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- PDB-4gnv: Crystal structure of beta-hexosaminidase 1 from Burkholderia ceno... -

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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 / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 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

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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

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Phasing

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

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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

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