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- PDB-4ygu: Crystal structure of a putative adhesin (BACEGG_01763) from Bacte... -

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Basic information

Entry
Database: PDB / ID: 4ygu
TitleCrystal structure of a putative adhesin (BACEGG_01763) from Bacteroides eggerthii DSM 20697 at 2.20 A resolution
Componentsputative adhesin
KeywordsCELL ADHESION / PF10988 family protein / DUF2807 / single-strabded right handed beta-helix fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / :
Function and homology information
Biological speciesBacteroides eggerthii DSM 20697 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative adhesin (BACEGG_01763) from Bacteroides eggerthii DSM 20697 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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: putative adhesin
B: putative adhesin
C: putative adhesin
D: putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,97524
Polymers79,5134
Non-polymers1,46220
Water3,567198
1
A: putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1896
Polymers19,8781
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1534
Polymers19,8781
Non-polymers2743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4639
Polymers19,8781
Non-polymers5858
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1715
Polymers19,8781
Non-polymers2924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.318, 101.555, 137.313
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
putative adhesin


Mass: 19878.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii DSM 20697 (bacteria)
Gene: BACEGG_01763 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7AH80
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 25-207) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 25-207) 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.67
Details: 1.0M lithium chloride, 22% polyethylene glycol 6000, 0.2M NDSB-256, 0.1M TRIS pH 8.67

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9792,0.9794,0.9116
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2014
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.91161
ReflectionResolution: 2.2→48.579 Å / Num. obs: 40038 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.05 % / Biso Wilson estimate: 36.546 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.157 / Net I/σ(I): 9.93 / Num. measured all: 322328
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
2.2-2.280.9441.1722.232659400839901.25199.6
2.28-2.370.9581.0472.532654390538901.11499.6
2.37-2.480.9431.0222.633199402240141.08899.8
2.48-2.610.9580.7663.531582393039220.81899.8
2.61-2.770.9650.5744.430021389738830.61599.6
2.77-2.980.9860.401632812391939110.42799.8
2.98-3.280.9940.2269.533192404940450.24199.9
3.28-3.760.9990.09116.631658407540650.09799.8
3.76-4.720.9990.06123.332404403740220.06699.6
4.720.9990.05326.832147433542960.05799.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHARPphasing
XDSJanuary 10, 2014 BUILT=20140307data scaling
BUSTER2.10.0refinement
XSCALEdata scaling
SHELXDphasing
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→48.579 Å / Cor.coef. Fo:Fc: 0.9514 / Cor.coef. Fo:Fc free: 0.9393 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
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. MAD PHASES WERE USED AS RESTRAINTS DURING THE REFINEMENT. 5. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 6. POLYETHYLENE GLYCOL FRAGMENTS (PEG AND PGE) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE. 7.1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAS BEEN MODELED INTO THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 2005 5.02 %RANDOM
Rwork0.2087 ---
obs0.2103 39954 99.66 %-
Displacement parametersBiso max: 180.24 Å2 / Biso mean: 64.6273 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.4258 Å20 Å20 Å2
2---1.4699 Å20 Å2
3---4.8957 Å2
Refine analyzeLuzzati coordinate error obs: 0.413 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 95 198 5255
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2360SINUSOIDAL10
X-RAY DIFFRACTIONt_trig_c_planes125HARMONIC2
X-RAY DIFFRACTIONt_gen_planes747HARMONIC5
X-RAY DIFFRACTIONt_it5103HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion687SEMIHARMONIC5
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_contact5374SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5103HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6855HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion1.65
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2626 132 4.55 %
Rwork0.2099 2769 -
all0.2123 2901 -
obs--99.66 %
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)
11.22960.2652-0.48722.68081.42915.17640.032-0.15-0.07430.47690.01520.06820.24130.1444-0.04720.54230.01690.0196-0.44060.0129-0.401717.106885.915662.5882
21.09580.03440.14513.87560.69815.0034-0.01910.20840.0333-0.73680.10160.2380.1481-0.1759-0.08250.6001-0.0533-0.0107-0.49890.014-0.485115.636466.887723.4735
31.04130.08540.48312.18231.37614.31040.0003-0.11050.0267-0.0506-0.0263-0.1499-0.35540.04690.0260.5648-0.00330.0192-0.491-0.001-0.455642.232161.123832.0866
41.69471.2572-0.8475.9217-1.20634.3330.1909-0.2846-0.17050.7146-0.2365-0.05670.04920.1070.04560.6079-0.02090.0186-0.59190.0245-0.57214.123939.791449.087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{ A|30-206 }0
2X-RAY DIFFRACTION2{ B|30-206 }0
3X-RAY DIFFRACTION3{ C|28-206 }0
4X-RAY DIFFRACTION4{ D|28-206 }0

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