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- PDB-4h41: Crystal structure of a putative alpha-L-fucosidase (BT_0435) from... -

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Basic information

Entry
Database: PDB / ID: 4h41
TitleCrystal structure of a putative alpha-L-fucosidase (BT_0435) from Bacteroides thetaiotaomicron VPI-5482 at 1.80 A resolution
Componentsputative alpha-L-fucosidase
KeywordsHYDROLASE / carbohydrate metabolism / host glycans / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Protein of unknown function DUF4434 / Domain of unknown function DUF5109 / Domain of unknown function (DUF4434) / : / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Protein of unknown function DUF4434 / Domain of unknown function DUF5109 / Domain of unknown function (DUF4434) / : / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-PG6 / Unknown ligand / DUF5109 domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative alpha-L-fucosidase (BT_0435) from Bacteroides thetaiotaomicron VPI-5482 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Refinement description
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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: putative alpha-L-fucosidase
B: putative alpha-L-fucosidase
C: putative alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,16023
Polymers120,2563
Non-polymers3,90420
Water14,358797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14230 Å2
ΔGint-59 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.670, 125.700, 80.010
Angle α, β, γ (deg.)90.000, 103.720, 90.000
Int Tables number4
Space group name H-MP1211
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING SUPPORT THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein putative alpha-L-fucosidase


Mass: 40085.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_0435, NP_809348.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8AAM9

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Non-polymers , 7 types, 817 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 28-366 OF 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 40.0% polyethylene glycol 400, 5.0% polyethylene glycol 3000, 0.1M MES pH 6.0, 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: 0.97895
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.8→29.135 Å / Num. all: 89110 / Num. obs: 89110 / % possible obs: 93.6 % / Redundancy: 12.7 % / Rsym value: 0.133 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.855.30.5952.12173941120.59560.5
1.85-1.95.60.492.52769349650.4972.3
1.9-1.958.50.4763.64655154680.47682.5
1.95-2.0112.60.44457722361530.44494.7
2.01-2.0813.90.3746.28770863110.374100
2.08-2.15140.3067.58486360750.306100
2.15-2.23140.2568.78248259050.256100
2.23-2.32140.2299.97855756120.229100
2.32-2.43140.20211.17616554350.202100
2.43-2.55140.17612.47257451690.176100
2.55-2.68140.16613.56976249690.166100
2.68-2.8514.10.1415.96540346520.14100
2.85-3.0414.10.11918.46175143850.119100
3.04-3.2914.10.10421.65749340750.104100
3.29-3.614.10.09424.65329137810.094100
3.6-4.02140.08727.74792834150.087100
4.02-4.6514.10.08329.64205629910.083100
4.65-5.6914.10.0928.83614825710.09100
5.69-8.05140.098272764219770.098100
8.05-29.13513.60.088301486010890.08898.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.135 Å / Cor.coef. Fo:Fc: 0.9455 / Cor.coef. Fo:Fc free: 0.9373 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. POLYETHYLENE GLYCOL FRAGMENTS (1PE,PE4,PG6,AND PG4) FROM THE CRYSTALLIZATION CONDITIONS AND SODIUM (NA) FROM THE PURIFICATION BUFFER HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. AN UNKNOWN LIGAND (UNL) WAS MODELED IN THE PUTATIVE ACTIVE SITE OF EACH PROTOMER. 5. 18 N-TERMINAL RESIDUES OF A AND C AND 11 RESIDUES OF B MOLECULES WERE NOT MODELED 6. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 7. THE REFINEMENT WAS RESTRAINED AGAINST THE SAD PHASES. 8. HYDROGEN ATOMS WERE INCLUDED IN THE REFINEMENT AND TREATED BY BUSTER AS CONTRIBUTING TO FCALC.
RfactorNum. reflection% reflectionSelection details
Rfree0.158 4444 4.99 %RANDOM
Rwork0.1331 ---
obs0.1343 89070 93.62 %-
Displacement parametersBiso max: 116.41 Å2 / Biso mean: 26.8024 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1--7.8224 Å20 Å25.0947 Å2
2--8.7222 Å20 Å2
3----0.8998 Å2
Refine analyzeLuzzati coordinate error obs: 0.169 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7899 0 250 797 8946
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4515SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes207HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2290HARMONIC5
X-RAY DIFFRACTIONt_it16269HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1002SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance5HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18648SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16269HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg29270HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion4.85
X-RAY DIFFRACTIONt_other_torsion3.17
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2306 215 5 %
Rwork0.1989 4085 -
all0.2004 4300 -
obs--93.62 %
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)
10.2776-0.11710.09041.29670.02130.392-0.0010.01450.0919-0.0506-0.026-0.2262-0.05190.00870.0271-0.0550.00470.0157-0.07240.00410.0063-6.493499.986523.8997
20.5075-0.3290.14411.001-0.13290.2826-0.0802-0.0411-0.01540.210.0352-0.104-0.05590.02750.0450.0019-0.0046-0.0359-0.06420.0148-0.0478-0.981165.637440.877
30.4039-0.1202-0.04080.76810.1650.53280.07130.1167-0.1048-0.1376-0.05950.0610.0326-0.0507-0.0118-0.02240.0164-0.0361-0.0275-0.0399-0.041-15.969567.00095.7573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|46 - 366 }A46 - 366
2X-RAY DIFFRACTION2{ B|39 - 366 }B39 - 366
3X-RAY DIFFRACTION3{ C|46 - 366 }C46 - 366

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