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- PDB-4e0e: Crystal structure of a DUF4450 family protein (BT_4147) from Bact... -

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Basic information

Entry
Database: PDB / ID: 4e0e
TitleCrystal structure of a DUF4450 family protein (BT_4147) from Bacteroides thetaiotaomicron VPI-5482 at 2.90 A resolution
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / DUF4450 FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF4450 / Domain of unknown function (DUF4450) / DUF4450 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BT_4147) from Bacteroides thetaiotaomicron VPI-5482 at 2.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Structure summary
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.5Oct 30, 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 uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)80,9464
Polymers80,9464
Non-polymers00
Water00
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)40,4732
Polymers40,4732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-30 kcal/mol
Surface area17520 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)40,4732
Polymers40,4732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-32 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.880, 146.470, 72.370
Angle α, β, γ (deg.)90.000, 99.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative uncharacterized protein


Mass: 20236.521 Da / Num. of mol.: 4 / Fragment: UNP residues 20-196
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_4147 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A074
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 20-196) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-196) 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.67
Details: 22.00% polyethylene glycol 3000, 0.1M CHES pH 9.67, 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: 0.97903,0.91837
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011
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
10.979031
20.918371
ReflectionResolution: 2.9→48.823 Å / Num. all: 46139 / Num. obs: 15744 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 2.931 % / Biso Wilson estimate: 81.292 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allRsym value% possible all
2.9-2.970.810.56923331121611660.6922.995.9
2.97-3.050.5980.3842.93359117111380.465397.2
3.05-3.140.5590.3553.23132114210900.4312.995.4
3.14-3.240.4020.2414.62761111610390.2992.793.1
3.24-3.340.2390.1616.82992106810250.1972.996
3.34-3.460.1770.1278.33088104410220.153397.9
3.46-3.590.1360.09710.63171105910370.1173.197.9
3.59-3.740.120.08511.528209439140.1033.196.9
3.74-3.90.1070.07912.327019269040.096397.6
3.9-4.090.0910.06414.326139008720.078396.9
4.09-4.320.070.05815.723628317940.07395.5
4.32-4.580.0670.0517.822438307860.0612.994.7
4.58-4.890.0670.04517.717207326700.0562.691.5
4.89-5.290.0520.04620.121747196940.0553.196.5
5.29-5.790.0550.04819.519276546300.0573.196.3
5.79-6.470.0620.05618.316655725380.0673.194.1
6.47-7.480.0660.0618.314995365040.072394
7.48-9.160.0440.04224.311234454020.0512.890.3
9.16-12.950.0270.03230.99093373060.039390.8
12.95-48.8230.0280.03334.15492001770.043.188.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.9→48.823 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9087 / Occupancy max: 1 / Occupancy min: 0.75 / 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. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 794 5.07 %RANDOM
Rwork0.1901 ---
obs0.1919 15665 95.93 %-
Displacement parametersBiso max: 137.6 Å2 / Biso mean: 59.6988 Å2 / Biso min: 27.89 Å2
Baniso -1Baniso -2Baniso -3
1-3.832 Å20 Å21.8583 Å2
2---4.6892 Å20 Å2
3---0.8572 Å2
Refine analyzeLuzzati coordinate error obs: 0.418 Å
Refinement stepCycle: LAST / Resolution: 2.9→48.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5321 0 0 0 5321
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2465SINUSOIDAL4
X-RAY DIFFRACTIONt_trig_c_planes127HARMONIC2
X-RAY DIFFRACTIONt_gen_planes793HARMONIC5
X-RAY DIFFRACTIONt_it5457HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion704SEMIHARMONIC5
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_contact5750SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5457HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7409HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion2.72
LS refinement shellResolution: 2.9→3.1 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2954 153 5.34 %
Rwork0.2339 2712 -
all0.2374 2865 -
obs--95.93 %
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)
12.4148-0.05421.56550.5285-0.07062.8352-0.02020.3386-0.1274-0.0144-0.01220.03780.0375-0.19320.0324-0.12990.02740.0603-0.1312-0.14330.08768.071584.760434.31
22.09890.14241.31030.71930.89022.4436-0.1312-0.1111-0.05470.02390.1314-0.01120.00170.3057-0.0002-0.09080.04090.0371-0.081-0.03210.018728.947289.962556.2052
32.2684-0.27241.65132.2713-0.22534.1972-0.1652-0.2961-0.0623-0.0559-0.0861-0.0872-0.37960.08620.2513-0.0894-0.0162-0.0172-0.18940.0639-0.055942.1068124.44151.1779
41.44730.58221.03291.72520.6952.6309-0.0940.356-0.1168-0.2126-0.00130.1556-0.25290.0350.09530.00420.0818-0.0403-0.11680.0127-0.07530.7545117.92823.5436
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 188
2X-RAY DIFFRACTION2B20 - 188
3X-RAY DIFFRACTION3C20 - 188
4X-RAY DIFFRACTION4D20 - 188

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