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- PDB-3bmx: Beta-N-hexosaminidase (YbbD) from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 3bmx
TitleBeta-N-hexosaminidase (YbbD) from Bacillus subtilis
ComponentsUncharacterized lipoprotein ybbD
KeywordsHYDROLASE / beta-N-hexosaminidase / Bacillus subtilis / TIM barrel / Glycosidase / Lipoprotein / Membrane / Palmitate
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 / extracellular region / plasma membrane
Similarity search - Function
Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-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 ...Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-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
ACETATE ION / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Beta-hexosaminidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFischer, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism
Authors: Litzinger, S. / Fischer, S. / Polzer, P. / Diederichs, K. / Welte, W. / Mayer, C.
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)142,34116
Polymers141,3492
Non-polymers99214
Water25,0051388
1
A: Uncharacterized lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2228
Polymers70,6741
Non-polymers5487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1198
Polymers70,6741
Non-polymers4447
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.385, 73.085, 83.567
Angle α, β, γ (deg.)79.79, 69.61, 88.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Uncharacterized lipoprotein ybbD / Beta-N-hexosaminidase / ORF1


Mass: 70674.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: wt168 / Gene: ybbD / Plasmid: PET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40406
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Diethylene glycol diethyl ether


Mass: 162.227 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1388 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 0.1M sodium acetate, 30-33 % PEG 1000, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99989 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2007
RadiationMonochromator: sagitally focused Si(111) mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.4→43 Å / Num. all: 227962 / Num. obs: 227962 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.25
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.65 / Num. unique all: 25215 / % possible all: 53.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUCCANEERphasing
ARP/wARPmodel building
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries: 1EX1, 1IIX, 1J8V, 1LQ2, 1X38

1ex1

1iix
PDB Unreleased entry

1j8v

1lq2

1x38


Resolution: 1.4→42.835 Å / FOM work R set: 0.923 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.166 11453 5.02 %random
Rwork0.127 ---
obs0.129 227962 90.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.003 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso max: 5.21 Å2 / Biso mean: 18.81 Å2 / Biso min: 81.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.262 Å2-5.86 Å22.47 Å2
2---1.195 Å2-2.03 Å2
3----1.251 Å2
Refine analyzeLuzzati coordinate error obs: 0.212 Å
Refinement stepCycle: LAST / Resolution: 1.4→42.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9526 0 65 1388 10979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719783
X-RAY DIFFRACTIONf_angle_d0.96736007
X-RAY DIFFRACTIONf_chiral_restr0.2161500
X-RAY DIFFRACTIONf_plane_restr0.0063036
X-RAY DIFFRACTIONf_dihedral_angle_d17.0545035
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4160.3851140.3152205231928
1.416-1.4330.3521300.2782467259731
1.433-1.450.3111520.2592727287935
1.45-1.4680.2693350.2155596593170
1.468-1.4880.2513650.1856676704184
1.488-1.5080.2223600.1727085744590
1.508-1.530.2163700.1567503787394
1.53-1.5530.2064080.1357730813897
1.553-1.5770.1964590.11978978356100
1.577-1.6030.1813920.11578938285100
1.603-1.630.164370.10579188355100
1.63-1.660.1644040.10579628366100
1.66-1.6920.1494190.09779068325100
1.692-1.7260.1554240.09679618385100
1.726-1.7640.1524190.09479408359100
1.764-1.8050.1494080.10379458353100
1.805-1.850.1494410.10779058346100
1.85-1.90.1633950.10680378432100
1.9-1.9560.1583920.10779448336100
1.956-2.0190.1524120.10579368348100
2.019-2.0910.1444470.10479548401100
2.091-2.1750.1464210.10279108331100
2.175-2.2740.1464240.10579138337100
2.274-2.3940.1474480.10779168364100
2.394-2.5440.154080.11179868394100
2.544-2.740.1384040.11379158319100
2.74-3.0160.1624280.12679368364100
3.016-3.4520.1624310.13779328363100
3.452-4.3490.1564020.12679588360100
4.349-42.8550.1654040.1517856826099

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