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Basic information

Entry
Database: PDB / ID: 3pet
TitleCrystal structure of a putative adhesin (BF0245) from Bacteroides fragilis NCTC 9343 at 2.07 A resolution
ComponentsPutative adhesin
KeywordsCELL ADHESION / RIGHT-HANDED BETA-HELIX / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyPectate Lyase C-like - #120 / Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / Pectate Lyase C-like / 3 Solenoid / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta / ACETATE ION / Lipoprotein
Function and homology information
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative adhesin (BF0245) from Bacteroides fragilis NCTC 9343 at 2.07 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
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 1.4Oct 16, 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 adhesin
B: Putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,81120
Polymers46,9032
Non-polymers2,90818
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,10011
Polymers23,4511
Non-polymers1,64810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7119
Polymers23,4511
Non-polymers1,2608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.590, 60.700, 205.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative adhesin / Putative lipoprotein


Mass: 23451.369 Da / Num. of mol.: 2 / Fragment: sequence database residues 25-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Strain: ATCC 25285 / NCTC 9343 / Gene: BF0202 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LIP7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 25-244) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 25-244) 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.5651.97DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop3.850.20M sodium chloride, 31.8% polyethylene glycol 300, 0.1M sodium acetate pH 3.85, NANODROP, temperature 293K, VAPOR DIFFUSION, SITTING DROP
2772vapor diffusion, sitting drop4.5GNF2 E12: 0.20M sodium chloride, 40.0% polyethylene glycol 300, 0.1M sodium acetate pH 4.5, NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL9-210.97893
SYNCHROTRONSSRL BL11-120.97954, 0.91837, 0.97917
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDJul 22, 2010
MARMOSAIC 325 mm CCD2CCDApr 8, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorMADMx-ray1
2Single crystal Si(111) bent monochromator (horizontal focusing)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978931
20.979541
30.918371
40.979171
ReflectionResolution: 2.07→45.392 Å / Num. obs: 30470 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.558 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 8.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.07-2.140.8142.22527853971,2100
2.14-2.230.62.92774259421,2100
2.23-2.330.5033.32628456271,2100
2.33-2.450.4353.72602055411,2100
2.45-2.610.39642773059011,2100
2.61-2.810.2975.32665756521,2100
2.81-3.090.1888.12628855961,2100
3.09-3.530.09814.22689056701,2100
3.53-4.440.06221.12681056791,2100
4.44-45.3920.04823.42732057761,299.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
SHELXphasing
SHARPphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.07→45.392 Å / Cor.coef. Fo:Fc: 0.9491 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
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. CHLORIDE (CL), ACETATE (ACT), POLYETHYLENE GLYCOL FRAGMENTS (PG4) MODELED ARE PRESENT PROTEIN/CRYSTALLIZATION/CRYO BUFFER. 3. NON-CRYSTALLOGRAPHIC RESTRAINTS WERE APPLIED DURING REFINEMENT (AUTONCS). 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. REFINEMENT WAS RESTRAINED TO THE MAD PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 1530 5.06 %RANDOM
Rwork0.1758 ---
obs0.1775 30217 --
Displacement parametersBiso max: 106.68 Å2 / Biso mean: 28.836 Å2 / Biso min: 11.08 Å2
Baniso -1Baniso -2Baniso -3
1--5.6207 Å20 Å20 Å2
2---0.9225 Å20 Å2
3---6.5433 Å2
Refinement stepCycle: LAST / Resolution: 2.07→45.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 151 304 3659
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1731SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes496HARMONIC5
X-RAY DIFFRACTIONt_it3465HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion484SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3788SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3465HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4641HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion2.71
LS refinement shellResolution: 2.07→2.14 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2175 143 5.18 %
Rwork0.1868 2617 -
all0.1884 2760 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2983-0.0592-0.02830.60880.16281.4290.01070.03130.04050.0072-0.0184-0.0073-0.114-0.04220.0078-0.00430.0131-0.009-0.05860.0162-0.05323.506419.17867.4819
20.4301-0.05660.13280.54020.23382.1809-0.02770.01340.0163-0.017-0.0412-0.0185-0.03140.02850.0689-0.02270.0026-0.0123-0.08640.0084-0.051534.5072-2.88885.745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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