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- PDB-3gza: Crystal structure of putative alpha-L-fucosidase (NP_812709.1) fr... -

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Basic information

Entry
Database: PDB / ID: 3gza
TitleCrystal structure of putative alpha-L-fucosidase (NP_812709.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.60 A resolution
Componentsputative alpha-L-fucosidase
KeywordsHYDROLASE / NP_812709.1 / putative alpha-L-fucosidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome
Similarity search - Function
Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel ...Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Putative exported fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of putative alpha-L-fucosidase (NP_812709.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,36714
Polymers101,5872
Non-polymers78112
Water22,2311234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-12 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.052, 81.532, 111.572
Angle α, β, γ (deg.)90.00, 103.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A23 - 460
2116B23 - 460

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein putative alpha-L-fucosidase / Putative exported fucosidase


Mass: 50793.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3798, NP_812709.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A169

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Non-polymers , 5 types, 1246 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1234 / 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 19-460 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.200M sodium citrate, 20.00% PEG-3350, No Buffer pH 8.2, 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: 0.91837,0.97828,0.97916
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 18, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978281
30.979161
ReflectionResolution: 1.6→28.072 Å / Num. obs: 133836 / % possible obs: 99.7 % / Redundancy: 3 % / Biso Wilson estimate: 16.908 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 6.547
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.642.90.36522885499000.365100
1.64-1.692.90.322.32818596490.32100
1.69-1.742.90.272.72758294140.27100
1.74-1.792.90.2173.32658790780.217100
1.79-1.852.90.1873.82591688230.187100
1.85-1.912.90.1644.32520085760.164100
1.91-1.982.90.1452427482500.14100
1.98-2.072.90.11462330879130.114100
2.07-2.1630.0957.12257076380.095100
2.16-2.2630.0857.72153272670.08599.9
2.26-2.3930.0817.92062669580.08199.9
2.39-2.5330.0817.41933665150.08199.8
2.53-2.730.0787.91829261410.07899.7
2.7-2.9230.0679.11711557350.06799.6
2.92-3.230.05710.41581552660.05799.4
3.2-3.5830.049121435947570.04999.2
3.58-4.1330.04712.71261941740.04798.9
4.13-5.0630.05211.61075935610.05298.7
5.06-7.1630.05710.9821827310.05798.2
7.16-28.0830.04514.2441414900.04595.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.6→28.072 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.578 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. ELECTRON DENSITY INDICATES THAT THE PEPTIDE BOND BETWEEN TYR 226 AND HIS 227 ON BOTH SUBUNITS IN THE ASYMMETRIC UNIT IS IN THE CIS-CONFIGURATION. TYR 226 AND HIS 227 ARE IN THE VICINITY OF THE PUTATIVE ACTIVE SITE. 5. AN UNKNOWN LIGAND (UNL) WAS MODELED INTO THE PUTATIVE ACTIVE IN CHAIN B. 6. 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE - HEPES) FROM THE PROTEIN BUFFER WAS MODELED IN THE PUTATIVE ACTIVE SITE OF CHAIN A. 7. ETHYLENE GLYCOLS (EDO) USED AS A CRYOPROTECTANT AND SODIUM IONS FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. 8. ELECTRON DENSITY BETWEEN RESUDES 260-266 ON THE B-SUBUNIT WAS DISORDERED, AND THESE RESIDUES WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.168 6726 5 %RANDOM
Rwork0.139 ---
obs0.14 133835 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 64.61 Å2 / Biso mean: 28.212 Å2 / Biso min: 8.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-1.1 Å2
2--0.35 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6906 0 58 1234 8198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227355
X-RAY DIFFRACTIONr_bond_other_d0.0030.025110
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.94210021
X-RAY DIFFRACTIONr_angle_other_deg1.283312393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6575933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92823.801371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.606151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1351557
X-RAY DIFFRACTIONr_chiral_restr0.110.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028351
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021560
X-RAY DIFFRACTIONr_nbd_refined0.2110.31396
X-RAY DIFFRACTIONr_nbd_other0.1970.35800
X-RAY DIFFRACTIONr_nbtor_refined0.1850.53526
X-RAY DIFFRACTIONr_nbtor_other0.0930.53800
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.51630
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0460.51
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.56
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0780.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.333
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.575
X-RAY DIFFRACTIONr_mcbond_it0.8031.54426
X-RAY DIFFRACTIONr_mcbond_other0.2661.51798
X-RAY DIFFRACTIONr_mcangle_it1.29127160
X-RAY DIFFRACTIONr_scbond_it2.10133067
X-RAY DIFFRACTIONr_scangle_it3.1554.52829
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5602 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.375
LOOSE THERMAL2.210
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 479 -
Rwork0.196 9417 -
all-9896 -
obs--100 %
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)
10.7626-0.01950.10850.44990.20490.9746-0.00760.1284-0.0029-0.06570.00540.0545-0.026-0.14480.0022-0.1705-0.00280.0167-0.18070.0119-0.162861.002878.032834.8798
20.39010.06170.40610.15810.26821.44190.0631-0.043-0.07240.11140.0587-0.0560.21450.1812-0.1219-0.10960.0417-0.0209-0.1404-0.0219-0.106494.659180.540985.4225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 460
2X-RAY DIFFRACTION2B23 - 460

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