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- PDB-3p69: Crystal structure of a putative secreted protein (BF4250) from Ba... -

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Basic information

Entry
Database: PDB / ID: 3p69
TitleCrystal structure of a putative secreted protein (BF4250) from Bacteroides fragilis NCTC 9343 at 2.05 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / CARBOHYDRATE METABOLISM / PUTATIVE GLYCOSIDE HYDROLASE / IG-LIKE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyImmunoglobulin-like - #4120 / : / DUF5018-related / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta / DUF5018 domain-containing protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BF4250) from Bacteroides fragilis NCTC 9343 at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Dec 24, 2014Group: Structure summary
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Feb 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 1.6Oct 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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,76310
Polymers29,1962
Non-polymers5678
Water4,792266
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0947
Polymers14,5981
Non-polymers4966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6693
Polymers14,5981
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.074, 127.074, 150.606
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Uncharacterized protein


Mass: 14598.162 Da / Num. of mol.: 2 / Fragment: sequence database residues 27-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF4250 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5L7M9
#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.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 27-159) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 27-159) 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: 4.01 Å3/Da / Density % sol: 69.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.7510M ammonium sulfate, 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: 0.97898,0.97922,0.91837,0.97881
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978981
20.979221
30.918371
40.978811
ReflectionResolution: 2.05→29.914 Å / Num. all: 29482 / Num. obs: 29482 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 40.336 Å2 / Rsym value: 0.089 / Net I/σ(I): 12.1
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.05-2.16.30.61350521531.259100
2.1-2.166.30.81321821040.976100
2.16-2.226.31.11300320730.699100
2.22-2.296.31.21234419610.617100
2.29-2.376.31.51211319180.512100
2.37-2.456.31.91183718810.399100
2.45-2.546.32.51154318340.304100
2.54-2.656.33.21082317190.243100
2.65-2.766.33.91059316770.197100
2.76-2.96.35.31005015950.142100
2.9-3.066.36.7953715110.11100
3.06-3.246.38.3908214440.084100
3.24-3.476.38.4855613630.078100
3.47-3.746.39.5792912590.067100
3.74-4.16.310.9744211860.056100
4.1-4.586.313658510530.046100
4.58-5.296.21358899480.045100
5.29-6.486.112.849538060.047100
6.48-9.17612.938266350.045100
9.17-29.9145.713.620503620.04397.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
BUSTER-TNTBUSTER 2.8.0refinement
SCALA3.3.15data processing
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.05→29.914 Å / Cor.coef. Fo:Fc: 0.9518 / Cor.coef. Fo:Fc free: 0.9409 / Occupancy max: 1 / Occupancy min: 0.5 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. GLYCEROL (GOL), USED AS A CRYOPROTECTANT AND CHLORIDE (CL) FROM THE PROTEIN BUFFER HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 1499 5.08 %RANDOM
Rwork0.1893 ---
obs0.1909 29479 --
Displacement parametersBiso max: 130.59 Å2 / Biso mean: 50.6401 Å2 / Biso min: 19.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.5352 Å20 Å20 Å2
2--1.5352 Å20 Å2
3----3.0704 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 33 266 2243
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d968SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes309HARMONIC5
X-RAY DIFFRACTIONt_it2073HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion283SEMIHARMONIC5
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_contact2488SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2073HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2821HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion4.08
X-RAY DIFFRACTIONt_other_torsion2.38
LS refinement shellResolution: 2.05→2.12 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.251 150 5.24 %
Rwork0.2113 2711 -
all0.2132 2861 -
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)
10.77151.429-0.36077.8114-3.37023.5556-0.13670.18830.08840.03090.34660.2262-0.3493-0.1951-0.21-0.05670.00390.0569-0.15630.0188-0.1011-0.884436.8107-0.0039
21.2826-0.43840.83370.8306-0.94122.14540.0054-0.11250.15180.08140.0179-0.0878-0.3369-0.0774-0.0234-0.011-0.02030.0445-0.1153-0.05940.00062.657720.109723.5346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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