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- PDB-3r67: Crystal structure of a putative glycosidase (BT_4094) from BACTER... -

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Basic information

Entry
Database: PDB / ID: 3r67
TitleCrystal structure of a putative glycosidase (BT_4094) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.30 A resolution
Componentsputative Glycosidase
KeywordsHYDROLASE / 5-bladed beta propeller fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-biology
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / glycosyltransferase activity
Similarity search - Function
Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glycosidase (BT_4094) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.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 1.4Nov 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: putative Glycosidase
B: putative Glycosidase
C: putative Glycosidase
D: putative Glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,17524
Polymers161,9334
Non-polymers1,24120
Water20,7891154
1
A: putative Glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9188
Polymers40,4831
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative Glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7325
Polymers40,4831
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: putative Glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8567
Polymers40,4831
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: putative Glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6704
Polymers40,4831
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.920, 101.650, 86.560
Angle α, β, γ (deg.)90.000, 111.630, 90.000
Int Tables number4
Space group name H-MP1211
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUGGESTS THAT A MONOMER IS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION

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Components

#1: Protein
putative Glycosidase


Mass: 40483.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_4094 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A0C7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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 GLY 0 FOLOWED BY RESIDUES 23-377 FOR EACH MONOMER 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2M MgFormate, 20.0% PEG-3350, No Buffer pH 5.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.90497,0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2010 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.904971
20.979251
ReflectionResolution: 2.3→29.811 Å / Num. all: 60752 / Num. obs: 60752 / % possible obs: 100 % / Redundancy: 3.8 % / Rsym value: 0.171 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.363.80.592.41705644570.59100
2.36-2.423.80.5392.61677443750.539100
2.42-2.493.80.4842.91627242450.484100
2.49-2.573.80.4531573941010.45100
2.57-2.663.80.4013.41533839950.401100
2.66-2.753.80.3523.91496239000.352100
2.75-2.853.80.314.41422937020.31100
2.85-2.973.90.2495.31382735900.249100
2.97-3.13.80.2056.41331934680.205100
3.1-3.253.90.16381276733100.163100
3.25-3.433.80.1299.91199131220.129100
3.43-3.643.80.10711.81144329800.107100
3.64-3.893.80.09312.91075727970.093100
3.89-4.23.80.0814.31003826120.08100
4.2-4.63.80.07315.3924224070.073100
4.6-5.143.80.0715.4834821760.07100
5.14-5.943.80.08312.9733819130.083100
5.94-7.273.80.08712.2627016430.087100
7.27-10.293.80.07114481012690.071100
10.29-29.8113.70.0511725196900.05195.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
BUSTER-TNT2.8.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.811 Å / Cor.coef. Fo:Fc: 0.9489 / Cor.coef. Fo:Fc free: 0.9136 / Occupancy max: 1 / Occupancy min: 0.25 / 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. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 5. ETHYLENE GLYCOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 3077 5.07 %RANDOM
Rwork0.1521 ---
obs0.1546 60731 --
Displacement parametersBiso max: 104.34 Å2 / Biso mean: 22.537 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.9976 Å20 Å2-0.0058 Å2
2--2.5702 Å20 Å2
3----1.5726 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11093 0 80 1154 12327
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5211SINUSOIDAL10
X-RAY DIFFRACTIONt_trig_c_planes289HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1708HARMONIC5
X-RAY DIFFRACTIONt_it11662HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1451SEMIHARMONIC5
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_contact14181SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11662HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15858HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4
X-RAY DIFFRACTIONt_other_torsion1.88
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2609 240 5.39 %
Rwork0.1857 4210 -
all0.1896 4450 -
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)
10.724-0.24610.00132.2504-0.33480.8739-0.0276-0.088-0.03280.24750.0570.0394-0.0209-0.017-0.0294-0.07840.02070.0097-0.08920.0077-0.066527.033916.20541.3556
20.67610.0210.17281.4545-0.120.72910.00230.0236-0.004-0.05470.026-0.020.01090.0323-0.0284-0.07890.00040.0291-0.0552-0.0148-0.038541.671136.14461.2153
30.480.3070.15631.510.17750.6104-0.01070.0039-0.06570.01220.0273-0.07680.0094-0.0388-0.0166-0.07720.00480.0243-0.05430.0076-0.025853.162711.074579.0388
41.07470.261-0.5031.26920.10141.2172-0.0661-0.0532-0.0186-0.00750.0369-0.05330.0474-0.04970.0292-0.10450.010.0042-0.0509-0.0046-0.059169.821843.142341.7941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|28 - A|376 }A28 - 376
2X-RAY DIFFRACTION2{ B|28 - B|376 }B28 - 376
3X-RAY DIFFRACTION3{ C|28 - C|376 }C28 - 376
4X-RAY DIFFRACTION4{ D|29 - D|376 }D29 - 376

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