[English] 日本語
Yorodumi
- PDB-6xmv: The crystal structure of Neisseria gonorrhoeae DolP (NGO1985) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xmv
TitleThe crystal structure of Neisseria gonorrhoeae DolP (NGO1985)
ComponentsHemolysin,Endolysin
KeywordsPROTEIN TRANSPORT / BON domain / lipoprotein / T4 lysozyme
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
BON domain profile. / BON domain / BON domain / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Endolysin / Hemolysin
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsLi, J. / Peterson Brown, L.E. / Reed, R.W. / Wierzbicki, I.H. / Sikora, A.E. / Korotkov, K.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI117235 United States
CitationJournal: To Be Published
Title: The structure and function of a new component of Bam complex in Neisseria
Authors: Wierzbicki, I.H. / Zielke, R.A. / Li, J. / Begum, A.A. / Baarda, B.I. / Peterson Brown, L.E. / Reed, R.W. / Korotkov, K.V. / Jerse, A.E. / Sikora, A.E.
History
DepositionJun 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemolysin,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0153
Polymers37,9441
Non-polymers712
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.040, 125.900, 47.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Hemolysin,Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 37943.969 Da / Num. of mol.: 1 / Mutation: C1054T, C1097A, K1162A
Source method: isolated from a genetically manipulated source
Details: BamG fragment 46-202
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: ATCC 700825 / FA 1090 / Gene: NGO_1985, e, T4Tp126 / Plasmid: pKV1435 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: Q5F5E4, UniProt: D9IEF7, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na acetate pH 4.5, 3M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→57.785 Å / Num. obs: 10641 / % possible obs: 98.6 % / Redundancy: 5.745 % / Biso Wilson estimate: 48.682 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.193 / Χ2: 0.944 / Net I/σ(I): 9.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.75-2.825.6331.2031.6345018097990.611.32798.8
2.82-2.95.8910.959242837347270.771.05299
2.9-2.985.9010.7622.6544207587490.8020.83598.8
2.98-3.076.0580.6773.1441867026910.8950.7498.4
3.07-3.186.0440.5563.7241526946870.8980.60899
3.18-3.295.9640.4364.6440086786720.9230.47799.1
3.29-3.415.9770.3246.2839276626570.9660.35499.2
3.41-3.555.510.2548.4933836206140.9720.2899
3.55-3.715.3980.21610.0132176095960.9720.23997.9
3.71-3.895.6870.17410.8832195785660.9850.19197.9
3.89-4.15.5030.13313.6329115515290.9880.14896
4.1-4.355.8660.10116.1231445435360.9950.11198.7
4.35-4.655.7850.08218.0528464944920.9950.0999.6
4.65-5.025.7530.08317.7326354614580.9940.09299.3
5.02-5.55.7410.09915.924804374320.9940.10998.9
5.5-6.155.7070.09816.0122373943920.9930.10899.5
6.15-7.15.6390.07716.9419853543520.9970.08599.4
7.1-8.75.4670.05423.7116403023000.9960.0699.3
8.7-12.35.1150.04427.9712482482440.9970.04998.4
12.3-57.7854.7340.04425.986581531390.9970.04990.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.32 Å57.78 Å
Translation4.32 Å57.78 Å

-
Processing

Software
NameVersionClassification
XSCALEVERSION May 1, 2016 BUILT=20160617data scaling
PHASER2.7.17phasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSVERSION May 1, 2016 BUILT=20160617data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HUK

2huk


Resolution: 2.75→57.785 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 953 4.92 %
Rwork0.2255 18405 -
obs0.2282 10641 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.82 Å2 / Biso mean: 55.0817 Å2 / Biso min: 18.05 Å2
Refinement stepCycle: final / Resolution: 2.75→57.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 2 13 2437
Biso mean--41.53 31.91 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0040.0362457
X-RAY DIFFRACTIONf_angle_d0.5674.573324
X-RAY DIFFRACTIONf_chiral_restr0.040.143384
X-RAY DIFFRACTIONf_plane_restr0.0040.042425
X-RAY DIFFRACTIONf_dihedral_angle_d14.1179.9441481
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7502-2.89520.38071240.3217269199
2.8952-3.07650.34551340.2801263898
3.0765-3.31410.34711370.2842263298
3.3141-3.64750.31981330.249264297
3.6475-4.17520.31600.2269249695
4.1752-5.25980.20621350.1716264998
5.2598-57.7850.24441300.1887265798

+
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