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Basic information

Entry
Database: PDB / ID: 4ler
TitleCrystal structure of a putative outer membrane protein, probably involved in nutrient binding (BVU_1254) from Bacteroides vulgatus ATCC 8482 at 1.42 A resolution
ComponentsPutative outer membrane protein, probably involved in nutrient binding
KeywordsSUGAR BINDING PROTEIN / SusD homolog / SusD-like_2 family (PF12771) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


SusD-like, tetratrico peptide repeats domain / SusD-like 2 / Starch-binding associating with outer membrane / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative outer membrane protein, probably involved in nutrient binding
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.42 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative outer membrane protein, probably involved in nutrient binding (BVU_1254) from Bacteroides vulgatus ATCC 8482 at 1.42 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 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 1.3Nov 27, 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 outer membrane protein, probably involved in nutrient binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3764
Polymers53,2691
Non-polymers1063
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.001, 71.001, 184.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative outer membrane protein, probably involved in nutrient binding


Mass: 53269.320 Da / Num. of mol.: 1 / Fragment: UNP residues 26-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_1254 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6KZT0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 26-493 OF 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.00M lithium chloride, 20.00% 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: BL11-1 / Wavelength: 0.91837,0.97891,0.97852
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 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
20.978911
30.978521
ReflectionResolution: 1.42→29.753 Å / Num. obs: 88866 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.315 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.43
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.43-1.480.9261.45420616443199.3
1.48-1.540.68425743016950199.4
1.54-1.610.562.55602516808199.6
1.61-1.70.4193.35560717676199.2
1.7-1.80.2824.75405515768199.6
1.8-1.940.1866.75826116962199.7
1.94-2.140.1189.85592917081199.3
2.14-2.440.07913.95574216295199.4
2.44-3.080.0617.25582116903199
3.08-29.7530.04322.95637516738198.8

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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
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.42→29.753 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 2.189 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.056
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. OTHER REFINEMENT REMARKS: 3. CHLORIDE (CL) IONS FROM PURIFICATION SOLUTIONS HAVE BEEN MODELED. 4. NEGATIVE DIFFERENCE DENSITY ON MANY CARBOXYLATE SIDE CHAINS IS LIKELY THE RESULT OF RADIATION DAMAGE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 4451 5 %RANDOM
Rwork0.1433 ---
obs0.1446 88746 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 59.72 Å2 / Biso mean: 27.0331 Å2 / Biso min: 16.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.42→29.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 3 550 4189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223895
X-RAY DIFFRACTIONr_bond_other_d0.0010.022608
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.9545317
X-RAY DIFFRACTIONr_angle_other_deg0.87636362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2025499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71424.639194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57215641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4211520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02828
X-RAY DIFFRACTIONr_mcbond_it1.99732385
X-RAY DIFFRACTIONr_mcbond_other1.33960
X-RAY DIFFRACTIONr_mcangle_it2.97553850
X-RAY DIFFRACTIONr_scbond_it4.06481510
X-RAY DIFFRACTIONr_scangle_it5.911111460
X-RAY DIFFRACTIONr_rigid_bond_restr1.53136503
X-RAY DIFFRACTIONr_sphericity_free5.9913568
X-RAY DIFFRACTIONr_sphericity_bonded3.63436393
LS refinement shellResolution: 1.424→1.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 298 -
Rwork0.249 5948 -
all-6246 -
obs--96.43 %

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