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- PDB-4mu9: Crystal structure of a putative glycosylhydrolase (BT_3782) from ... -

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Basic information

Entry
Database: PDB / ID: 4mu9
TitleCrystal structure of a putative glycosylhydrolase (BT_3782) from Bacteroides thetaiotaomicron VPI-5482 at 1.89 A resolution
ComponentsGlycoside hydrolase family 73
KeywordsHYDROLASE / Glycosyl hydrolase family 76 / PF03663 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Predicted O-glycosyl hydrolase / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Glycoside hydrolase family 73
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glycosylhydrolase (BT_3782) from Bacteroides thetaiotaomicron VPI-5482 at 1.89 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 73
B: Glycoside hydrolase family 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,18120
Polymers84,7122
Non-polymers1,47018
Water12,737707
1
A: Glycoside hydrolase family 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0299
Polymers42,3561
Non-polymers6738
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside hydrolase family 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,15311
Polymers42,3561
Non-polymers79710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.230, 61.220, 63.750
Angle α, β, γ (deg.)91.430, 90.280, 114.120
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glycoside hydrolase family 73


Mass: 42355.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_3782 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A184
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 707 / Source method: isolated from a natural source / Formula: H2O
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 25-387 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20.00% polyethylene glycol 10000, 8.00% ethylene glycol, 0.1M HEPES pH 7.5, 0.005M mannan, 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: 0.91837,0.97947,0.97876
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2013
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
20.979471
30.978761
ReflectionResolution: 1.89→28.033 Å / Num. obs: 42443 / % possible obs: 69 % / Observed criterion σ(I): -3 / Redundancy: 1.94 % / Biso Wilson estimate: 20.477 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.89-1.960.4371.7529052651123.1
1.96-2.040.3192.252454763141.8
2.04-2.130.2462.868946309159
2.13-2.240.1773.694178627179.5
2.24-2.380.1414.295608777179
2.38-2.560.115592098501177.9
2.56-2.820.0856.399159224182.5
2.82-3.230.0578.396018981180.1
3.23-4.060.04311.896509141182.8
4.06-28.030.03513.399789631186.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
XSCALEdata scaling
BUSTER-TNTrefinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.89→28.033 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.9302 / Occupancy max: 1 / Occupancy min: 0.23 / 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 TO ACCOUNT FOR THE ...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 TO ACCOUNT 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. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS) 5. EDO (ETHYLENE GLYCOL) AND EPE (HEPES) LIGANDS FROM CRYO- AND CRYS CONDITIONS ARE MODELED INT THE STRUCTURE. 6. THERE IS DISORDERED LOOP IN THE MODELED STRUCTURE 67-70.
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 2203 5.19 %RANDOM
Rwork0.1498 ---
obs0.152 42441 76.46 %-
Displacement parametersBiso max: 99.12 Å2 / Biso mean: 22.5195 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-3.3322 Å2-2.3502 Å2-0.5559 Å2
2---3.8233 Å24.7217 Å2
3---0.4911 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å
Refinement stepCycle: LAST / Resolution: 1.89→28.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5852 0 94 707 6653
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2143SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes150HARMONIC2
X-RAY DIFFRACTIONt_gen_planes884HARMONIC5
X-RAY DIFFRACTIONt_it6178HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion747SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_utility_angle2HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7685SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6178HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8349HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion16.78
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2292 51 5.4 %
Rwork0.1997 894 -
all0.2013 945 -
obs--76.46 %
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)
10.3117-0.05020.12390.41630.05730.3137-0.005-0.030.0724-0.0323-0.007-0.01980.01510.02090.012-0.0450.0137-0.001-0.0003-0.0402-0.02579.11986.68936.9852
20.2588-0.0369-0.06210.27980.09750.22860.0255-0.0287-0.06140.0026-0.02920.00160.004-0.01290.0037-0.03650.0177-0.00140.0081-0.0329-0.025810.4275-19.54237.5141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|25-387 }
2X-RAY DIFFRACTION2{ B|25-387 }

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