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- PDB-4jja: Crystal structure of a DUF1343 family protein (BF0379) from Bacte... -

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Basic information

Entry
Database: PDB / ID: 4jja
TitleCrystal structure of a DUF1343 family protein (BF0379) from Bacteroides fragilis NCTC 9343 at 1.30 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / PF07075 family protein / DUF1343 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyExo-beta-N-acetylmuramidase NamZ / : / : / Exo-beta-N-acetylmuramidase NamZ, N-terminal / Exo-beta-N-acetylmuramidase NamZ, C-terminal / peptidoglycan beta-N-acetylmuramidase activity / Conserved hypothetical exported protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BF0379) from Bacteroides fragilis NCTC 9343 at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0827
Polymers42,5861
Non-polymers4966
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.655, 47.702, 59.732
Angle α, β, γ (deg.)90.000, 98.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein


Mass: 42586.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF0379, BF9343_0369, YP_210109.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5LI79
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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 20-389 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: 1.87 Å3/Da / Density % sol: 34.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0M lithium chloride, 20.0% polyethylene glycol 6000, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979183
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.3→29.686 Å / Num. all: 75685 / Num. obs: 75685 / % possible obs: 97.7 % / Redundancy: 3.6 % / Rsym value: 0.089 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.3330.4911.51419347470.49183.7
1.33-1.373.50.441.71875553320.4495.4
1.37-1.413.70.3562.11942452580.35697.8
1.41-1.453.70.2962.51900051510.29698.1
1.45-1.53.70.2373.11847250020.23798.2
1.5-1.553.70.1923.91784248350.19298.6
1.55-1.613.70.174.31735447070.1798.7
1.61-1.683.70.1494.91666945260.14999
1.68-1.753.70.1355.31603743510.13599.1
1.75-1.843.70.1195.81535641750.11999.3
1.84-1.943.70.1066.51468439960.10699.5
1.94-2.063.70.0927.31388237930.09299.7
2.06-2.23.60.08581285835270.08599.8
2.2-2.373.60.0867.71212533450.08699.8
2.37-2.63.60.0877.51095930510.08799.8
2.6-2.913.50.0857.5976827780.085100
2.91-3.363.40.0758.6827324670.075100
3.36-4.113.70.05911.2773420950.05999.9
4.11-5.813.70.05512.2612916360.055100
5.81-29.6863.50.0689.732339130.06898.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→29.686 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.362 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.044
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL (GOL) FROM THE CRYOPROTECTANT AND CL ION FROM CRYSTALLIZATION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.151 3800 5 %RANDOM
Rwork0.1189 ---
obs0.1206 75638 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.44 Å2 / Biso mean: 16.7691 Å2 / Biso min: 5.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.17 Å2
2--0.49 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 31 327 3173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223197
X-RAY DIFFRACTIONr_bond_other_d0.0010.022274
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9834361
X-RAY DIFFRACTIONr_angle_other_deg1.03735567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64723.493146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83115574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6221524
X-RAY DIFFRACTIONr_chiral_restr0.1160.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213564
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02653
X-RAY DIFFRACTIONr_mcbond_it1.7231.51913
X-RAY DIFFRACTIONr_mcbond_other0.8261.5760
X-RAY DIFFRACTIONr_mcangle_it2.57623147
X-RAY DIFFRACTIONr_scbond_it3.39631284
X-RAY DIFFRACTIONr_scangle_it4.7834.51194
X-RAY DIFFRACTIONr_rigid_bond_restr1.65735471
X-RAY DIFFRACTIONr_sphericity_free10.1133336
X-RAY DIFFRACTIONr_sphericity_bonded4.39535371
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 208 -
Rwork0.225 4531 -
all-4739 -
obs--83.24 %

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