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- PDB-3poh: Crystal structure of an endo-beta-N-acetylglucosaminidase (BT_398... -

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Basic information

Entry
Database: PDB / ID: 3poh
TitleCrystal structure of an endo-beta-N-acetylglucosaminidase (BT_3987) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.55 A resolution
ComponentsEndo-beta-N-acetylglucosaminidase F1
KeywordsHYDROLASE / TIM BARREL / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


hypothetical protein (bacova_03559) / Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich ...hypothetical protein (bacova_03559) / Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Endo-beta-N-acetylglucosaminidase F1
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an endo-beta-N-acetylglucosaminidase (BT_3987) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-N-acetylglucosaminidase F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7322
Polymers49,6631
Non-polymers691
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.449, 74.449, 133.913
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC STATE IN SOLUTION.

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Components

#1: Protein Endo-beta-N-acetylglucosaminidase F1


Mass: 49662.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: 226186 / Gene: BT_3987 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A0N4
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 27-476) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 27-476) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0M NaCitrate, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9795,0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2010
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97951
30.97931
ReflectionResolution: 1.55→29.712 Å / Num. obs: 62783 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.663 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.55-1.610.3572.5315001216294.1
1.61-1.670.2793.7375531116999.7
1.67-1.750.2126.25996312610100
1.75-1.840.159.66649311729100
1.84-1.950.10214.26520611497100
1.95-2.10.07519.36827512062100
2.1-2.310.06223.96781912066100
2.31-2.650.05227.76858412305100
2.65-3.330.04332.56555711978100
3.330.03437665361215799.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→29.712 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.173 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.069
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.IMIDAZOLE (IMD) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1636 3178 5.1 %RANDOM
Rwork0.1361 ---
obs0.1375 62730 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.58 Å2 / Biso mean: 23.5834 Å2 / Biso min: 8.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 5 612 3942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223715
X-RAY DIFFRACTIONr_bond_other_d0.0010.022485
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9675124
X-RAY DIFFRACTIONr_angle_other_deg0.92736172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44525.581172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47115642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0351514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02730
X-RAY DIFFRACTIONr_mcbond_it1.52332317
X-RAY DIFFRACTIONr_mcbond_other0.453943
X-RAY DIFFRACTIONr_mcangle_it2.43653780
X-RAY DIFFRACTIONr_scbond_it3.6681398
X-RAY DIFFRACTIONr_scangle_it5.558111293
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 233 -
Rwork0.18 4104 -
all-4337 -
obs--94.61 %
Refinement TLS params.Method: refined / Origin x: 56.7396 Å / Origin y: 19.5617 Å / Origin z: 63.7909 Å
111213212223313233
T0.0223 Å2-0.012 Å20.0044 Å2-0.0139 Å2-0.014 Å2--0.0249 Å2
L0.5002 °20.2288 °2-0.0231 °2-0.4103 °2-0.0242 °2--0.468 °2
S-0.0474 Å °0.054 Å °-0.0242 Å °-0.0581 Å °0.0445 Å °-0.0304 Å °0.0128 Å °-0.0235 Å °0.0029 Å °

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