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- PDB-4pys: The crystal structure of beta-N-acetylhexosaminidase from Bactero... -

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Basic information

Entry
Database: PDB / ID: 4pys
TitleThe crystal structure of beta-N-acetylhexosaminidase from Bacteroides fragilis NCTC 9343
Componentsbeta-N-acetylhexosaminidase
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily ...Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.822 Å
AuthorsTan, K. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of beta-N-acetylhexosaminidase from Bacteroides fragilis NCTC 9343
Authors: Tan, K. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-N-acetylhexosaminidase
B: beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,54220
Polymers118,3992
Non-polymers1,14418
Water10,881604
1
A: beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,86311
Polymers59,1991
Non-polymers66410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6799
Polymers59,1991
Non-polymers4808
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.820, 96.820, 315.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsExperimentally unknown. It is predicted to be a monomer.

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Components

#1: Protein beta-N-acetylhexosaminidase


Mass: 59199.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF9343_3009 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)magic / References: UniProt: Q5LAT3, UniProt: D1JST6*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Magnesium chloride, 0.1M HEPES:NaOH, 15%(v/v) PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2014 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.82→34.5 Å / Num. all: 134406 / Num. obs: 134406 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 4.5 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 32
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.6 / Num. unique all: 6620 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.822→34.032 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 6739 5.02 %random
Rwork0.1645 ---
obs0.1657 134251 99.59 %-
all-134251 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.822→34.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7853 0 68 604 8525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078158
X-RAY DIFFRACTIONf_angle_d1.07111046
X-RAY DIFFRACTIONf_dihedral_angle_d13.2352970
X-RAY DIFFRACTIONf_chiral_restr0.0791138
X-RAY DIFFRACTIONf_plane_restr0.0051418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.822-1.84270.28982080.24074142X-RAY DIFFRACTION99
1.8427-1.86440.24812040.22584247X-RAY DIFFRACTION100
1.8644-1.88720.27052270.21184168X-RAY DIFFRACTION100
1.8872-1.9110.20632130.19994199X-RAY DIFFRACTION100
1.911-1.93620.23552250.18764263X-RAY DIFFRACTION100
1.9362-1.96270.20771990.18214185X-RAY DIFFRACTION100
1.9627-1.99070.20762300.17714204X-RAY DIFFRACTION100
1.9907-2.02050.20912190.17244224X-RAY DIFFRACTION100
2.0205-2.0520.18542100.17024203X-RAY DIFFRACTION100
2.052-2.08570.20882350.16794193X-RAY DIFFRACTION100
2.0857-2.12160.18562190.16194233X-RAY DIFFRACTION100
2.1216-2.16020.20632110.16664244X-RAY DIFFRACTION100
2.1602-2.20170.19492010.16824275X-RAY DIFFRACTION100
2.2017-2.24670.19262480.16734175X-RAY DIFFRACTION100
2.2467-2.29550.19352340.16574234X-RAY DIFFRACTION100
2.2955-2.34890.20382380.16294207X-RAY DIFFRACTION100
2.3489-2.40760.18482260.16594245X-RAY DIFFRACTION100
2.4076-2.47270.22362210.16734254X-RAY DIFFRACTION100
2.4727-2.54540.17492390.16134248X-RAY DIFFRACTION100
2.5454-2.62760.18562190.15924259X-RAY DIFFRACTION100
2.6276-2.72140.18982390.15984206X-RAY DIFFRACTION100
2.7214-2.83040.20172230.16784284X-RAY DIFFRACTION100
2.8304-2.95910.1742260.16384288X-RAY DIFFRACTION100
2.9591-3.1150.20672220.17374297X-RAY DIFFRACTION100
3.115-3.310.19152150.16944278X-RAY DIFFRACTION99
3.31-3.56530.18072480.15534275X-RAY DIFFRACTION99
3.5653-3.92370.17862020.14934346X-RAY DIFFRACTION99
3.9237-4.49030.16112260.13744325X-RAY DIFFRACTION99
4.4903-5.65310.16182760.14714366X-RAY DIFFRACTION99
5.6531-34.03780.20772360.19284445X-RAY DIFFRACTION95
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)
11.09120.1595-0.37561.64730.30992.64050.00780.03240.155-0.17120.01310.1587-0.3216-0.0341-0.0730.14520.0215-0.03290.1562-0.03070.208334.2383-25.478226.6059
26.2262-0.031-2.41043.53161.36973.6907-0.1264-1.089-0.12960.8296-0.11430.41310.377-0.28370.21580.34910.01390.04860.588-0.0670.435815.728-32.682251.0184
32.2005-0.8518-0.32411.6190.10221.9354-0.1245-0.279-0.31030.27730.05250.30640.1474-0.11610.04140.17440.00840.0290.2011-0.01480.198633.8811-40.831742.6084
40.95960.02850.40871.2181-0.0953.9333-0.0049-0.1127-0.10220.319-0.0354-0.03670.47290.12020.03270.22920.00220.02590.1899-0.02180.1744-9.7773-22.308870.145
52.7430.76940.49491.75340.97091.4301-0.0970.37960.261-0.3423-0.08340.4613-0.1228-0.27520.13910.1972-0.0198-0.02660.3943-0.0510.3115-29.2947-16.997341.8212
61.86490.06890.35462.082-0.02861.6022-0.15690.29370.036-0.11920.0793-0.1096-0.07550.2140.07960.1118-0.06290.0170.2744-0.02640.1452-6.8863-9.851447.1
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 228 )
2X-RAY DIFFRACTION2chain 'A' and (resid 229 through 313 )
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 518 )
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 157 )
5X-RAY DIFFRACTION5chain 'B' and (resid 158 through 367 )
6X-RAY DIFFRACTION6chain 'B' and (resid 368 through 518 )

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