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- PDB-4fs7: Crystal structure of a leucine-rich repeat protein (BACOVA_04585)... -

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Basic information

Entry
Database: PDB / ID: 4fs7
TitleCrystal structure of a leucine-rich repeat protein (BACOVA_04585) from Bacteroides ovatus ATCC 8483 at 1.19 A resolution
ComponentsUncharacterized protein
KeywordsPROTEIN BINDING / leucine-rich repeats / extracellular protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyBspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.19 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical leucine rich repeat protein (BACOVA_04585) from Bacteroides ovatus ATCC 8483 at 1.19 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 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 1.3Feb 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4293
Polymers44,3041
Non-polymers1242
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.199, 84.416, 121.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 44304.445 Da / Num. of mol.: 1 / Fragment: UNP residues 22-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_04585 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M397
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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 22-414 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 293 K
Details: 0.200M sodium fluoride 20.00% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97949,0.97915
DetectorType: MAR MAR325 / Detector: CCD / Date: Jan 11, 2012 / Details: DOUBLE CRYSTAL MONOCHROMATOR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979491
30.979151
ReflectionResolution: 1.19→29.278 Å / Num. obs: 119592 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.858 Å2 / Rmerge F obs: 0.165 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.061 / Net I/σ(I): 9.11 / Num. measured all: 430225
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.19-1.230.9730.5131.63902121843210840.67796.5
1.23-1.280.7750.42524342423659233120.55798.5
1.28-1.340.6370.3532.44445823997237280.4698.9
1.34-1.410.4640.263.24261722880227170.33799.3
1.41-1.50.3220.184.44430523638234890.23299.4
1.5-1.610.1980.1156.94173822084219910.14799.6
1.61-1.780.1220.0789.74610124296241860.09999.5
1.78-2.030.0630.046154292522591223800.05899.1
2.03-2.560.0350.03221.34407023410227250.04197.1
2.560.0260.02825.84156623299209330.03589.8

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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
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.19→29.278 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.204 / SU ML: 0.024 / Cross valid method: THROUGHOUT
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. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. 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. 4. ETHYLENE GLYCOL (EDO) USED AS A CRYOPROTECTANT HAS BEEN MODELED INTO THE STRUCTURE. 5. AN UNEXPLAINED DIFFEREANCE ELECTRON DENSITY NEAR TYR314 WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.157 5966 5 %RANDOM
Rwork0.131 ---
obs0.132 119524 99.07 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2---0.96 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.19→29.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 8 568 3580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223358
X-RAY DIFFRACTIONr_bond_other_d0.0010.022373
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9864583
X-RAY DIFFRACTIONr_angle_other_deg0.99335874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51424.694147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3815648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1921515
X-RAY DIFFRACTIONr_chiral_restr0.1090.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.54332025
X-RAY DIFFRACTIONr_mcbond_other1.2843815
X-RAY DIFFRACTIONr_mcangle_it3.65153355
X-RAY DIFFRACTIONr_scbond_it5.20181333
X-RAY DIFFRACTIONr_scangle_it7.474111195
X-RAY DIFFRACTIONr_rigid_bond_restr1.88835731
X-RAY DIFFRACTIONr_sphericity_free12.9375576
X-RAY DIFFRACTIONr_sphericity_bonded5.59555634
LS refinement shellResolution: 1.19→1.221 Å
RfactorNum. reflection% reflection
Rfree0.245 410 -
Rwork0.224 8275 -
all-8685 -
obs--98.61 %

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