[English] 日本語
Yorodumi
- PDB-7w1c: Crystal structure of Klebsiella pneumoniae K1 capsule-specific po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w1c
TitleCrystal structure of Klebsiella pneumoniae K1 capsule-specific polysaccharide lyase in a P1 crystal form
ComponentsK1 LYASE
KeywordsVIRAL PROTEIN / BETA-HELIX / POLYSACCHARIDE LYASE / TAIL SPIKE PROTEIN
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / Lyases / symbiont entry into host cell via disruption of host cell envelope / virus tail / adhesion receptor-mediated virion attachment to host cell / lyase activity
Similarity search - Function
: / K1 capsule-specific polysaccharide lyase, N-terminal domain / K1 capsule-specific polysaccharide lyase, C-terminal domain / K1 capsule-specific polysaccharide lyase, Rider domain / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
IMIDAZOLE / (2S)-2-hydroxybutanedioic acid / Depolymerase, capsule K1-specific
Similarity search - Component
Biological speciesKlebsiella phage NTUH-K2044-K1-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.48 Å
AuthorsTu, I.F. / Huang, K.F. / Wu, S.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST-108-2113-M-001-008 Taiwan
Academia Sinica (Taiwan)AS-KPQ-110-ITAR-11 Taiwan
CitationJournal: J.Biomed.Sci. / Year: 2022
Title: Structural and biological insights into Klebsiella pneumoniae surface polysaccharide degradation by a bacteriophage K1 lyase: implications for clinical use.
Authors: Tu, I.F. / Lin, T.L. / Yang, F.L. / Lee, I.M. / Tu, W.L. / Liao, J.H. / Ko, T.P. / Wu, W.J. / Jan, J.T. / Ho, M.R. / Chou, C.Y. / Wang, A.H. / Wu, C.Y. / Wang, J.T. / Huang, K.F. / Wu, S.H.
History
DepositionNov 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: K1 LYASE
B: K1 LYASE
C: K1 LYASE
D: K1 LYASE
E: K1 LYASE
F: K1 LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)436,96954
Polymers432,7846
Non-polymers4,18548
Water72,7994041
1
A: K1 LYASE
B: K1 LYASE
C: K1 LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,45227
Polymers216,3923
Non-polymers2,06024
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21750 Å2
ΔGint22 kcal/mol
Surface area57960 Å2
MethodPISA
2
D: K1 LYASE
E: K1 LYASE
F: K1 LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,51727
Polymers216,3923
Non-polymers2,12524
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21310 Å2
ΔGint16 kcal/mol
Surface area57630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.281, 100.574, 125.033
Angle α, β, γ (deg.)80.500, 70.320, 83.430
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
K1 LYASE


Mass: 72130.633 Da / Num. of mol.: 6 / Mutation: D391A, D392A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella phage NTUH-K2044-K1-1 (virus)
Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A068Q5Q5
#2: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4041 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% (W/V) PEG 4000, 0.2 M IMIDAZOLE MALATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 27, 2014
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. obs: 656693 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.44
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 64500 / % possible all: 95.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
SOLOMONphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.48→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.479 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 32922 5 %RANDOM
Rwork0.137 ---
obs0.139 623420 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.19 Å2 / Biso mean: 21.99 Å2 / Biso min: 5.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20.24 Å2-0.51 Å2
2--0.77 Å2-1.4 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.48→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28913 0 286 4041 33240
Biso mean--35 36.83 -
Num. residues----3824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01929830
X-RAY DIFFRACTIONr_bond_other_d0.0020.0227533
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.93940550
X-RAY DIFFRACTIONr_angle_other_deg1.0163.00363000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14953826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78823.6151300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.007154422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.26515189
X-RAY DIFFRACTIONr_chiral_restr0.1170.24591
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0234728
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027264
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_rigid_bond_restr5.577357363
X-RAY DIFFRACTIONr_sphericity_free35.20551484
X-RAY DIFFRACTIONr_sphericity_bonded11.541559323
LS refinement shellResolution: 1.48→1.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 2355 -
Rwork0.206 44494 -
all-46849 -
obs--93.66 %

+
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