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- PDB-3p02: Crystal structure of a protein of unknown function (BACOVA_00267)... -

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Basic information

Entry
Database: PDB / ID: 3p02
TitleCrystal structure of a protein of unknown function (BACOVA_00267) from Bacteroides ovatus at 1.55 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / 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) / hypothetical protein (bacova_03559) / Lipocalin / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a protein of unknown function (BACOVA_00267) from Bacteroides ovatus at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 27, 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 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 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 1.5Nov 27, 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)37,1427
Polymers36,7691
Non-polymers3726
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.920, 61.920, 96.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT A MONOMER IS A SIGNIFICANT OLIGOMERIC STATE IN SOLUTION.

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Components

#1: Protein Uncharacterized protein


Mass: 36769.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_00267 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7LR42
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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 23-338 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 19.50% polyethylene glycol 3350, 0.2570M lithium acetate, 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: 0.86700,0.97925,0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8671
20.979251
30.979131
ReflectionResolution: 1.55→29.466 Å / Num. all: 45435 / Num. obs: 45435 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 13.713 Å2 / Rsym value: 0.114 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.55-1.594.10.8771.61368033000.87798.8
1.59-1.634.20.7421.91328231940.74298.8
1.63-1.684.20.6382.21305731380.63898.8
1.68-1.734.20.5362.61256530260.53699.2
1.73-1.794.20.4273.31226629470.42799.1
1.79-1.854.20.3344.11184728500.33499.1
1.85-1.924.20.2635.21158227880.26399.5
1.92-24.10.26.61102226620.299.5
2-2.094.10.1767.81068225780.17699.6
2.09-2.194.10.14891016624510.14899.8
2.19-2.314.10.12410.2970723490.12499.9
2.31-2.454.10.10811.4929422490.10899.9
2.45-2.624.10.09512.3863821030.09599.9
2.62-2.834.10.08113.6809319600.08199.9
2.83-3.14.10.06616752818380.066100
3.1-3.474.10.0519.3675916610.05100
3.47-440.0521.2593114740.05100
4-4.940.04322.6501012600.043100
4.9-6.933.90.04519391510140.045100
6.93-29.4663.50.04718.121015930.04798.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
SCALA3.3.15data processing
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.55→29.466 Å / Cor.coef. Fo:Fc: 0.9603 / Cor.coef. Fo:Fc free: 0.9495 / Occupancy max: 1 / Occupancy min: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2286 5.04 %RANDOM
Rwork0.1646 ---
obs0.1659 45381 --
Displacement parametersBiso max: 100.62 Å2 / Biso mean: 21.216 Å2 / Biso min: 6.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.7679 Å20 Å20 Å2
2--0.4268 Å20 Å2
3---1.3411 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 0 24 489 3040
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1385SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes443HARMONIC5
X-RAY DIFFRACTIONt_it2869HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion370SEMIHARMONIC5
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_contact3809SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2869HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3935HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion4.36
X-RAY DIFFRACTIONt_other_torsion2.66
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2494 175 5.31 %
Rwork0.2186 3122 -
all0.2202 3297 -
Refinement TLS params.Method: refined / Origin x: 35.2493 Å / Origin y: 44.684 Å / Origin z: 25.3416 Å
111213212223313233
T-0.0033 Å20.0006 Å2-0.0005 Å2--0.0458 Å20.0029 Å2---0.0354 Å2
L0.2113 °2-0.107 °2-0.0347 °2-0.3671 °20.2404 °2--0.564 °2
S-0.0041 Å °-0.0232 Å °0.0189 Å °0.039 Å °-0.0084 Å °-0.0022 Å °-0.0215 Å °-0.0118 Å °0.0124 Å °

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