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- PDB-4dwe: Crystal structure of a putative polysaccharide deacetylase (BACOV... -

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Basic information

Entry
Database: PDB / ID: 4dwe
TitleCrystal structure of a putative polysaccharide deacetylase (BACOVA_03992) from Bacteroides ovatus ATCC 8483 at 2.01 A resolution
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / Hypothetical protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / CSAP
Function / homologyPutative polysaccharide deacetylase / Putative polysaccharide deacetylase / Putative phage tail component domain protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_03992) from Bacteroides ovatus ATCC 8483 at 2.01 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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 1.5Nov 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

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Assembly

Deposited unit
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9038
Polymers56,2591
Non-polymers6457
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.762, 72.975, 95.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein uncharacterized protein


Mass: 56258.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_03992 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M1K9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 21-499 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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17M sodium acetate, 25.5% polyethylene glycol 4000, 15.0% Glycerol, 0.1M tris hydrochloride pH 8.5, 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: 0.91837,0.9796,0.97925
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: double crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97961
30.979251
ReflectionResolution: 2.01→29.571 Å / Num. obs: 32317 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.32 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.01-2.080.4371.810567572195.2
2.08-2.170.3442.313280657198.1
2.17-2.260.2712.811064549497.9
2.26-2.380.2363.312311610397.2
2.38-2.530.2033.812030605097.3
2.53-2.730.1544.911549606495.6
2.73-30.1116.812322596298.1
3-3.430.0710.612257600397.7
3.43-4.320.04216.211656596295.8
4.320.0371912272602896.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.01→29.571 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.127 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.148
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. GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 1596 4.9 %RANDOM
Rwork0.1486 ---
obs0.1509 32268 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.23 Å2 / Biso mean: 30.3165 Å2 / Biso min: 13.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---1.8 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.01→29.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 42 426 4213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.023892
X-RAY DIFFRACTIONr_bond_other_d0.0040.022631
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9535268
X-RAY DIFFRACTIONr_angle_other_deg1.37136401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2035465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67524.802202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44115658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5721518
X-RAY DIFFRACTIONr_chiral_restr0.1080.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024333
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02809
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 107 -
Rwork0.197 2048 -
all-2155 -
obs--98.04 %
Refinement TLS params.Method: refined / Origin x: 4.991 Å / Origin y: 1.155 Å / Origin z: 7.286 Å
111213212223313233
T0.0026 Å2-0.007 Å20.0039 Å2-0.0289 Å2-0.0028 Å2--0.0187 Å2
L0.4199 °2-0.1138 °20.0504 °2-0.3061 °2-0.022 °2--0.3516 °2
S-0.005 Å °-0.016 Å °0.0034 Å °-0.006 Å °0.0191 Å °0.0067 Å °0.002 Å °-0.0194 Å °-0.0141 Å °

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