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- PDB-4onz: Crystal structure of a putative glycoside hydrolase (BACOVA_02161... -

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Basic information

Entry
Database: PDB / ID: 4onz
TitleCrystal structure of a putative glycoside hydrolase (BACOVA_02161) from Bacteroides ovatus ATCC 8483 at 1.85 A resolution
Componentsputative glycoside hydrolase
KeywordsHYDROLASE / PF04041 family / DUF377 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyMannoside 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 / Unknown ligand / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glycoside hydrolase (BACOVA_02161) from Bacteroides ovatus ATCC 8483 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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 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: putative glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9054
Polymers40,8341
Non-polymers713
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.575, 50.331, 85.631
Angle α, β, γ (deg.)90.000, 94.380, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein putative glycoside hydrolase


Mass: 40834.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_02161, ZP_02065187.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7LWF7
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-381 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.0M lithium chloride, 20.0% polyethylene glycol 6000, 0.1M citric acid pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97953,0.97899
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979531
30.978991
ReflectionResolution: 1.85→29.521 Å / Num. all: 28087 / Num. obs: 28087 / % possible obs: 96.9 % / Redundancy: 3.2 % / Rsym value: 0.096 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.93.10.621.2633420380.6294.3
1.9-1.953.30.4771.6670920240.47798.4
1.95-2.013.30.4061.9645519640.40698
2.01-2.073.30.3462.2636019340.34698.4
2.07-2.143.10.2762.7580318450.27696.2
2.14-2.213.10.2293.3518116850.22992.4
2.21-2.293.40.2033.7592817550.20399.1
2.29-2.393.30.1634.5563617020.16398.8
2.39-2.493.20.155525716230.1598.5
2.49-2.623.10.1216.1465615010.12195.1
2.62-2.763.20.1047.1458014280.10495.6
2.76-2.933.40.0878.2469413910.08798.7
2.93-3.133.30.06910.3442313240.06998.5
3.13-3.383.20.05811.2384512010.05897.2
3.38-3.73.20.0512.9347510800.0594.8
3.7-4.143.40.05210.5345210190.05298.4
4.14-4.783.30.05610.229869040.05698.3
4.78-5.853.10.0648.623277430.06494.5
5.85-8.273.30.0738.119445980.07397.8
8.27-29.5213.10.0598.410143280.05994

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→29.521 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.305 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.131
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN 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. AN UNKNOWN LIGAND (UNL) IS MODELED INTO THE PUTATIVE ACTIVE SITE BASED ON A SIMILAR STRUCTURE WITH PDB CODE 3TAW.
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 1433 5.1 %RANDOM
Rwork0.1562 ---
obs0.1585 28082 96.53 %-
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: 81.77 Å2 / Biso mean: 26.3568 Å2 / Biso min: 12.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0.56 Å2
2--0.49 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 8 268 2998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022920
X-RAY DIFFRACTIONr_bond_other_d0.0010.022787
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9713973
X-RAY DIFFRACTIONr_angle_other_deg0.73136464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6275373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.824.681141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.73915502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.181515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
X-RAY DIFFRACTIONr_mcbond_it1.6063.3321405
X-RAY DIFFRACTIONr_mcbond_other1.6063.3281404
X-RAY DIFFRACTIONr_mcangle_it2.5616.2131762
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 85 -
Rwork0.249 1940 -
all-2025 -
obs--93.92 %
Refinement TLS params.Method: refined / Origin x: 7.97 Å / Origin y: 7.824 Å / Origin z: 22.265 Å
111213212223313233
T0.0436 Å20.0351 Å20.0109 Å2-0.0526 Å20.005 Å2--0.0078 Å2
L1.1926 °2-0.1019 °20.1765 °2-0.7016 °2-0.0489 °2--0.4234 °2
S0.1011 Å °0.1514 Å °0.0197 Å °-0.0321 Å °-0.0746 Å °-0.0361 Å °0.0086 Å °0.0212 Å °-0.0265 Å °

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