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- PDB-4l8j: Crystal structure of a Putative efflux transporter (BACEGG_01895)... -

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Basic information

Entry
Database: PDB / ID: 4l8j
TitleCrystal structure of a Putative efflux transporter (BACEGG_01895) from Bacteroides eggerthii DSM 20697 at 2.06 A resolution
ComponentsPutative efflux transporter
KeywordsTRANSPORT PROTEIN / HlyD family secretion protein / PF00529 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Efflux pump adaptor protein, beta barrel domain / Helix hairpin bin / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Beta Barrel / Orthogonal Bundle ...conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Efflux pump adaptor protein, beta barrel domain / Helix hairpin bin / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / :
Similarity search - Component
Biological speciesBacteroides eggerthii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.06 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative efflux transporter (BACEGG_01895) from Bacteroides eggerthii DSM 20697 at 2.06 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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 1.4Nov 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

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Assembly

Deposited unit
A: Putative efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2526
Polymers36,7491
Non-polymers5035
Water3,135174
1
A: Putative efflux transporter
hetero molecules

A: Putative efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,50412
Polymers73,4992
Non-polymers1,00510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10430 Å2
ΔGint-37 kcal/mol
Surface area37610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.536, 69.536, 187.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-403-

PEG

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Components

#1: Protein Putative efflux transporter


Mass: 36749.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Strain: DSM 20697 / Gene: BACEGG_01895, ZP_03459111.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7AHL2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 24-350) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 24-350) 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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.83
Details: 12.0% polyethylene glycol 8000, 0.1M sodium chloride, 0.1M CAPS pH 9.83, 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: 0.97871, 0.91837, 0.97817
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013
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
10.978711
20.918371
30.978171
ReflectionResolution: 2.06→46.486 Å / Num. obs: 29410 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.746 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.06-2.130.8842.218362272799.9
2.13-2.220.6712.920096304099.9
2.22-2.320.4444.117630286199.9
2.32-2.440.3585.319081281599.9
2.44-2.590.2557.119311288599.9
2.59-2.790.1849.518537291799.9
2.79-3.070.10415.9192322939100
3.07-3.520.06424.219664301699.9
3.52-4.420.04234.518857297199.6
4.420.03737.919142323999.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.06→46.486 Å / Cor.coef. Fo:Fc: 0.9367 / Cor.coef. Fo:Fc free: 0.9229 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. PEG FRAGMENTS (PEG) FROM THE CRYSTALLIZATION AND GLYCEROL (GOL) USED ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. PEG FRAGMENTS (PEG) FROM THE CRYSTALLIZATION AND GLYCEROL (GOL) USED AS A CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE.3. THE REFINEMEMT WAS RESTRAINED AGAINST THE MAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1493 5.08 %RANDOM
Rwork0.208 ---
obs0.2093 29369 99.84 %-
Displacement parametersBiso max: 116.81 Å2 / Biso mean: 46.9515 Å2 / Biso min: 24.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.2986 Å20 Å20 Å2
2--0.2986 Å20 Å2
3----0.5972 Å2
Refine analyzeLuzzati coordinate error obs: 0.339 Å
Refinement stepCycle: LAST / Resolution: 2.06→46.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 33 174 2741
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1261SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes382HARMONIC5
X-RAY DIFFRACTIONt_it2636HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion360SEMIHARMONIC5
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_contact3041SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2636HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3575HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion2.71
LS refinement shellResolution: 2.06→2.13 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2498 146 5.2 %
Rwork0.2195 2662 -
all0.2211 2808 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: 21.2691 Å / Origin y: 10.4219 Å / Origin z: 54.4325 Å
111213212223313233
T-0.1195 Å2-0.0094 Å20.0126 Å2-0.0037 Å2-0.0327 Å2---0.0273 Å2
L0.3815 °20.5029 °20.5026 °2-0.5143 °20.4669 °2--0.8057 °2
S-0.0866 Å °0.1685 Å °0.0389 Å °-0.0685 Å °0.1559 Å °0.0211 Å °-0.0639 Å °0.1765 Å °-0.0693 Å °
Refinement TLS groupSelection details: { A|25 - 350 }

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