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- PDB-3on6: Crystal structure of an exo-alpha-1,6-mannosidase (bacova_03626) ... -

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Basic information

Entry
Database: PDB / ID: 3on6
TitleCrystal structure of an exo-alpha-1,6-mannosidase (bacova_03626) from bacteroides ovatus at 1.70 a resolution
ComponentsUncharacterized protein
KeywordsHYDROLASE / ALPHA/ALPHA TOROID FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


Metal-independent alpha-mannosidase / Metal-independent alpha-mannosidase (GH125) / DUF1237 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Bacterial protein of unknown function (BACOVA_03626) from Bacteroides ovatus at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
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 1.4Oct 30, 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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,72516
Polymers106,9182
Non-polymers80714
Water21,3661186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-17 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.613, 91.138, 99.124
Angle α, β, γ (deg.)90.000, 92.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 6 / Auth seq-ID: 39 - 481 / Label seq-ID: 19 - 461

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A POSSIBLE OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 53459.109 Da / Num. of mol.: 2 / Fragment: sequence database residues 22-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_03626 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7M0J6
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1186 / 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 ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 22-481 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: 2.18 Å3/Da / Density % sol: 43.54 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.00M LiCl, 20.00% PEG-6000, 0.1M HEPES pH 7.0, 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: 0.91162,0.97944,0.97886
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2010 / 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
10.911621
20.979441
30.978861
ReflectionResolution: 1.7→29.044 Å / Num. obs: 100307 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.103 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.42
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.760.41623660518530194.5
1.76-1.830.3482.43741818886195.3
1.83-1.910.2833611618243195.1
1.91-2.020.2213.84077620575195
2.02-2.140.1654.93558617968195.4
2.14-2.310.1316.23853519452195.6
2.31-2.540.1087.33761518964196.5
2.54-2.90.0839.33725718822196.4
2.9-3.660.0514.53849419443196.6
3.66-29.0440.03320.53809519311197

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.044 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.119 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.086
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. 6. CHLORIDE (CL) AND POLYETHYLENE GLYCROL (PEG) FROM THE CRYSTALLIZATION AND ETHYLENE GLYCOL(EDO) USED AS A CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1663 5002 5 %RANDOM
Rwork0.1333 ---
obs0.135 100282 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.66 Å2 / Biso mean: 11.8343 Å2 / Biso min: 3.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.04 Å2
2--0.3 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7143 0 47 1186 8376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227586
X-RAY DIFFRACTIONr_bond_other_d0.0010.025222
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.94310294
X-RAY DIFFRACTIONr_angle_other_deg0.891312743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99824.699366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.983151323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3791534
X-RAY DIFFRACTIONr_chiral_restr0.090.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021562
X-RAY DIFFRACTIONr_mcbond_it0.6831.54542
X-RAY DIFFRACTIONr_mcbond_other0.221.51818
X-RAY DIFFRACTIONr_mcangle_it1.18827373
X-RAY DIFFRACTIONr_scbond_it2.10433044
X-RAY DIFFRACTIONr_scangle_it3.3894.52907
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6032 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.285
LOOSE THERMAL0.9710
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 364 -
Rwork0.201 7041 -
all-7405 -
obs--99.42 %
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)
10.2288-0.04130.01570.24060.0250.2989-0.0071-0.0315-0.0020.0283-0.00110.0043-0.00010.00460.00830.0097-0.00290.00440.0178-0.00040.016213.101331.594737.401
20.3324-0.0279-0.0650.1911-0.00130.323-0.0010.02690.0028-0.0204-0.00050.00920.013-0.01340.00150.0218-0.0005-0.00180.0048-0.00450.023122.876820.8199-4.8843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 481
2X-RAY DIFFRACTION2B39 - 481

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