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- PDB-4ei0: Crystal structure of a DUF4466 family protein (PARMER_03218) from... -

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Basic information

Entry
Database: PDB / ID: 4ei0
TitleCrystal structure of a DUF4466 family protein (PARMER_03218) from Parabacteroides merdae ATCC 43184 at 2.00 A resolution
Componentsuncharacterized hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF14725 family protein / DUF4466 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF4466 / Domain of unknown function DUF4466 / PARMER_03128-like, N-terminal / Domain of unknown function (DUF4466) / Immunoglobulin-like / Sandwich / Mainly Beta / DUF4466 domain-containing protein
Function and homology information
Biological speciesParabacteroides merdae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (PARMER_03218) from Parabacteroides merdae ATCC 43184 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 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: uncharacterized hypothetical protein
B: uncharacterized hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5313
Polymers69,4392
Non-polymers921
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-11 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.749, 85.879, 128.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein uncharacterized hypothetical protein


Mass: 34719.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae (bacteria) / Strain: ATCC 43184 / Gene: PARMER_03218 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7AIG2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 23-333) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 23-333) 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 5.0% Glycerol, 19.0% polyethylene glycol 4000, 19.0% 2-propanol, 0.1M sodium citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→29.469 Å / Num. obs: 47406 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.338 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.070.7061.622873864297.5
2.07-2.150.5152.223198870698.3
2.15-2.250.4062.823882912398.3
2.25-2.370.3033.522843899197.5
2.37-2.520.2354.624565908498.8
2.52-2.710.1676.122990875098.4
2.71-2.990.19.623621912597.8
2.99-3.420.05915.723714885298.3
3.42-4.30.03623.222979878597.1
4.30.02927.423271883896.5

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Phasing

PhasingMethod: SAD

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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: SAD / Resolution: 2→29.469 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.887 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.148
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.GLYCEROL (GOL) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 2396 5.1 %RANDOM
Rwork0.1742 ---
obs0.1764 47345 99.12 %-
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: 157.07 Å2 / Biso mean: 51.4653 Å2 / Biso min: 28.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--1.2 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2→29.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4641 0 6 355 5002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.024795
X-RAY DIFFRACTIONr_bond_other_d0.0050.023142
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9636521
X-RAY DIFFRACTIONr_angle_other_deg1.18537738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.40625.437206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75915804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7651512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025398
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02934
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 146 -
Rwork0.252 3065 -
all-3211 -
obs--98.77 %
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)
10.4439-0.2180.35981.0994-1.06852.25650.017-0.0055-0.0034-0.10280.08340.07030.0303-0.2345-0.10040.0204-0.00450.01030.0331-0.00250.038632.5344.745413.8564
20.71080.2354-0.73960.7156-0.68152.74590.008-0.0395-0.06680.02190.02250.0419-0.0063-0.2738-0.03050.030.0092-0.03570.0644-0.01610.125432.209643.615477.7522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 171
2X-RAY DIFFRACTION1A172 - 333
3X-RAY DIFFRACTION2B32 - 171
4X-RAY DIFFRACTION2B172 - 333

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