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- PDB-3rh3: Crystal structure of an Uncharacterized DUF3829-like protein (BT_... -

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Basic information

Entry
Database: PDB / ID: 3rh3
TitleCrystal structure of an Uncharacterized DUF3829-like protein (BT_1908) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution
ComponentsUncharacterized DUF3829-like protein
KeywordsStructural Genomics / Unknown function / All alpha protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-Biology
Function / homology
Function and homology information


Uncharacterised protein PF12889, C-terminal DUF3829 / : / DUF3829-like, C-terminal domain / Uncharacterised protein PF12889, N-terminal DUF3829 / : / Domain of unknown function (DUF6845) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DUF3829 domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an Uncharacterized DUF3829-like protein (BT_1908) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 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 1.4Oct 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 DUF3829-like protein
B: Uncharacterized DUF3829-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3108
Polymers60,8932
Non-polymers4166
Water3,063170
1
A: Uncharacterized DUF3829-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6774
Polymers30,4471
Non-polymers2303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized DUF3829-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6334
Polymers30,4471
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.409, 50.547, 87.943
Angle α, β, γ (deg.)90.000, 107.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized DUF3829-like protein


Mass: 30446.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_1908 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A6H6
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 27-289 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20.0% polyethylene glycol 3350 0.2M ammonium chloride, 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: 0.91162,0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979341
ReflectionResolution: 2.1→29.324 Å / Num. obs: 31006 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.033 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.24
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.11-2.190.4042.211616596291.7
2.19-2.270.3372.710784545295.6
2.27-2.380.2613.312487630995.9
2.38-2.50.213.911289571095.2
2.5-2.660.1734.811844597394.5
2.66-2.860.1226.211424577594.8
2.86-3.150.0868.211625588793.9
3.15-3.60.05911.111175566091.7
3.6-4.530.04414.911106562290.6
4.530.03415.611618589293

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.324 Å / Cor.coef. Fo:Fc: 0.9304 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.33 / 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. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 4. POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION AND ETHYLENE GLYCOL (EDO) USED AS A CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE. 5.THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 1561 5.05 %RANDOM
Rwork0.2121 ---
obs0.2137 30927 --
Displacement parametersBiso max: 118.14 Å2 / Biso mean: 49.7869 Å2 / Biso min: 25.42 Å2
Baniso -1Baniso -2Baniso -3
1--8.9895 Å20 Å2-4.7088 Å2
2--1.3986 Å20 Å2
3---7.5909 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3663 0 27 170 3860
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1832SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes114HARMONIC2
X-RAY DIFFRACTIONt_gen_planes563HARMONIC5
X-RAY DIFFRACTIONt_it3822HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion505SEMIHARMONIC5
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_contact4675SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3822HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5166HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion2.8
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2484 145 5.15 %
Rwork0.2122 2671 -
all0.2141 2816 -
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)
10.49660.3487-0.43721.2715-0.35462.24340.00380.13510.0596-0.04480.1250.0406-0.0953-0.1869-0.1288-0.05550.03190.084-0.130.0176-0.149-27.232415.346272.3961
20.8783-0.0921-0.64111.2084-0.31741.145-0.0328-0.0201-0.01210.06390.07190.1080.0765-0.1291-0.0391-0.0884-0.02580.0609-0.0919-0.006-0.0879-20.661944.05150.9284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|34 - A|289 }A34 - 289
2X-RAY DIFFRACTION2{ B|34 - B|289 }B34 - 289

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