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- PDB-4mxt: Crystal structure of an Outer-membrane lipoprotein carrier protei... -

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Basic information

Entry
Database: PDB / ID: 4mxt
TitleCrystal structure of an Outer-membrane lipoprotein carrier protein (BACUNI_04723) from Bacteroides uniformis ATCC 8492 at 1.40 A resolution
ComponentsUncharacterized protein
KeywordsPROTEIN TRANSPORT / LolA-like prokaryotic lipoproteins and lipoprotein localization factors fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyOuter membrane lipoprotein carrier protein LolA / Lipoprotein localisation LolA/LolB/LppX / Outer membrane lipoprotein carrier protein LolA-like / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / Mainly Beta / DI(HYDROXYETHYL)ETHER / Outer membrane lipoprotein carrier protein LolA
Function and homology information
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACUNI_04723) from Bacteroides uniformis ATCC 8492 at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: 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 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0333
Polymers21,8211
Non-polymers2122
Water4,486249
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0666
Polymers43,6422
Non-polymers4244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3290 Å2
ΔGint12 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.262, 42.802, 64.550
Angle α, β, γ (deg.)90.000, 104.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein


Mass: 21820.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: BACUNI_04723 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7VAU1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 28-216) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 28-216) 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.20M di-ammonium tartrate, 20.)% polyethylene glycol 3350, 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: 0.91837,0.97971,0.97894
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 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
10.918371
20.979711
30.978941
ReflectionResolution: 1.4→27.049 Å / Num. obs: 36767 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.93 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.4-1.450.381.78448595679.7
1.45-1.510.2752.29541686388.1
1.51-1.580.173.510200701492.9
1.58-1.660.1284.69442656892.4
1.66-1.760.0936.19106648189
1.76-1.90.0648.810246713593.2
1.9-2.090.04413.39998693592.8
2.09-2.390.03616.89513668589.4
2.39-3.010.0319.99986688391.9
3.010.02125.39705665588.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
PHENIX1.8.2refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→27.049 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 0.13 / σ(F): 1.9 / Phase error: 16.44 / Stereochemistry target values: MLHL
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.POLYETHYLENE GLYCOL FRAGMENTS (PEG) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflection
Rfree0.1733 1850 5.03 %
Rwork0.1428 --
obs0.1443 36766 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.39 Å2 / Biso mean: 20.263 Å2 / Biso min: 8.3 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 14 249 1749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111831
X-RAY DIFFRACTIONf_angle_d1.3652534
X-RAY DIFFRACTIONf_chiral_restr0.086270
X-RAY DIFFRACTIONf_plane_restr0.006337
X-RAY DIFFRACTIONf_dihedral_angle_d13.987727
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.401-1.43890.25121190.22532516263590
1.4389-1.48120.22281260.18462689281596
1.4812-1.5290.19411500.15612718286898
1.529-1.58370.19321470.13632711285898
1.5837-1.64710.17871480.12512708285698
1.6471-1.7220.16351330.12022697283097
1.722-1.81280.16791300.12792662279296
1.8128-1.92640.18171660.12442755292198
1.9264-2.0750.1631500.11622689283998
2.075-2.28380.16381480.12352640278895
2.2838-2.6140.14131480.13962747289598
2.614-3.29240.17341550.15572672282795
3.2924-27.05370.1811300.15532712284294

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