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- PDB-4e9k: Crystal structure of a DUF4465 family protein (BACOVA_04221) from... -

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Basic information

Entry
Database: PDB / ID: 4e9k
TitleCrystal structure of a DUF4465 family protein (BACOVA_04221) from Bacteroides ovatus ATCC 8483 at 2.31 A resolution
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF14717 family protein / DUF4465 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF4465 / Protein of unknown function DUF4465 / Domain of unknown function (DUF4465) / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.31 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_04221) from Bacteroides ovatus ATCC 8483 at 2.31 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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 6, 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: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8385
Polymers27,4541
Non-polymers3844
Water1,65792
1
A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,67610
Polymers54,9072
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_576x,-y+2,-z+3/21
Buried area3180 Å2
ΔGint-121 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.156, 93.156, 103.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-300-

SO4

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein hypothetical protein


Mass: 27453.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_04221 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M287
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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 22-261 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: 4.07 Å3/Da / Density % sol: 69.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.4M ammonium sulfate, 0.1M MES pH 6.0, 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: 0.91837,0.97975,0.97908
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2012
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
10.918371
20.979751
30.979081
ReflectionResolution: 2.31→45.108 Å / Num. obs: 20538 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.557 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.31-2.390.8752.113629196899.9
2.39-2.490.7652.3133792077100
2.49-2.60.5683.313835195399.9
2.6-2.740.3974.6149142083100
2.74-2.910.2686.8141721993100
2.91-3.130.15811.313713198399.5
3.13-3.450.08918.413896208199.7
3.45-3.940.05728.6145062044100
3.94-4.950.03738.113533208999.9
4.950.03443.714686226799.6

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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
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.31→45.108 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 10.054 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.155
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. SULFATE (SO4) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 1041 5.1 %RANDOM
Rwork0.1785 ---
obs0.1798 20507 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 182.3 Å2 / Biso mean: 55.8103 Å2 / Biso min: 27.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2--1.2 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.31→45.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 20 92 2029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021993
X-RAY DIFFRACTIONr_bond_other_d0.0010.021277
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9542716
X-RAY DIFFRACTIONr_angle_other_deg0.8613.0013116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04725.3100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82615313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.213154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 65 -
Rwork0.263 1256 -
all-1321 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 32.219 Å / Origin y: 87.165 Å / Origin z: 60.487 Å
111213212223313233
T0.0551 Å2-0.0076 Å20.0185 Å2-0.078 Å2-0.0169 Å2--0.0129 Å2
L1.7536 °20.4842 °2-0.2134 °2-0.6736 °2-0.0325 °2--1.4157 °2
S0.0147 Å °0.2348 Å °-0.0705 Å °-0.0119 Å °-0.0053 Å °-0.0186 Å °0.1156 Å °-0.0396 Å °-0.0094 Å °

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