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- PDB-4ef2: Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC... -

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Basic information

Entry
Database: PDB / ID: 4ef2
TitleCrystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 2.10 A resolution
ComponentsPheromone cOB1/lipoprotein, YaeC family
KeywordsMETHIONINE-BINDING PROTEIN / periplasmic methionine binding protein / NLPA lipoprotein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Lipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SELENOMETHIONINE / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lipoprotein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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

Downloads & links

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Assembly

Deposited unit
A: Pheromone cOB1/lipoprotein, YaeC family
B: Pheromone cOB1/lipoprotein, YaeC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1029
Polymers54,9412
Non-polymers1,1617
Water1,76598
1
A: Pheromone cOB1/lipoprotein, YaeC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9585
Polymers27,4711
Non-polymers4884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pheromone cOB1/lipoprotein, YaeC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1434
Polymers27,4711
Non-polymers6733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.225, 75.691, 143.815
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pheromone cOB1/lipoprotein, YaeC family


Mass: 27470.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_2496 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q831K8

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Non-polymers , 6 types, 105 molecules

#2: Chemical ChemComp-MSE / SELENOMETHIONINE


Type: L-peptide linking / Mass: 196.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2Se
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 28-272) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 28-272) 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 30.0% polyethylene glycol 400, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97966,0.97901
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2012
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
20.979661
30.979011
ReflectionResolution: 2.1→28.763 Å / Num. obs: 28845 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.876 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.170.7461.46344348464.9
2.17-2.260.5521.98913487381.8
2.26-2.360.3452.69143492188.5
2.36-2.490.2283.810809570994.8
2.49-2.640.1595.29729521494.1
2.64-2.850.1047.611397575297.3
2.85-3.130.06911.211199551097.6
3.13-3.590.04118.111247560596
3.59-4.510.02428.910207532093.9
4.510.01737.111189555795.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→28.763 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.455 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.191
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 RECORD CONTAINS 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.PEG FRAGMENTS (PEG, PGE AND PE8) FROM THE CRYSTALLIZATION SOLUTION AND CHLORIDE (CL) FROM THE PURIFICATION BUFFER HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 6.SELENO-METHIONINE (MSE) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON PUTATIVE ASSIGNMENT OF FUNCTION FROM PROTEIN STRUCTURE COMPARISONS AND ANOMALOUS DIFFERENCE FOURIER ELECTRON DENSITY MAPS. 7.RAMACHANDRAN OUTLIERS AT PHE84 IN BOTH PROTEIN ARE SUPPORTED BY ELECTRON DENSITY AND LIE IN THE VICINITY OF THE PUTATIVE ACTIVE SITE. 8.NCS RESTRAINTS WERE APPLIED USING REFMAC's LOCAL NCS OPTION (NCSR LOCAL). NCS GROUP 1 CHAIN A (30-270 TO CHAIN B (30-270) COUNT: 8183, RMS: 0.12, WEIGHT: 0.05.
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1458 5.1 %RANDOM
Rwork0.1875 ---
obs0.1898 28794 95.25 %-
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: 121.37 Å2 / Biso mean: 52.5789 Å2 / Biso min: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å20 Å20 Å2
2---0.87 Å20 Å2
3---4.69 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 68 98 3912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.023911
X-RAY DIFFRACTIONr_bond_other_d0.0060.022556
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9735319
X-RAY DIFFRACTIONr_angle_other_deg1.46536330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3595492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80826.322174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34615646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.003158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214315
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02693
X-RAY DIFFRACTIONr_nbd_refined0.2140.2861
X-RAY DIFFRACTIONr_nbd_other0.2150.22331
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21863
X-RAY DIFFRACTIONr_nbtor_other0.1080.21610
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.140.214
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 80 -
Rwork0.297 1518 -
all-1598 -
obs--77.95 %
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)
12.74551.9690.35463.91080.18950.9602-0.05060.107-0.0231-0.1610.11490.15010.0073-0.0961-0.06420.13490.03340.00080.08130.01460.019313.717810.251831.738
22.60850.9029-0.29913.9902-1.01371.94950.05840.0327-0.3265-0.05050.0540.23570.1577-0.2892-0.11240.2146-0.0115-0.04230.32540.07880.09654.190837.80496.9745
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 270
2X-RAY DIFFRACTION2B30 - 270

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