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

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Basic information

Entry
Database: PDB / ID: 3owr
TitleCrystal structure of a putative secreted protein (BF4250) from Bacteroides fragilis NCTC 9343 at 1.81 A resolution
Componentsuncharacterized hypothetical 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 / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Lipoprotein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.81 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 1.81 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 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 1.6Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized hypothetical protein
B: uncharacterized hypothetical protein
C: uncharacterized hypothetical protein
D: uncharacterized hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,17911
Polymers58,3934
Non-polymers7867
Water8,197455
1
A: uncharacterized hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7042
Polymers14,5981
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9824
Polymers14,5981
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: uncharacterized hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7993
Polymers14,5981
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: uncharacterized hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6932
Polymers14,5981
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.967, 103.967, 59.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: 33 - 159 / Label seq-ID: 8 - 134

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
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 hypothetical protein


Mass: 14598.162 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF4250 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5L7M9
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.33
Details: 45.5% polyethylene glycol 600, 0.1M phosphate-citrate pH 4.33, 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: 0.97903,0.97922,0.91837
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
10.979031
20.979221
30.918371
ReflectionResolution: 1.81→46.496 Å / Num. obs: 58472 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.884 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 12.74
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.81-1.870.6892.22224954081100
1.87-1.950.5092.9256236223199.9
1.95-2.040.3694244625908199.9
2.04-2.150.4095.6358215899199.9
2.15-2.280.3867.44415856041100
2.28-2.460.3099.24699059531100
2.46-2.70.22212.14480156701100
2.7-3.090.13817.34651958811100
3.09-3.890.07128.34642758971100
3.89-46.4960.0537.4467186046199.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.81→46.496 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 4.435 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.105
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM TLS GROUP ASSIGNMENT. 5. PHOSPHATE (PO4) AND POLYETHYLENE GLYCOL FRAGMENTS (PG4,PEG) FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 2956 5.1 %RANDOM
Rwork0.1661 ---
obs0.1679 58470 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74 Å2 / Biso mean: 22.3316 Å2 / Biso min: 9.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 1.81→46.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 47 455 4354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224080
X-RAY DIFFRACTIONr_bond_other_d0.0010.022668
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9495566
X-RAY DIFFRACTIONr_angle_other_deg0.80836565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4135540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.424.643168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86615661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4721519
X-RAY DIFFRACTIONr_chiral_restr0.0830.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02793
X-RAY DIFFRACTIONr_mcbond_it1.61632595
X-RAY DIFFRACTIONr_mcbond_other0.50631057
X-RAY DIFFRACTIONr_mcangle_it2.59854195
X-RAY DIFFRACTIONr_scbond_it4.05281485
X-RAY DIFFRACTIONr_scangle_it5.769111355
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1426 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.885
BLOOSE POSITIONAL1.115
CLOOSE POSITIONAL0.965
DLOOSE POSITIONAL0.875
ALOOSE THERMAL1.8310
BLOOSE THERMAL1.8210
CLOOSE THERMAL2.6410
DLOOSE THERMAL2.6910
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 183 -
Rwork0.257 4149 -
all-4332 -
obs--99.93 %
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)
10.46330.17630.46660.3220.1581.80250.0045-0.0168-0.05760.04340.0227-0.01960.0807-0.049-0.02730.0316-0.01530.00160.02120.00320.018642.960933.672926.4863
20.3190.00810.06910.6997-0.34830.88750.01510.01540.0224-0.062-0.01250.00940.033-0.058-0.00270.0495-0.0190.00440.0493-0.00930.017238.212436.034258.4017
30.42040.12340.08261.00110.6862.02870.00610.0091-0.0426-0.00460.03-0.0372-0.03520.1338-0.0360.0233-0.021-0.00660.05690.01420.043619.02098.061971.0186
40.58110.0923-0.26990.3479-0.0720.9394-0.013-0.05820.01050.01490.00610.0047-0.04780.01510.00690.0284-0.0161-0.01110.0480.01130.024616.326312.870838.9444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 159
2X-RAY DIFFRACTION2B32 - 159
3X-RAY DIFFRACTION3C32 - 159
4X-RAY DIFFRACTION4D31 - 159

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