[English] 日本語
Yorodumi
- PDB-1gvm: CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gvm
TitleCHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE
ComponentsAUTOLYSIN
KeywordsCHOLINE-BINDING DOMAIN / CELL WALL ATTACHMENT
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
Cholin Binding / left handed beta-beta-3-solenoid / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. ...Cholin Binding / left handed beta-beta-3-solenoid / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
CHOLINE ION / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / Autolysin
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFernandez-Tornero, C. / Lopez, R. / Garcia, E. / Gimenez-Gallego, G. / Romero, A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Two New Crystal Forms of the Choline-Binding Domain of the Major Pneumococcal Autolysin: Insights Into the Dynamics of the Active Dimeric
Authors: Fernandez-Tornero, C. / Garcia, E. / Lopez, R. / Gimenez-Gallego, G. / Romero, A.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: A Novel Solenoid Fold in the Cell Wall Anchoring Domain of the Pneumococcal Virulence Factorlyta
Authors: Fernandez-Tornero, C. / Lopez, R. / Garcia, E. / Gimenez-Gallego, G. / Romero, A.
History
DepositionFeb 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: AUTOLYSIN
B: AUTOLYSIN
C: AUTOLYSIN
D: AUTOLYSIN
E: AUTOLYSIN
F: AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,66728
Polymers95,2606
Non-polymers2,40722
Water1,42379
1
A: AUTOLYSIN
B: AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,58710
Polymers31,7532
Non-polymers8338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: AUTOLYSIN
D: AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4829
Polymers31,7532
Non-polymers7297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: AUTOLYSIN
F: AUTOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5989
Polymers31,7532
Non-polymers8447
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.717, 85.390, 204.136
Angle α, β, γ (deg.)90.00, 96.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99957, -0.01022, -0.02753), (-0.01794, 0.95479, 0.29676), (0.02325, 0.29712, -0.95456)29.17724, -1.03858, 6.48181
2given(0.35487, 0.88639, -0.2973), (0.88348, -0.42196, -0.20349), (-0.30582, -0.19044, -0.93285)21.75259, -10.66553, 67.84927
3given(-0.41713, 0.77704, 0.47139), (-0.87492, -0.48371, 0.02314), (0.24599, -0.40277, 0.88162)29.90285, 14.57103, 52.50802
4given(-0.50289, 0.86387, 0.02885), (-0.84371, -0.49786, 0.20075), (0.18778, 0.07661, 0.97922)51.17114, 33.0355, 65.55295
5given(0.30394, 0.93954, 0.15776), (0.92603, -0.25245, -0.28059), (-0.2238, 0.23137, -0.94678)37.76469, 6.25918, 80.43757

-
Components

#1: Protein
AUTOLYSIN / / MAJOR AUTOLYSIN / N-ACETYLMURAMOYL-L-ALANINE AMIDASE / MUREIN HYDROLASE / MUCOPEPTIDE ...MAJOR AUTOLYSIN / N-ACETYLMURAMOYL-L-ALANINE AMIDASE / MUREIN HYDROLASE / MUCOPEPTIDE AMINOHYDROLASE / CELL WALL HYDROLASE


Mass: 15876.638 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Plasmid: PCE17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RB791
References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase
#2: Chemical
ChemComp-CHT / CHOLINE ION / Choline


Mass: 104.171 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C5H14NO
#3: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALA D 194, DISORDERED SIDE-CHAIN IN PDB ENTRY. THE FIRST THREE RESIDUES OF EACH CHAIN (GLY185, ...ALA D 194, DISORDERED SIDE-CHAIN IN PDB ENTRY. THE FIRST THREE RESIDUES OF EACH CHAIN (GLY185, GLY186, ILE187) ARE ARTIFACTS FROM THE CLONING PROCEDURE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 %
Crystal growpH: 6.4
Details: 30% PEG 4000, 0.2 M NA-ACETATE, 0.1 M AMMONIUM-ACETATE, PH 6.4, 0.15 M CHOLINE-CL, 0.4 MM DDAO.
Crystal grow
*PLUS
Temperature: 295 K / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1droppH6.5
3100 mM1dropNaCl
4150 mMcholine chloride1drop
530 %(w/v)PEG40001reservoir
60.2 Mammonium acetate1reservoir
70.1 Msodium citrate1reservoirpH6.4
80.4 mMDDAO1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→33 Å / Num. obs: 23628 / % possible obs: 98.5 % / Observed criterion σ(I): 8 / Redundancy: 3.2 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.4 / % possible all: 98.7
Reflection
*PLUS
Lowest resolution: 33 Å / Num. measured all: 74838 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 98.7 % / Rmerge(I) obs: 0.28

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HCX

1hcx


Resolution: 2.8→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 740335.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1790 8 %RANDOM
Rwork0.226 ---
obs0.226 22605 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.0206 Å2 / ksol: 0.436606 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å21.27 Å2
2--7.59 Å20 Å2
3----6.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 0 162 79 6651
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 301 8 %
Rwork0.322 3461 -
obs--99 %
Refinement
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
LS refinement shell
*PLUS
Lowest resolution: 2.95 Å

+
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