[English] 日本語
Yorodumi
- PDB-5kkd: Truncated hemolysin A Y134A from P. mirabilis at 2.1 Angstroms re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kkd
TitleTruncated hemolysin A Y134A from P. mirabilis at 2.1 Angstroms resolution crystallized in a high salt condition
ComponentsHemolysin
KeywordsTOXIN / hemolysin / two partner secretion / beta solenoid / beta helix
Function / homology
Function and homology information


catalytic activity / cell outer membrane / toxin activity / killing of cells of another organism
Similarity search - Function
Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Hemagglutinin repeat / Hemagglutinin repeat / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 Å
AuthorsNovak, W.R.P. / Bhattacharyya, B. / Weaver, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1050435 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Proteolysis of truncated hemolysin A yields a stable dimerization interface.
Authors: Novak, W.R. / Bhattacharyya, B. / Grilley, D.P. / Weaver, T.M.
History
DepositionJun 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jun 21, 2017Group: Structure summary / Category: entity / Item: _entity.pdbx_mutation
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemolysin
B: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8703
Polymers50,7742
Non-polymers961
Water2,918162
1
A: Hemolysin
B: Hemolysin
hetero molecules

A: Hemolysin
B: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7406
Polymers101,5484
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7660 Å2
ΔGint-51 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.080, 69.080, 234.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Hemolysin


Mass: 25387.025 Da / Num. of mol.: 2 / Mutation: Y134A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: hpmA / Plasmid: PET24A+ / Production host: Escherichia coli (E. coli) / References: UniProt: P16466
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1M LiSO4, 2% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 33020 / % possible obs: 100 % / Redundancy: 24.1 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.129 / Net I/av σ(I): 31.958 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.13-2.1720.10.7881100
2.17-2.2121.80.6911100
2.21-2.2522.80.581100
2.25-2.2923.50.561100
2.29-2.34240.5271100
2.34-2.4240.4491100
2.4-2.4624.10.3991100
2.46-2.5324.20.3641100
2.53-2.624.10.3091100
2.6-2.6824.10.2551100
2.68-2.78240.2111100
2.78-2.89240.1881100
2.89-3.0224.30.1541100
3.02-3.1824.30.1271100
3.18-3.3824.60.1081100
3.38-3.6424.90.1041100
3.64-4.0125.60.1131100
4.01-4.59260.1071100
4.59-5.7826.40.081199.9
5.78-5025.20.056199.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→47.82 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.24
RfactorNum. reflection% reflection
Rfree0.1951 1650 5.01 %
Rwork0.1701 --
obs0.1714 32913 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.43 Å2 / Biso mean: 44.53 Å2 / Biso min: 20.42 Å2
Refinement stepCycle: final / Resolution: 2.13→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 5 162 3117
Biso mean--69.1 47.39 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073022
X-RAY DIFFRACTIONf_angle_d0.8184124
X-RAY DIFFRACTIONf_chiral_restr0.06481
X-RAY DIFFRACTIONf_plane_restr0.005565
X-RAY DIFFRACTIONf_dihedral_angle_d14.3691789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1278-2.19040.24951500.21772483263399
2.1904-2.26110.25121500.190925242674100
2.2611-2.34190.23681380.198825652703100
2.3419-2.43570.23681290.186925412670100
2.4357-2.54650.20291120.189426162728100
2.5465-2.68080.21351260.186825712697100
2.6808-2.84870.25231280.189225862714100
2.8487-3.06860.20921380.185925982736100
3.0686-3.37740.19411470.164326022749100
3.3774-3.86590.1621490.157726342783100
3.8659-4.86990.16711340.140126862820100
4.8699-47.83220.18361490.172528573006100
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)
16.95890.60021.35468.2018-0.59756.3617-0.1941-0.00780.66650.32360.05930.5977-1.2421-0.21290.28340.8307-0.0021-0.03210.2690.03340.44518.945344.2154-8.8551
25.7723-1.0171.31972.4802-0.91284.2584-0.2755-0.34850.4472-0.06890.05770.2592-0.9286-0.38960.18740.62550.1262-0.09290.26040.010.42843.149738.1971-7.7764
33.72731.9858-0.92263.8686-0.15263.30530.1164-0.31410.39660.4422-0.06620.0538-1.2165-0.2476-0.08470.71830.075-0.12290.2631-0.02670.34938.555738.62821.771
45.4178-0.6345-0.71813.8005-1.50933.8145-0.2050.2070.6204-0.31370.1587-0.1408-0.6669-0.1833-0.00120.5006-0.0286-0.08090.1906-0.00610.31699.572934.3726-15.7577
51.8555-0.2038-1.28151.46340.37655.9597-0.1039-0.15350.15630.1371-0.0111-0.1217-0.486-0.04860.06850.3701-0.0287-0.07010.20030.02970.289110.525828.6977-7.9281
66.189-2.97551.81571.9228-0.22344.8297-0.05510.53661.24530.2487-0.08410.3954-1.0086-1.40090.10920.41950.1566-0.02230.51610.00130.5461-5.398529.007-15.8612
75.2456-0.67783.01372.4261-0.36148.1807-0.02690.0759-0.03210.03130.0167-0.0935-0.15760.11990.00610.2383-0.0508-0.01370.13080.02970.240313.159120.5693-15.2165
84.6004-0.0654-0.16114.39391.44942.1889-0.1016-0.2493-0.2330.1425-0.10410.26140.2904-0.42660.23090.2902-0.0186-0.02290.37490.06610.3172-0.912418.1685-20.7566
95.9656-0.20282.37173.50061.98013.6866-0.11380.3464-1.0873-0.420.16290.16220.94580.4598-0.13010.82610.17680.0380.333-0.00450.566223.484-12.7287-15.5685
103.25990.23431.05023.8289-0.89162.3917-0.0339-0.1467-0.8925-0.030.08760.02841.07240.3937-0.10840.72960.1680.08540.28550.06110.526722.4263-10.9533-9.7521
112.6734-0.0803-0.06262.6364-0.27243.6697-0.01850.0792-0.281-0.161-0.0199-0.03950.53110.30480.01170.31530.00680.01470.2330.00630.250520.21863.1098-16.7384
126.8226-0.9873-4.29063.57063.06366.32710.0373-0.5651-0.02420.07450.074-0.2646-0.07391.0103-0.07790.272-0.01390.00110.4223-0.00620.278328.205913.8971-19.5443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 49 )A31 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 71 )A50 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 107 )A72 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 123 )A108 - 123
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 159 )A124 - 159
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 173 )A160 - 173
7X-RAY DIFFRACTION7chain 'A' and (resid 174 through 216 )A174 - 216
8X-RAY DIFFRACTION8chain 'A' and (resid 217 through 234 )A217 - 234
9X-RAY DIFFRACTION9chain 'B' and (resid 30 through 62 )B30 - 62
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 107 )B63 - 107
11X-RAY DIFFRACTION11chain 'B' and (resid 108 through 210 )B108 - 210
12X-RAY DIFFRACTION12chain 'B' and (resid 211 through 233 )B211 - 233

+
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://pdbjlc1.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