[English] 日本語
Yorodumi
- PDB-5g5u: Crystal structure of NagZ H174A mutant from Pseudomonas aeruginosa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g5u
TitleCrystal structure of NagZ H174A mutant from Pseudomonas aeruginosa
ComponentsBETA-HEXOSAMINIDASE
KeywordsHYDROLASE / CELL-WALL RECYCLING / ANTIBIOTIC RESISTANCE / GLYCO HYDROLASE / N-ACETYLGLUCOSAMINIDASE / BETA-HEXOSAMINIDASE / PEPTIDOGLYCAN
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division ...beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division / response to antibiotic / cytoplasm
Similarity search - Function
Beta-hexosaminidase, bacterial / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / 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 speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAcebron, I. / Artola-Recolons, C. / Mahasenan, K. / Mobashery, S. / Hermoso, J.A.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Catalytic Cycle of the N-Acetylglucosaminidase NagZ from Pseudomonas aeruginosa.
Authors: Acebron, I. / Mahasenan, K.V. / De Benedetti, S. / Lee, M. / Artola-Recolons, C. / Hesek, D. / Wang, H. / Hermoso, J.A. / Mobashery, S.
History
DepositionJun 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-HEXOSAMINIDASE
B: BETA-HEXOSAMINIDASE


Theoretical massNumber of molelcules
Total (without water)76,5012
Polymers76,5012
Non-polymers00
Water6,612367
1
A: BETA-HEXOSAMINIDASE


Theoretical massNumber of molelcules
Total (without water)38,2511
Polymers38,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-HEXOSAMINIDASE


Theoretical massNumber of molelcules
Total (without water)38,2511
Polymers38,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.231, 75.620, 76.720
Angle α, β, γ (deg.)90.00, 110.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein BETA-HEXOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / N-ACETYL-BETA-GLUCOSAMINIDASE / NAGZ


Mass: 38250.605 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: BOTH PROTEIN CHAINS CONTAIN A HIS RESIDUE AT POSITION -1 FROM THE FUSION TAG USED FOR PURIFICATION. THE SEQUENCE INCLUDES THE SINGLE-POINT MUTATION H174A THAT MAKES THIS PROTEIN INACTIVE
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HZK0, beta-N-acetylhexosaminidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXPERIMENTAL SEQUENCE CONTAINS A HIS-TAG FOR PURIFICATION. THERE IS A PUNCTUAL MUTATION AT ...THE EXPERIMENTAL SEQUENCE CONTAINS A HIS-TAG FOR PURIFICATION. THERE IS A PUNCTUAL MUTATION AT POSITION 174 (H174A)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 6
Details: 30% PEG 8000 100 MM SODIUM CACODYLATE PH 6.0 200 MM SODIUM ACETATE PH 6.0 5 MM EDTA

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97945
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2015 / Details: KB MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.25→60.2 Å / Num. obs: 32273 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 22.69 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.8
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.7 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APO STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA

Resolution: 2.25→60.202 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1658 5.1 %
Rwork0.1741 --
obs0.1771 32245 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→60.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 0 367 5449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085191
X-RAY DIFFRACTIONf_angle_d0.9867038
X-RAY DIFFRACTIONf_dihedral_angle_d18.8783154
X-RAY DIFFRACTIONf_chiral_restr0.051775
X-RAY DIFFRACTIONf_plane_restr0.005946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.31630.2491250.20132555X-RAY DIFFRACTION98
2.3163-2.3910.24491210.19012529X-RAY DIFFRACTION98
2.391-2.47650.26711290.19162580X-RAY DIFFRACTION99
2.4765-2.57560.2361330.19042551X-RAY DIFFRACTION99
2.5756-2.69290.30651560.19452513X-RAY DIFFRACTION99
2.6929-2.83480.24131410.1882566X-RAY DIFFRACTION99
2.8348-3.01240.26521430.18942534X-RAY DIFFRACTION98
3.0124-3.2450.28211440.18822555X-RAY DIFFRACTION99
3.245-3.57150.22411490.16872537X-RAY DIFFRACTION98
3.5715-4.08820.19171440.1492515X-RAY DIFFRACTION98
4.0882-5.15030.17851330.14682564X-RAY DIFFRACTION98
5.1503-60.22360.22741400.17452588X-RAY DIFFRACTION97
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)
11.16410.23170.00961.57560.13021.7140.01880.03090.2255-0.0605-0.02780.0704-0.1816-0.01980.07620.0468-0.01270.01070.0566-0.00820.0889-24.8465-1.174897.1033
20.89250.2036-0.19090.6567-0.24051.1578-0.10.11650.3279-0.20280.1526-0.0288-0.26970.01960.01290.1845-0.09930.00690.152-0.01140.2215-6.01512.961392.8729
34.10852.0262-0.33771.31120.56021.7224-0.20420.31960.0515-0.23270.124-0.0073-0.14460.08480.13610.1529-0.06670.04650.1221-0.0070.1921-7.81931.239883.484
41.1930.58680.32851.50750.8881.89680.005-0.0650.0714-0.11230.06640.00570.00360.0002-0.03760.0754-0.01810.00480.08350.03110.1489-15.86810.482797.9492
51.92120.48210.22051.8252-0.2812.09090.00930.0023-0.21920.0157-0.0957-0.24640.21010.08750.05570.0832-0.01230.03010.08030.00440.1293-23.236443.295497.191
60.43770.12360.20971.34880.48291.9620.0385-0.0296-0.4022-0.03020.0382-0.0450.3114-0.0438-0.04340.1615-0.01890.03160.10720.01420.2761-38.958525.3893101.2081
71.1287-0.00740.25671.11410.07991.8907-0.00320.1559-0.2252-0.29170.06380.10020.25-0.11230.06130.1537-0.05570.00930.1259-0.0250.1713-44.237531.613287.5357
80.92740.2759-0.08551.1106-0.5962.097-0.04790.061-0.0513-0.11410.05260.0257-0.12180.10040.04590.0936-0.02640.02770.1145-0.03790.1617-34.226241.278893.9976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 0 THROUGH 71 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 72 THROUGH 227 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 228 THROUGH 256 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 257 THROUGH 332 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 0 THROUGH 71 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 72 THROUGH 136 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 137 THROUGH 227 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 228 THROUGH 332 )

+
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://pdbjlvh1.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