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- PDB-3qc2: Crystal structure of a glycosyl hydrolase (BACOVA_03624) from Bac... -

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Basic information

Entry
Database: PDB / ID: 3qc2
TitleCrystal structure of a glycosyl hydrolase (BACOVA_03624) from Bacteroides ovatus at 2.30 A resolution
Componentsglycosyl hydrolase
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


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 / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides ovatus (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 glycosyl hydrolase (BACOVA_03624) from Bacteroides ovatus at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
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 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycosyl hydrolase
B: glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3368
Polymers82,6112
Non-polymers7256
Water6,233346
1
A: glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5623
Polymers41,3061
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7745
Polymers41,3061
Non-polymers4694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.070, 137.070, 81.042
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLUGLUAA28 - 3366 - 314
21HISHISGLUGLUBB28 - 3366 - 314
12VALVALPROPROAA346 - 386324 - 364
22VALVALPROPROBB346 - 386324 - 364
DetailsCRYSTAL PACKING SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein glycosyl hydrolase


Mass: 41305.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_03624, ZP_02066624.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7M0J4
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 24-386) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 24-386) 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 40.0% polyethylene glycol 300, 0.1M phosphate-citrate pH 4.2, Additive: 0.003 M fructose, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9795,0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2010
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97951
30.97931
ReflectionResolution: 2.3→28.31 Å / Num. obs: 38497 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.59 % / Biso Wilson estimate: 37.479 Å2 / Rmerge F obs: 0.259 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.145 / Net I/σ(I): 8.84 / Num. measured all: 215276
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.381.1090.7051.5318669744366710.87489.6
2.38-2.480.9350.6161.822681791778090.76198.6
2.48-2.590.7970.532.221391744573490.65498.7
2.59-2.730.6270.4012.922215774976490.49598.7
2.73-2.90.4210.2734.221701754374550.33798.8
2.9-3.120.2840.1866.121563748674170.2399.1
3.12-3.430.1570.10810.121576750974400.13499.1
3.43-3.930.0910.06615.421953766175910.08299.1
3.93-4.930.0550.04520.821481752274620.05699.2
4.930.0520.04222.522046774376500.05298.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
REFMAC5.5.0109refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→28.31 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.262 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.214
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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. POLYEYHYLENE GLYCOL FRAGMENTS FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE 3.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. THE MODELING OF A CIS PEPTIDE BETWEEN GLY 39 AND GLY 40 ON THE A AND B-SUBUNITS IS SUPPORTED BY ELECTRON DENSITY. 6. EVEN THOUGH ASN 77 ON THE B-SUBUNIT IS FLAGGED AS A RAMACHANDRAN OUTLIER IN MOLPROBITY, ITS MODELING IS SUPPORTED BY ELECTRON DENSITY.7. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 8.UNEXPLAINED ELECTRON DENSITIES NEAR THE SIDECHAINS OF LYS 202 ON THE A AND B CHAINS WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 1931 5 %RANDOM
Rwork0.1844 36537 --
obs0.1864 38468 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.65 Å2 / Biso mean: 27.6448 Å2 / Biso min: 7.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5662 0 47 346 6055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225925
X-RAY DIFFRACTIONr_bond_other_d0.0030.024060
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9458052
X-RAY DIFFRACTIONr_angle_other_deg0.79839836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9385728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.54223.679280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.14815894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0041531
X-RAY DIFFRACTIONr_chiral_restr0.0740.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021281
X-RAY DIFFRACTIONr_mcbond_it0.3261.53592
X-RAY DIFFRACTIONr_mcbond_other0.0511.51452
X-RAY DIFFRACTIONr_mcangle_it0.62125801
X-RAY DIFFRACTIONr_scbond_it0.85132333
X-RAY DIFFRACTIONr_scangle_it1.334.52244
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4596 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.290.5
MEDIUM THERMAL0.262
LS refinement shellResolution: 2.299→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 128 -
Rwork0.244 2496 -
all-2624 -
obs--92.82 %
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)
10.86560.05570.38140.98230.33770.9498-0.0401-0.1060.04070.02070.0480.0089-0.0796-0.017-0.00790.0408-0.0343-0.01710.06810.0030.039220.882-38.411520.7368
20.84320.27320.46060.55490.25070.9643-0.03280.05250.1038-0.0691-0.05570.0343-0.15190.0510.08850.0362-0.0011-0.02520.03170.01420.04131.1771-56.4398-15.5298
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 386
2X-RAY DIFFRACTION2B28 - 386

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