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- PDB-3nfv: Crystal structure of an alginate lyase (BACOVA_01668) from Bacter... -

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Basic information

Entry
Database: PDB / ID: 3nfv
TitleCrystal structure of an alginate lyase (BACOVA_01668) from Bacteroides ovatus at 1.95 A resolution
Componentsalginate lyase
KeywordsLYASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


periplasmic space / lyase activity
Similarity search - Function
Alginate lyase domain / Alginate lyase / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Alginate lyase domain-containing protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an alginate lyase (BACOVA_01668) from Bacteroides ovatus at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,97916
Polymers44,0521
Non-polymers92715
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.115, 54.133, 75.361
Angle α, β, γ (deg.)90.000, 105.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alginate lyase


Mass: 44051.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_01668 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7LV19
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 20-400) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-400) 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20.000000000% iso-Propanol, 20.000000000% PEG-4000, 0.1M Citrate pH 5.6, 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: 0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.95→43.402 Å / Num. obs: 31230 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.621 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-2.020.472.310715308297.6
2.02-2.10.3433.210920305599.3
2.1-2.20.272411883326199.9
2.2-2.310.223510632291498.9
2.31-2.460.1766.312052324299.8
2.46-2.650.1447.611557310799.8
2.65-2.910.1139.611353306199.5
2.91-3.330.0861311669314099.9
3.33-4.190.05717.711440313998.5
4.19-43.4020.05819.111345322698.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→43.402 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.259 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.137
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. ISOPROPANOL (IPA) AND ETHYLENE GLYCOL (EDO) MODELED IS PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1572 5 %RANDOM
Rwork0.156 ---
obs0.158 31217 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.31 Å2 / Biso mean: 23.042 Å2 / Biso min: 7.84 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20.03 Å2
2--0.72 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 60 415 3507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223211
X-RAY DIFFRACTIONr_bond_other_d0.0020.022275
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9764325
X-RAY DIFFRACTIONr_angle_other_deg0.9335560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3795399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46424.859142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56315576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9211514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213511
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02615
X-RAY DIFFRACTIONr_mcbond_it1.87431934
X-RAY DIFFRACTIONr_mcbond_other0.5723775
X-RAY DIFFRACTIONr_mcangle_it2.79753117
X-RAY DIFFRACTIONr_scbond_it4.76781277
X-RAY DIFFRACTIONr_scangle_it6.642111199
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 108 -
Rwork0.217 2127 -
all-2235 -
obs--96.84 %

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