[English] 日本語
Yorodumi
- PDB-4gyj: Crystal structure of mutant (D318N) bacillus subtilis family 3 gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gyj
TitleCrystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1)
ComponentsUncharacterized lipoprotein ybbD
KeywordsHYDROLASE/substrate / TIM-BARREL / HYDROLASE / HYDROLASE-substrate complex
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / peptidoglycan turnover / peptidoglycan biosynthetic process / beta-N-acetylglucosaminidase activity / cell wall organization / regulation of cell shape / carbohydrate metabolic process / extracellular region / plasma membrane
Similarity search - Function
: / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily ...: / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBacik, J.P. / Mark, B.L.
CitationJournal: Chem.Biol. / Year: 2012
Title: Active Site Plasticity within the Glycoside Hydrolase NagZ Underlies a Dynamic Mechanism of Substrate Distortion.
Authors: Bacik, J.P. / Whitworth, G.E. / Stubbs, K.A. / Vocadlo, D.J. / Mark, B.L.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Structure summary
Revision 1.2Jan 28, 2015Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_distant_solvent_atoms / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / refine / refine_hist / software / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _refine.ls_number_reflns_all / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _software.classification / _software.name / _software.version / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized lipoprotein ybbD
B: Uncharacterized lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8976
Polymers142,4612
Non-polymers1,4354
Water19,2581069
1
A: Uncharacterized lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9483
Polymers71,2311
Non-polymers7182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9483
Polymers71,2311
Non-polymers7182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.450, 73.390, 83.430
Angle α, β, γ (deg.)98.65, 110.14, 92.43
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Uncharacterized lipoprotein ybbD / ORF1


Mass: 71230.641 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 18-642 / Mutation: D318N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU01660, NagZ, ybbD, yzbA / Production host: Escherichia coli (E. coli) / References: UniProt: P40406
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid


Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][<C3O2>]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1069 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 296 K / pH: 7.5
Details: 22% PEG3350, pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9749
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9749 Å / Relative weight: 1
ReflectionResolution: 1.65→38.61 Å / Num. obs: 147692 / % possible obs: 95.8 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.07 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.07 / Net I/σ(I): 11.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.742 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
MxDCdata collection
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BMX

3bmx


Resolution: 1.65→38.61 Å / SU ML: 0.41 / σ(F): 1.97 / Phase error: 20.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 7241 5.06 %
Rwork0.163 --
obs0.164 147676 95.8 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.38 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6931 Å21.589 Å21.3117 Å2
2---3.6265 Å24.1466 Å2
3---0.9334 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9293 0 98 1069 10460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099590
X-RAY DIFFRACTIONf_angle_d1.1513026
X-RAY DIFFRACTIONf_dihedral_angle_d19.6523672
X-RAY DIFFRACTIONf_chiral_restr0.0721523
X-RAY DIFFRACTIONf_plane_restr0.0071696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66880.34552500.28354618X-RAY DIFFRACTION94
1.6688-1.68840.28452410.26524515X-RAY DIFFRACTION95
1.6884-1.7090.31632360.24864719X-RAY DIFFRACTION94
1.709-1.73060.26632100.2434540X-RAY DIFFRACTION95
1.7306-1.75340.26142320.22934655X-RAY DIFFRACTION95
1.7534-1.77740.26752430.22114624X-RAY DIFFRACTION94
1.7774-1.80280.27312440.21254629X-RAY DIFFRACTION95
1.8028-1.82970.25272290.19634656X-RAY DIFFRACTION94
1.8297-1.85830.22892270.18314620X-RAY DIFFRACTION96
1.8583-1.88880.19862370.17444657X-RAY DIFFRACTION94
1.8888-1.92130.21262490.17534650X-RAY DIFFRACTION96
1.9213-1.95630.23522740.1694614X-RAY DIFFRACTION95
1.9563-1.99390.20642740.174648X-RAY DIFFRACTION96
1.9939-2.03460.2182430.16324639X-RAY DIFFRACTION95
2.0346-2.07880.18552540.16214659X-RAY DIFFRACTION95
2.0788-2.12720.18762610.15944647X-RAY DIFFRACTION96
2.1272-2.18040.22670.15754663X-RAY DIFFRACTION96
2.1804-2.23930.19932630.15824681X-RAY DIFFRACTION96
2.2393-2.30520.19132600.15854686X-RAY DIFFRACTION97
2.3052-2.37960.19522450.15064700X-RAY DIFFRACTION96
2.3796-2.46460.1882520.15214728X-RAY DIFFRACTION96
2.4646-2.56330.18532520.15514680X-RAY DIFFRACTION97
2.5633-2.67990.20472660.1584693X-RAY DIFFRACTION97
2.6799-2.82120.19192690.15974729X-RAY DIFFRACTION97
2.8212-2.99790.18362590.15714729X-RAY DIFFRACTION97
2.9979-3.22920.19692570.1634733X-RAY DIFFRACTION97
3.2292-3.5540.18222580.15894747X-RAY DIFFRACTION98
3.554-4.06780.16172250.14214781X-RAY DIFFRACTION98
4.0678-5.12310.14992630.1334784X-RAY DIFFRACTION98
5.1231-38.61720.15522380.1664774X-RAY DIFFRACTION98
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)
11.2099-0.4125-0.12611.48170.3521.0234-0.05120.0893-0.02-0.03730.0011-0.02010.05610.08190.03270.0613-0.0296-0.02120.05940.00720.052433.9432-38.2055-13.2515
22.0402-0.23790.34972.0456-0.16431.86960.00980.08760.2710.0194-0.04390.1852-0.3098-0.0660.01910.13710.01610.01440.1012-0.01160.151216.6788-7.8473-6.3331
31.07460.1437-0.46871.739-0.16331.5423-0.0044-0.1559-0.01330.1676-0.0085-0.0889-0.06230.1277-0.00350.08510.0231-0.01210.110.02910.060533.8419-16.5626-48.9755
41.567-0.0755-0.55652.0834-0.46851.7244-0.14350.0913-0.2738-0.27030.15310.32960.571-0.27990.00010.3462-0.1016-0.03360.1847-0.00480.188519.5703-48.417-56.4594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 25:428)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 429:642)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 26:428)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 429:642)

+
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