_angle_d14.8521222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0202-2.06720.3061120.23352765287797
2.0672-2.11890.23291710.20812773294499
2.1189-2.17620.26071520.195528112963100
2.1762-2.24020.19351200.170528462966100
2.2402-2.31250.19761360.18528502986100
2.3125-2.39510.25851350.19128092944100
2.3951-2.4910.22961300.195228933023100
2.491-2.60440.24851570.188128473004100
2.6044-2.74170.21941400.194528322972100
2.7417-2.91340.21771360.18529053041100
2.9134-3.13830.22891510.190328643015100
3.1383-3.4540.20341520.169928773029100
3.454-3.95350.18561380.141429333071100
3.9535-4.97970.12291520.129729453097100
4.9797-42.40580.18211470.157731223269100
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)
10.88350.2176-0.4305-0.0908-0.17840.6361-0.32630.34640.1487-0.05460.1958-0.0656-0.0061-0.1601-0.00010.3409-0.0442-0.01150.59010.06720.398256.534728.043227.6501
20.8635-0.0168-0.5810.482-0.57940.9558-0.01080.60710.1166-0.3015-0.00490.3057-0.0029-0.35490.00090.3326-0.0332-0.0270.72880.03390.394137.426127.279528.6216
31.12960.5673-0.77190.6556-0.02570.8124-0.21220.26370.56430.0565-0.026-0.0415-0.21830.3292-0.00090.3015-0.0622-0.02160.50570.08680.424244.404232.635538.6517
42.8984-1.6331-1.04631.40350.40581.3422-0.21120.4607-0.3319-0.1684-0.00770.11770.092-0.1678-0.00070.2759-0.0527-0.00770.56140.04970.398536.088123.505237.0266
50.35110.3117-0.07820.7156-0.12570.3045-0.2697-0.5402-0.52790.63890.13840.41110.47560.2252-0.00070.44280.04050.14080.54990.13360.503735.761916.057954.6889
60.6351-0.4862-0.43180.43960.22660.635-0.15420.02090.03490.07650.04450.0167-0.0394-0.07600.2894-0.0022-0.00270.51370.06290.403231.901531.498948.3154
71.68490.0803-1.10230.4763-0.07151.1401-0.1004-0.00240.03830.01010.0841-0.00380.06-0.0571-00.2911-0.02050.00120.49110.07060.371436.767329.793643.3638
80.3253-0.45380.31560.6455-0.43130.695-0.34070.9301-1.3067-0.19660.0447-0.05740.4494-0.30080.00140.5094-0.00830.07870.6449-0.020.694947.830212.207532.9091
91.3143-0.231-0.89371.6628-0.54320.595-0.25030.05160.3164-0.48460.09770.7501-0.1417-0.3824-0.00180.445-0.0151-0.10410.343-0.0410.51434.278821.4486-0.3594
101.41831.19390.11831.40360.84161.1345-0.11750.08080.1084-1.07350.02310.22890.4074-0.06780.00040.5955-0.0484-0.07190.35370.00030.392544.740321.3302-6.2371
112.61971.20870.01241.4486-0.59210.4782-0.08470.05460.4506-0.2549-0.01480.2818-0.1481-0.1176-0.0010.4713-0.0201-0.06690.27790.00260.418643.817529.44582.3937
121.0126-0.8689-0.60471.5035-0.27711.066-0.2478-0.2163-0.08090.1272-0.0777-0.082-0.06910.0236-00.4007-0.1144-0.02710.43240.00720.298752.146825.117315.335
130.00720.06350.03770.17750.13720.1870.0553-0.6634-0.18890.0545-0.0054-0.06270.39250.0606-0.00060.436-0.0283-0.03370.43190.04730.351455.149418.091418.1334
140.79250.3205-0.41060.72130.52540.7294-0.0928-0.2523-0.1372-0.2393-0.0731-0.29460.08510.549-0.00140.4094-0.01350.03050.35510.04620.360359.116324.62122.8291
150.2237-0.0696-0.06760.0784-0.09330.2215-0.14790.5485-0.0750.0143-0.2305-0.55840.4770.6737-0.00050.4716-0.02590.11330.4675-0.03930.52658.599815.04530.2814
161.59481.07410.78270.88710.78931.068-0.075-0.10550.0509-0.0657-0.1142-0.0507-0.0187-0.0733-0.00010.3746-0.02720.01520.2584-0.00770.33150.355825.24332.5626
171.0970.06110.6960.6924-0.22161.05570.2463-0.63370.96610.1933-0.97841.5512-0.7024-1.5329-0.00580.5998-0.05420.06990.7547-0.21760.698432.028322.750513.0338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 66 through 89 )A66 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 111 )A90 - 111
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 126 )A112 - 126
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 173 )A127 - 173
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 195 )A174 - 195
6X-RAY DIFFRACTION6chain 'A' and (resid 196 through 215 )A196 - 215
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 260 )A216 - 260
8X-RAY DIFFRACTION8chain 'A' and (resid 261 through 273 )A261 - 273
9X-RAY DIFFRACTION9chain 'B' and (resid 69 through 102 )B69 - 102
10X-RAY DIFFRACTION10chain 'B' and (resid 103 through 126 )B103 - 126
11X-RAY DIFFRACTION11chain 'B' and (resid 127 through 160 )B127 - 160
12X-RAY DIFFRACTION12chain 'B' and (resid 161 through 183 )B161 - 183
13X-RAY DIFFRACTION13chain 'B' and (resid 184 through 195 )B184 - 195
14X-RAY DIFFRACTION14chain 'B' and (resid 196 through 215 )B196 - 215
15X-RAY DIFFRACTION15chain 'B' and (resid 216 through 225 )B216 - 225
16X-RAY DIFFRACTION16chain 'B' and (resid 226 through 260 )B226 - 260
17X-RAY DIFFRACTION17chain 'B' and (resid 261 through 273 )B261 - 273

+
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