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- PDB-3lk6: Beta-N-hexosaminidase N318D mutant (YBBD_N318D) from bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 3lk6
TitleBeta-N-hexosaminidase N318D mutant (YBBD_N318D) from bacillus subtilis
ComponentsLipoprotein ybbD
KeywordsHYDROLASE / bacillus subtilis / hexosaminidase / Cell membrane / 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
DI(HYDROXYETHYL)ETHER / Beta-hexosaminidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsKrug, M.
CitationJournal: To be Published
Title: Beta-N-hexosaminidase N318D mutant (YBBD_N318D) from bacillus subtilis
Authors: Krug, M. / Fischer, S. / Diederichs, K. / Boos, W. / Mayer, C.
History
DepositionJan 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein ybbD
B: Lipoprotein ybbD
C: Lipoprotein ybbD
D: Lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,20827
Polymers271,0994
Non-polymers2,10823
Water1,35175
1
A: Lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2226
Polymers67,7751
Non-polymers4475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4358
Polymers67,7751
Non-polymers6607
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3287
Polymers67,7751
Non-polymers5546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2226
Polymers67,7751
Non-polymers4475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.315, 99.149, 139.861
Angle α, β, γ (deg.)90.11, 90.05, 89.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 31:321 or resseq 323:642 )
211chain B and (resseq 31:321 or resseq 323:642 )
311chain C and (resseq 31:321 or resseq 323:642 )
411chain D and (resseq 31:321 or resseq 323:642 )

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Components

#1: Protein
Lipoprotein ybbD / ORF1


Mass: 67774.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU01660, ybbD, yzbA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P40406
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate, pH 4.9 and varying concentrations of polyethylene glycol 1000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2009
RadiationMonochromator: Si(111)monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→48.988 Å / Num. all: 68607 / Num. obs: 64490 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.88 % / Biso Wilson estimate: 41.578 Å2 / Net I/σ(I): 10.08
Reflection shellResolution: 2.88→3.05 Å / Redundancy: 1.66 % / Mean I/σ(I) obs: 2.74 / Num. unique all: 9481 / % possible all: 85.4

