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- PDB-4lb8: Crystal structure of a DUF4848 family protein (BT3222) from Bacte... -

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Basic information

Entry
Database: PDB / ID: 4lb8
TitleCrystal structure of a DUF4848 family protein (BT3222) from Bacteroides thetaiotaomicron VPI-5482 at 2.49 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF16140 family protein / DUF4848 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyImmunoglobulin-like - #3900 / Protein of unknown function DUF4848 / Domain of unknown function (DUF4848) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER / DUF4848 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.49 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BT3222) from Bacteroides thetaiotaomicron VPI-5482 at 2.49 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
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)33,5708
Polymers33,1811
Non-polymers3907
Water1,42379
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,14116
Polymers66,3622
Non-polymers77914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area9260 Å2
ΔGint-91 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.595, 140.829, 89.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 33180.859 Da / Num. of mol.: 1 / Fragment: UNP residues 22-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3222 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8A2T3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 22-310 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.20M lithium chloride, 20.00% polyethylene glycol 3350, 0.20M lithium chloride, 20.00% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.9786,0.97805
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.97861
30.978051
ReflectionResolution: 2.49→29.357 Å / Num. obs: 14384 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.579 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 8.96
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.49-2.580.6341.246532622194
2.58-2.680.4231.742082501193.4
2.68-2.80.3132.449042647197.5
2.8-2.950.2353.250632741197
2.95-3.140.1474.850722744196.2
3.14-3.380.0977.446342589194.2
3.38-3.710.0581145672542194.7
3.71-4.250.0415.650332730197
4.25-5.330.03119.845362550193.3
5.33-29.3570.02922.549722686194.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNTrefinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.49→29.357 Å / Cor.coef. Fo:Fc: 0.9357 / Cor.coef. Fo:Fc free: 0.8971 / 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. 3.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.CHLORIDE (CL) AND PEG3350 FRAGMENTS (PEG) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 720 5.03 %RANDOM
Rwork0.1804 ---
obs0.1826 14309 97.88 %-
Displacement parametersBiso max: 123.6 Å2 / Biso mean: 52.8535 Å2 / Biso min: 17.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.5792 Å20 Å20 Å2
2--12.8965 Å20 Å2
3----13.4756 Å2
Refine analyzeLuzzati coordinate error obs: 0.323 Å
Refinement stepCycle: LAST / Resolution: 2.49→29.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 19 79 2256
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1033SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes319HARMONIC5
X-RAY DIFFRACTIONt_it2212HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion282SEMIHARMONIC5
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_contact2525SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2212HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2976HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion2.94
LS refinement shellResolution: 2.49→2.69 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2958 174 6.05 %
Rwork0.2173 2701 -
all0.222 2875 -
obs--97.88 %
Refinement TLS params.Method: refined / Origin x: 10.0725 Å / Origin y: 74.7043 Å / Origin z: -7.4107 Å
111213212223313233
T-0.1322 Å2-0.0174 Å2-0.0378 Å2--0.0797 Å2-0.0046 Å2---0.0039 Å2
L0.372 °20.4757 °2-0.0967 °2-2.9632 °2-0.3171 °2--0.2391 °2
S-0.1331 Å °0.0748 Å °0.0215 Å °-0.276 Å °0.155 Å °0.1659 Å °0.0323 Å °-0.0258 Å °-0.0219 Å °
Refinement TLS groupSelection details: { A|38 - 310 }

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