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- PDB-3osd: Crystal structure of a putative glycosyl hydrolase (BT2157) from ... -

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Basic information

Entry
Database: PDB / ID: 3osd
TitleCrystal structure of a putative glycosyl hydrolase (BT2157) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution
Componentsputative glycosyl hydrolase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


alpha-3'-ketoglucosidase / hydrolase activity, acting on glycosyl bonds / plasma membrane
Similarity search - Function
3-keto-disaccharide hydrolase / 3-keto-alpha-glucoside-1,2-lyase-like domain / Exo-inulinase; domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / 3-keto-disaccharide hydrolase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glycosyl hydrolase (BT2157) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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
Revision 1.5Oct 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)30,62414
Polymers29,8631
Non-polymers76113
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.420, 87.420, 97.182
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUGGESTS THAT A DIMER IS THE PREDOMINANT OLIGOMERIZATION STATE IN SOLUTION. HOWEVER, NONE OF THE CRYSTAL PACKING INTERFACES ARE PREDICTED TO BE STABLE DIMERIZATION INTERFACES SUGGESTING THAT MONOMERS PACKED INTO THE LATTICE UNDER THE CRYSTALLIZATION CONDITIONS.

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Components

#1: Protein putative glycosyl hydrolase / Probable secreted glycosyl hydrolase


Mass: 29863.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_2157 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A5T1
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 27-290) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 27-290) 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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2M K3Citrate, 20.0% PEG-3350, No Buffer pH 8.3, 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: 0.91162,0.97918,0.97903
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979181
30.979031
ReflectionResolution: 1.8→29.454 Å / Num. all: 35272 / Num. obs: 35272 / % possible obs: 99.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 23.083 Å2 / Rsym value: 0.082 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.855.90.8022.11515325550.80299
1.85-1.95.90.6172.81478724880.61798.8
1.9-1.955.90.4973.51428424140.49799
1.95-2.015.90.3784.51387523430.37899.2
2.01-2.085.90.2945.71356822870.29499.1
2.08-2.155.90.23871309122170.23899.3
2.15-2.235.90.20581258921300.20599.4
2.23-2.325.90.1689.41227020840.16899.4
2.32-2.435.90.14110.91180120050.14199.5
2.43-2.555.90.11713.11116018930.11799.7
2.55-2.685.90.09914.91076418370.09999.6
2.68-2.855.90.08117.71013017310.08199.7
2.85-3.045.80.06720.6954516370.06799.7
3.04-3.295.80.05225.9886315270.05299.9
3.29-3.65.80.04231820114180.04299.9
3.6-4.025.70.03935.5741212960.03999.9
4.02-4.655.70.04140.1658811610.041100
4.65-5.695.60.03942.954829860.039100
5.69-8.055.40.0439.442787930.0499.9
8.05-29.4544.90.03444.822804700.03497.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.454 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 3.793 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.094
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 5. POTASSIUM (K) ION AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION AND CRYOPROTECTION SOLUTIONS ARE MODELED RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1836 1769 5 %RANDOM
Rwork0.1595 ---
obs0.1607 35247 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 77.54 Å2 / Biso mean: 31.9631 Å2 / Biso min: 16.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 46 395 2525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222256
X-RAY DIFFRACTIONr_bond_other_d0.0010.021557
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9423048
X-RAY DIFFRACTIONr_angle_other_deg0.85633811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg75289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29426.083120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06515385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.415156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
X-RAY DIFFRACTIONr_mcbond_it0.7361.51344
X-RAY DIFFRACTIONr_mcbond_other0.2071.5559
X-RAY DIFFRACTIONr_mcangle_it1.31322161
X-RAY DIFFRACTIONr_scbond_it2.1233912
X-RAY DIFFRACTIONr_scangle_it3.2374.5873
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 114 -
Rwork0.222 2429 -
all-2543 -
obs--98.76 %
Refinement TLS params.Method: refined / Origin x: 37.612 Å / Origin y: 19.606 Å / Origin z: -22.755 Å
111213212223313233
T0.0162 Å20.0083 Å2-0.0096 Å2-0.0147 Å2-0.0219 Å2--0.0739 Å2
L1.1627 °20.1871 °20.3002 °2-1.6427 °2-0.1011 °2--1.2924 °2
S-0.0196 Å °-0.0564 Å °0.1014 Å °-0.0466 Å °0 Å °0.0737 Å °0.1227 Å °0.0032 Å °0.0195 Å °

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