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- PDB-3nvd: Structure of YBBD in complex with pugnac -

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Basic information

Entry
Database: PDB / ID: 3nvd
TitleStructure of YBBD in complex with pugnac
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 / Chem-OAN / Beta-hexosaminidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.836 Å
AuthorsDiederichs, K.
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
DepositionJul 8, 2010Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 4, 2010ID: 3CQM
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references / Non-polymer description
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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)142,53211
Polymers141,3492
Non-polymers1,1839
Water27,5091527
1
A: Uncharacterized lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3636
Polymers70,6741
Non-polymers6895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized lipoprotein ybbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1695
Polymers70,6741
Non-polymers4944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.473, 73.206, 83.788
Angle α, β, γ (deg.)79.83, 69.45, 88.22
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized lipoprotein ybbD / 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, beta-N-acetylhexosaminidase

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Non-polymers , 5 types, 1536 molecules

#2: Chemical ChemComp-OAN / O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE / PUGNAc / PUGNAc


Mass: 353.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H19N3O7 / Comment: inhibitor*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1527 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M SODIUM ACETATE, 27% PEG 1000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9792
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2007
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.836→48.549 Å / Num. obs: 104555 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 1.985 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.55
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 1.977 / Num. unique all: 16575 / % possible all: 91.5

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BMX

3bmx


Resolution: 1.836→48.549 Å / σ(F): 1.99 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.246 5644 5.4 %
Rwork0.1871 --
obs0.1908 104555 93.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.973 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4641 Å20.5494 Å22.5924 Å2
2--0.6775 Å2-5.372 Å2
3----2.1416 Å2
Refinement stepCycle: LAST / Resolution: 1.836→48.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9526 0 79 1527 11132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0179776
X-RAY DIFFRACTIONf_angle_d1.61113193
X-RAY DIFFRACTIONf_dihedral_angle_d16.3453770
X-RAY DIFFRACTIONf_chiral_restr0.0831488
X-RAY DIFFRACTIONf_plane_restr0.0081710
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.837-1.86870.31512460.275467183
1.8687-1.90270.3092520.2555495189
1.9027-1.93930.30482310.2461504991
1.9393-1.97880.29332690.2454494389
1.9788-2.02180.31792770.2281505290
2.0218-2.06890.2932650.2235499990
2.0689-2.12060.30112700.2167503190
2.1206-2.17790.2482530.2111506891
2.1779-2.2420.27552720.2077501990
2.242-2.31430.28872630.203501690
2.3143-2.3970.25622720.202497189
2.397-2.49290.24292880.2006501889
2.4929-2.60630.2282740.1942499290
2.6063-2.74360.26372730.1901493389
2.7436-2.91530.24442650.1755497889
2.9153-3.14020.24962420.1751487688
3.1402-3.45570.22152470.1673488487
3.4557-3.95460.21562410.1477487587
3.9546-4.97810.21172450.1403492188
4.9781-28.59890.20852900.1826504690
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)
10.12110.0069-0.03060.1872-0.00580.15170.0063-0.0119-0.01630.0038-0.0098-0.0153-0.00940.00270.00020.0037-0.0087-0.00640.01950.01110.004867.820757.86685.6825
20.0447-0.0691-0.09980.25920.12690.2269-0.0060.03120.00670.0126-0.0136-0.02030.0071-0.00090.0072-0.0071-0.0226-0.00110.03210.00590.006637.342443.588148.9911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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