[English] 日本語
Yorodumi
- PDB-4gnv: Crystal structure of beta-hexosaminidase 1 from Burkholderia ceno... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gnv
TitleCrystal structure of beta-hexosaminidase 1 from Burkholderia cenocepacia J2315 with bound N-Acetyl-D-Glucosamine
ComponentsBeta-hexosaminidase 1
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell division / cytoplasm
Similarity search - Function
Beta-hexosaminidase, bacterial / : / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of beta-hexosaminidase 1 from Burkholderia cenocepacia J2315 with bound N-Acetyl-D-Glucosamine
Authors: Davies, D.R. / Abendroth, J. / Staker, B. / Stewart, L.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Beta-hexosaminidase 1
B: Beta-hexosaminidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8188
Polymers76,2342
Non-polymers5846
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-47 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.970, 89.310, 67.150
Angle α, β, γ (deg.)90.000, 91.730, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-hexosaminidase 1 / Beta-hexosaminidase 2


Mass: 38116.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656
Gene: nagZ1, nagZ2, BceJ2315_10000, BceJ2315_27960, BCAL1010, BCAL2860
Production host: Escherichia coli (E. coli) / References: UniProt: B4EA43, beta-N-acetylhexosaminidase
#2: 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
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 1.93 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: EBS Internal tracking number 234629b12: BuceA.18451.a.B1.PW36254 at 20 mg/mL in 25 mM HEPES (pH 7.0), 500 mM NaCl, 2 mM DTT, 0.025% Sodium Azide, 5% glycerol. 0.4 uL x 0.4 uL drop with ...Details: EBS Internal tracking number 234629b12: BuceA.18451.a.B1.PW36254 at 20 mg/mL in 25 mM HEPES (pH 7.0), 500 mM NaCl, 2 mM DTT, 0.025% Sodium Azide, 5% glycerol. 0.4 uL x 0.4 uL drop with Morpheus Screen B12: 90 mM Halogens (NaF, NaBr, NaI), 0.1 M Tris/Bicine pH 8.5, 37.5% MPD-PEG1000-PEG3500, SOAK 1 week with 10 mM N-acetyl-D-glucosamine, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 1.5→67.12 Å / Num. all: 551832 / Num. obs: 85727 / % possible obs: 97.8 % / Redundancy: 6.11 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 28.22
Reflection shellResolution: 1.5→1.539 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 4.57 / % possible all: 84.57

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.99 Å
Translation2.5 Å38.99 Å

-
Processing

Software
NameVersionClassificationNB
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→67.12 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1702 / WRfactor Rwork: 0.1432 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.906 / SU B: 2.092 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0695 / SU Rfree: 0.0704 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 4519 5 %RANDOM
Rwork0.1479 ---
obs0.1493 90246 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 41.45 Å2 / Biso mean: 14.266 Å2 / Biso min: 3.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.06 Å2
2--0.63 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.5→67.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 34 630 5766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195308
X-RAY DIFFRACTIONr_bond_other_d0.0010.023505
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9657246
X-RAY DIFFRACTIONr_angle_other_deg0.9338506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8955704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54522.5224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56415833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2481553
X-RAY DIFFRACTIONr_chiral_restr0.080.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021121
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 288 -
Rwork0.229 5425 -
all-5713 -
obs--84.57 %
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)
13.3674-0.14951.46221.0102-0.15961.36480.06120.1152-0.19770.0570.0110.0290.1040.0098-0.07220.03890.00560.00660.0135-0.01240.024213.9067-26.00253.3124
20.37330.08970.0410.42110.23530.4574-0.0120.0443-0.00690.0069-0.01070.05410.005-0.03310.02270.02360.00480.00190.01440.00430.02279.4533-13.42517.9514
30.51430.0754-0.07770.4769-0.02580.4144-0.01640.03850.04280.00410.0014-0.0253-0.06430.04120.0150.0326-0.0042-0.00350.01840.00840.026820.9928-1.015214.1738
41.23780.39050.20220.85780.49020.3645-0.02980.07270.0078-0.03470.0735-0.0512-0.00160.0656-0.04370.0180.00750.00290.0383-0.00110.031932.0643-12.25887.5459
50.7798-0.1402-0.22750.31650.2390.611-0.019-0.0094-0.09040.04070.02490.01640.0829-0.0237-0.00590.02590.00280.00150.00940.00870.020814.896-19.31314.1239
67.29136.6063-0.50917.0783-3.27830.7514-0.16310.04070.2174-0.10830.19080.2221-0.0036-0.047-0.02760.08730.05940.01240.04540.01080.05240.12882.823920.5176
71.7405-0.4460.52740.6907-0.35340.6276-0.0043-0.0216-0.1086-0.00330.05780.06130.0957-0.0159-0.05350.0291-0.013-0.00470.04760.01180.01036.8593-22.548250.1788
80.27630.0911-0.11890.5868-0.08970.53490.011-0.09950.01550.0272-0.042-0.0434-0.04060.05650.03110.0165-0.0075-0.01320.0457-0.00280.020118.8927-5.35442.6218
90.54450.0552-0.1230.63060.01970.57550.038-0.05740.10330.0313-0.03210.0519-0.1243-0.0279-0.00590.04320.01340.00240.0285-0.02430.02955.01544.002442.2174
101.12880.31320.22880.4735-0.55631.7555-0.005-0.1530.02430.12470.06120.0492-0.1298-0.1969-0.05630.05260.02170.01910.0905-0.00760.0292-3.3454-9.731954.0526
113.4409-0.5712-0.34110.5557-0.04640.4902-0.0002-0.0507-0.1183-0.0431-0.00510.05550.0907-0.02710.00530.02340-0.00390.01840.00080.007211.0973-16.999534.2035
123.63222.01492.781916.79733.95332.51660.00070.02490.035-0.0553-0.0111-0.2201-0.0130.05470.01040.0038-0.01360.0080.11480.02430.058831.4735-8.182934.869
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 21
2X-RAY DIFFRACTION2A22 - 92
3X-RAY DIFFRACTION3A93 - 222
4X-RAY DIFFRACTION4A223 - 282
5X-RAY DIFFRACTION5A283 - 331
6X-RAY DIFFRACTION6A332 - 341
7X-RAY DIFFRACTION7B4 - 57
8X-RAY DIFFRACTION8B58 - 142
9X-RAY DIFFRACTION9B143 - 251
10X-RAY DIFFRACTION10B252 - 302
11X-RAY DIFFRACTION11B303 - 330
12X-RAY DIFFRACTION12B331 - 341

+
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