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BMX

3bmx


Resolution: 2.88→48.988 Å / SU ML: 0.4 / Isotropic thermal model: isotropic and tls / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 3261 5.06 %5% of the reflections selected randomly by the program uniqueify
Rwork0.1713 ---
obs0.1728 64427 93.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.667 Å2 / ksol: 0.334 e/Å3
Refinement stepCycle: LAST / Resolution: 2.88→48.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18989 0 137 75 19201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619470
X-RAY DIFFRACTIONf_angle_d0.96126234
X-RAY DIFFRACTIONf_dihedral_angle_d16.0367413
X-RAY DIFFRACTIONf_chiral_restr0.0622965
X-RAY DIFFRACTIONf_plane_restr0.0043394
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4721X-RAY DIFFRACTIONPOSITIONAL
12B4721X-RAY DIFFRACTIONPOSITIONAL0.019
13C4709X-RAY DIFFRACTIONPOSITIONAL0.02
14D4721X-RAY DIFFRACTIONPOSITIONAL0.019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.92190.4075890.31761691X-RAY DIFFRACTION58
2.9219-2.96750.26671430.26162718X-RAY DIFFRACTION95
2.9675-3.01620.28361400.25012650X-RAY DIFFRACTION96
3.0162-3.06820.31551470.25412733X-RAY DIFFRACTION97
3.0682-3.1240.31661460.26232763X-RAY DIFFRACTION96
3.124-3.1840.28921420.23642706X-RAY DIFFRACTION96
3.184-3.2490.28651260.20882710X-RAY DIFFRACTION96
3.249-3.31960.24341530.20612740X-RAY DIFFRACTION96
3.3196-3.39680.19081260.18212642X-RAY DIFFRACTION95
3.3968-3.48180.18681460.17432756X-RAY DIFFRACTION95
3.4818-3.57590.1891510.15642675X-RAY DIFFRACTION95
3.5759-3.68110.17511360.16912760X-RAY DIFFRACTION96
3.6811-3.79980.21251430.16532651X-RAY DIFFRACTION95
3.7998-3.93560.18851360.15592694X-RAY DIFFRACTION95
3.9356-4.09310.18971500.15422697X-RAY DIFFRACTION95
4.0931-4.27930.18421390.14242708X-RAY DIFFRACTION95
4.2793-4.50480.16541500.12412665X-RAY DIFFRACTION95
4.5048-4.78680.13321640.11262688X-RAY DIFFRACTION96
4.7868-5.1560.14221430.11862748X-RAY DIFFRACTION96
5.156-5.67420.15641430.12382711X-RAY DIFFRACTION96
5.6742-6.49360.14621490.13742702X-RAY DIFFRACTION97
6.4936-8.17510.15791520.1442713X-RAY DIFFRACTION95
8.1751-48.99550.17521470.15642645X-RAY DIFFRACTION94
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.064-0.21640.03480.3175-0.04870.3466-0.04960.01440.0157-0.08110.07460.0968-0.20870.1594-0.02110.1586-0.0723-0.0380.0839-0.00210.03926.3738-10.219925.9673
20.04080.0329-0.08950.0652-0.00780.1205-0.1196-0.1175-0.1913-0.08180.02120.078-0.0081-0.07170.07120.01650.00750.01220.23910.02490.1226
30.0261-0.00140.01740.0272-0.09020.3017-0.0684-0.07740.19970.0296-0.0675-0.1257-0.47050.14530.01310.0476-0.21060.0679-0.30710.1396-0.4935
40.6313-0.20430.16640.2128-0.09410.0737-0.061-0.2108-0.25870.19840.07040.0839-0.0645-0.0456-0.0066-0.04840.0098-0.01540.0592-0.066-0.0074
50.17640.1817-0.07060.1390.04680.2736-0.0149-0.02410.06990.04330.03210.05480.20120.0662-0.00660.17210.06880.0291-0.01650.01180.0332
61.3162-0.07570.30.03480.07240.2509-0.110.06450.29090.0903-0.0010.03460.0927-0.03990.09050.0344-0.00570.00860.19610.03240.0512
70.08520.0027-0.05510.0377-0.11260.4521-0.06210.1453-0.1529-0.13650.0235-0.06220.41770.11950.01120.00750.17030.0609-0.1275-0.18-0.7051
80.34670.0883-0.25550.1251-0.02020.19510.04350.19290.156-0.11560.02310.0375-0.0132-0.1882-0.006-0.172-0.0793-0.04490.0454-0.04120.0175
90.2046-0.23060.09650.29590.05660.4649-0.0107-0.06090.018-0.05250.0322-0.07890.2345-0.1649-0.0150.1768-0.06620.0370.08360.0050.0596
101.1760.02060.17380.0465-0.01630.2152-0.1071-0.12060.4061-0.1118-0.05560.01010.04070.08020.07-0.0456-0.02480.06190.172-0.03670.0097
110.02510.0033-0.07970.03730.02130.179-0.052-0.0045-0.05160.02-0.0060.0540.2322-0.05620.0080.1299-0.1109-0.06820.0562-0.0472-0.1422
120.3919-0.2373-0.1060.19140.09620.0575-0.0382-0.13850.18660.13390.0416-0.18210.06620.02580.0104-0.03720.0020.04360.04710.0553-0.0025
130.22780.12470.00790.1036-0.01730.2372-0.04060.0029-0.01350.10210.0292-0.0304-0.2299-0.0440.01940.16950.0476-0.0410.029-0.01310.0155
140.0773-0.0175-0.11740.06190.00150.14-0.07980.0841-0.21550.0506-0.0264-0.0606-0.01930.08870.09510.00610.00690.00930.2142-0.04850.1056
150.02340.00010.10.00050.02640.3188-0.11520.04060.268-0.0028-0.09480.141-0.4002-0.10110.02060.01580.18560.084-0.2002-0.0685-0.4024
160.68770.15410.06360.17430.15430.1449-0.06040.1904-0.2125-0.09120.0133-0.0453-0.05480.02870.02540.0065-0.0179-0.01740.08020.0253-0.0007
Refinement TLS groupSelection details: chain D and resid 427:642)

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