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- PDB-4hxc: Crystal structure of a putative glycosyl hydrolase (BACUNI_00951)... -

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Basic information

Entry
Database: PDB / ID: 4hxc
TitleCrystal structure of a putative glycosyl hydrolase (BACUNI_00951) from Bacteroides uniformis ATCC 8492 at 2.15 A resolution
Componentsputative glycosyl hydrolase
KeywordsHYDROLASE / PF06439 family protein / DUF1080 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Exo-inulinase; domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 3-keto-disaccharide hydrolase domain-containing protein
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glycosyl hydrolase (BACUNI_00951) from Bacteroides uniformis ATCC 8492 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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 1.4Oct 30, 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: putative glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9146
Polymers29,4711
Non-polymers4425
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.537, 91.537, 99.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

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Components

#1: Protein putative glycosyl hydrolase


Mass: 29471.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: ATCC 8492 / Gene: ZP_02069537.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V066
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 30-291) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 30-291) 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: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium fluoride 20% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.9792,0.97868
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97921
30.978681
ReflectionResolution: 2.15→29.461 Å / Num. obs: 22690 / % possible obs: 93 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.567 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.230.4212.17635401087.7
2.23-2.320.3942.37594404792.5
2.32-2.420.2937424380291.6
2.42-2.550.1974.48662430195.8
2.55-2.710.1645.28301414294.8
2.71-2.920.126.98322425596.4
2.92-3.210.0759.97715397492
3.21-3.670.04715.18369412194.6
3.67-4.610.03620.57593394590.6
4.610.02723.68611423694.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.15→29.461 Å / Cor.coef. Fo:Fc: 0.9443 / Cor.coef. Fo:Fc free: 0.9201 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4.POLYETHYLENE GLYCOL FRAGMENTS (PGE,PEG) FROM THE CRYSTALLIZATION AND 1,2-ETHANEDIOL (EDO),USED AS A CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1163 5.14 %RANDOM
Rwork0.1838 ---
obs0.1857 22639 96.14 %-
Displacement parametersBiso max: 96.92 Å2 / Biso mean: 31.999 Å2 / Biso min: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.4825 Å20 Å20 Å2
2--0.4825 Å20 Å2
3----0.9651 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 2.15→29.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 29 184 2218
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d960SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes300HARMONIC5
X-RAY DIFFRACTIONt_it2104HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion258SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2421SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2104HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2843HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.22
X-RAY DIFFRACTIONt_other_torsion2.98
LS refinement shellResolution: 2.15→2.25 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2264 154 5.5 %
Rwork0.2075 2646 -
all0.2086 2800 -
obs--96.14 %
Refinement TLS params.Method: refined / Origin x: 26.5198 Å / Origin y: 1.8899 Å / Origin z: 87.8037 Å
111213212223313233
T-0.0732 Å20.0087 Å20.0087 Å2--0.1011 Å2-0.0172 Å2---0.097 Å2
L1.7791 °2-0.5783 °2-1.1522 °2-1.4575 °21.4343 °2--2.356 °2
S-0.1941 Å °-0.0657 Å °-0.1244 Å °0.1122 Å °-0.0427 Å °0.1515 Å °0.2296 Å °0.083 Å °0.2368 Å °
Refinement TLS groupSelection details: { A|37 - 291 }

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