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- PDB-4qni: Crystal structure of an auxiliary nutrient binding protein (BT350... -

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Basic information

Entry
Database: PDB / ID: 4qni
TitleCrystal structure of an auxiliary nutrient binding protein (BT3507) from Bacteroides thetaiotaomicron VPI-5482 at 2.30 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domain protein / N-terminal- PF08522 family (DUF1735) / C-terminal - PF14274 family (DUF4361) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Uncharacterised protein PF14274, DUF4361 / Domain of unknown function DUF4361 / Domain of unknown function DUF4973 / BT_3044-like, C-terminal / Domain of unknown function (DUF4973) / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BT3507) from Bacteroides thetaiotaomicron VPI-5482 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,60310
Polymers37,9411
Non-polymers6629
Water1,76598
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,41240
Polymers151,7644
Non-polymers2,64836
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area45270 Å2
ΔGint-73 kcal/mol
Surface area105430 Å2
MethodPISA
2
A: Uncharacterized protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)308,82580
Polymers303,5288
Non-polymers5,29672
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area18480 Å2
ΔGint-34 kcal/mol
Surface area56880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.922, 96.922, 158.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 37941.039 Da / Num. of mol.: 1 / Fragment: UNP residues 22-353
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_3507 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8A201
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (22-353) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (22-353) 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.40M tri-Sodium Citrate, 0.1M sodium HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97932,0.95369,0.97903
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 26, 2014
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.953691
30.979031
ReflectionResolution: 2.3→28.576 Å / Num. obs: 17102 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.333 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.71
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.380.8751.6115453010196.5
2.38-2.480.652.1130403353199.9
2.48-2.590.4972.81214031171100
2.59-2.730.3643.9125193259199.5
2.73-2.90.2256.2124703190199.9
2.9-3.120.13310.21231231461100
3.12-3.430.07318.1124093186199.9
3.43-3.930.04131.5121153219199.4
3.93-4.930.02250.3124553165199.9
4.93-28.5760.01959.5127443253199.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→28.576 Å / Cor.coef. Fo:Fc: 0.9558 / Cor.coef. Fo:Fc free: 0.9355 / 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 EXPERIMENTAL (MAD) PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. CITRATE (CIT) FROM THE CRYSTALLIZATION, CHLORIDE (CL) FROM THE PURIFICATION AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. RAMACHANDRAN OUTLIER AT RESIDUE 36 IS IN A REGION OF SUBOPTIMAL ELECTRON DENSITY THAT IS DIFFICULT TO MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 864 5.05 %RANDOM
Rwork0.1825 ---
obs0.1848 17101 99.81 %-
Displacement parametersBiso max: 132 Å2 / Biso mean: 58.5742 Å2 / Biso min: 30.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.9779 Å20 Å20 Å2
2---0.9779 Å20 Å2
3---1.9559 Å2
Refine analyzeLuzzati coordinate error obs: 0.302 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 42 98 2648
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1155SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes385HARMONIC5
X-RAY DIFFRACTIONt_it2605HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion347SEMIHARMONIC5
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_contact2900SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2605HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3538HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.92
X-RAY DIFFRACTIONt_other_torsion2.97
LS refinement shellResolution: 2.3→2.44 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.276 149 5.52 %
Rwork0.2008 2552 -
all0.2049 2701 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: 44.5254 Å / Origin y: 19.78 Å / Origin z: 24.4276 Å
111213212223313233
T-0.0548 Å2-0.0138 Å20.0814 Å2--0.187 Å20.012 Å2---0.1049 Å2
L0.8917 °20.0462 °20.087 °2-1.0959 °21.1012 °2--3.2325 °2
S0.0353 Å °0.011 Å °0.0432 Å °-0.1004 Å °-0.0532 Å °-0.0899 Å °-0.0915 Å °-0.095 Å °0.0179 Å °
Refinement TLS groupSelection details: { A|29 - 353 }

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