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- PDB-4i95: Crystal structure of a Lipocalin-like protein (BACEGG_00036) from... -

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Basic information

Entry
Database: PDB / ID: 4i95
TitleCrystal structure of a Lipocalin-like protein (BACEGG_00036) from Bacteroides eggerthii DSM 20697 at 1.81 A resolution
ComponentsPutative uncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Lipocalin-like domain of PF13924 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyUncharacterised protein PF14869 family, DUF4488 / Lipocalin / Beta Barrel / Mainly Beta / Unknown ligand / :
Function and homology information
Biological speciesBacteroides eggerthii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACEGG_00036) from Bacteroides eggerthii DSM 20697 at 1.81 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 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 1.3Feb 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 1.4Oct 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

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,7324
Polymers32,7322
Non-polymers02
Water5,278293
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein

A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)65,4648
Polymers65,4644
Non-polymers04
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area13110 Å2
ΔGint-60 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.067, 103.067, 114.975
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Putative uncharacterized protein


Mass: 16365.923 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Strain: DSM 20697 / Gene: BACEGG_00036 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7ACC1
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 23-163) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 23-163) 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0000M lithium chloride, 20.0000% polyethylene glycol 6000, 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: BL12-2 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→48.331 Å / Num. obs: 33477 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.921 Å2 / Rmerge(I) obs: 0.193 / Net I/σ(I): 15.74
Reflection shell

Rmerge(I) obs: 0.016 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.81-1.872.91236093053100
1.87-1.954.51404103515100
1.95-2.0461281023311100
2.04-2.157.81309153369100
2.15-2.2810.41280773165100
2.28-2.4612.71318803393100
2.46-2.715.31263923238100
2.7-3.0922.1133569336399.9
3.09-3.8933.31318363417100
3.8939132442365399.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→48.331 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.392 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107
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 RECORDS CONTAIN 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.AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE IN BOTH MONOMERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 1693 5.1 %RANDOM
Rwork0.1738 ---
obs0.1753 33450 99.98 %-
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: 90.51 Å2 / Biso mean: 26.9803 Å2 / Biso min: 10.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.35 Å2-0 Å2
2---0.35 Å2-0 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.81→48.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 16 293 2517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192348
X-RAY DIFFRACTIONr_bond_other_d0.0050.022209
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9653212
X-RAY DIFFRACTIONr_angle_other_deg1.04435115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2665298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.82324.561114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61615372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3871511
X-RAY DIFFRACTIONr_chiral_restr0.1120.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212678
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02545
X-RAY DIFFRACTIONr_mcbond_it2.6392.8971120
X-RAY DIFFRACTIONr_mcbond_other2.642.8971119
X-RAY DIFFRACTIONr_mcangle_it3.6375.3811403
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 127 -
Rwork0.263 2295 -
all-2422 -
obs--99.96 %
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)
11.86310.31530.05351.8804-0.44061.4446-0.04360.1236-0.0182-0.12130.0422-0.09880.01690.00810.00140.0143-0.00040.00340.011-0.00450.007231.9317-0.565117.1439
21.8375-0.3681-0.47041.6770.22831.218-0.0142-0.1899-0.09380.0870.0347-0.086-0.030.058-0.02050.02050.0105-0.01250.0309-0.00140.023636.04771.90340.2128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 163
2X-RAY DIFFRACTION2B27 - 163

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