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- PDB-4ntl: Crystal structure of a lipoprotein, YaeC family (EF3198) from Ent... -

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Basic information

Entry
Database: PDB / ID: 4ntl
TitleCrystal structure of a lipoprotein, YaeC family (EF3198) from Enterococcus faecalis V583 at 1.80 A resolution
ComponentsLipoprotein, YaeC family
KeywordsTRANSPORT PROTEIN / NLPA lipoprotein / PF03180 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
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
ACETATE ION / Lipoprotein, YaeC family
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.799 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a lipoprotein, YaeC family (EF3198) from Enterococcus faecalis V583 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: Lipoprotein, YaeC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,33112
Polymers27,6771
Non-polymers65411
Water5,044280
1
A: Lipoprotein, YaeC family
hetero molecules

A: Lipoprotein, YaeC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,66224
Polymers55,3532
Non-polymers1,30922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3800 Å2
ΔGint-189 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.161, 97.161, 144.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-301-

ZN

21A-571-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lipoprotein, YaeC family / YaeC family lipoprotein


Mass: 27676.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: EF_3198, I574_00285, NP_816800.1, OO5_00380 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q82Z74

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Non-polymers , 5 types, 291 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 27-272) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 27-272) 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6
Details: 0.2000M zinc acetate, 10.0000% polyethylene glycol 8000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979347,0.918401,0.979261
DetectorType: ADSC Q315 / Detector: CCD / Date: Oct 17, 2013 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9793471
20.9184011
30.9792611
ReflectionResolution: 1.799→29.013 Å / Num. all: 32421 / Num. obs: 32421 / % possible obs: 100 % / Redundancy: 13.8 % / Rsym value: 0.168 / Net I/σ(I): 11.3
Reflection shell

Rmerge(I) obs: 0.019 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.799-1.8513.60.33223723661.911100
1.85-1.914.10.33241923021.928100
1.9-1.9513.40.53008022431.232100
1.95-2.0114.313079421600.708100
2.01-2.0814.11.33010921310.543100
2.08-2.1514.21.82905020410.399100
2.15-2.23141.82784619830.393100
2.23-2.3213.41.82552119090.345100
2.32-2.4314.23.42590618280.211100
2.43-2.5514.13.92464917480.179100
2.55-2.6814.14.52351216710.157100
2.68-2.85145.32223615840.133100
2.85-3.0413.85.82074414980.117100
3.04-3.2913.861924713960.112100
3.29-3.613.36.11725912930.105100
3.6-4.0212.55.81480311840.109100
4.02-4.65137.11361810450.089100
4.65-5.6913.28.3118929000.075100
5.69-8.0513.58.997437200.069100
8.05-29.01312.31151604190.05497.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.799→29.013 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 4.326 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.WATERS WERE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4.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. 5. ZINC (ZN) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED INTO THE STRUCTURE. THE MODELING OF ZINC IS SUPPORTED BY ANOMALOUS DIFFERENCE ELECTRON DENSITY MAPS.6. 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 7.SODIUM (NA) FROM THE PURIFICATION BUFFER AND ACETATE (ACT) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 1640 5.1 %RANDOM
Rwork0.179 ---
obs0.1807 32352 99.52 %-
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: 115.29 Å2 / Biso mean: 29.1971 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.799→29.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 26 280 2192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022036
X-RAY DIFFRACTIONr_bond_other_d0.0010.021989
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9942766
X-RAY DIFFRACTIONr_angle_other_deg0.80734636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8595275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.45227.12894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30815367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.914152
X-RAY DIFFRACTIONr_chiral_restr0.0920.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022337
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02407
X-RAY DIFFRACTIONr_mcbond_it3.2533.9571006
X-RAY DIFFRACTIONr_mcbond_other3.2043.9491003
X-RAY DIFFRACTIONr_mcangle_it4.1917.3661263
LS refinement shellResolution: 1.799→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 122 -
Rwork0.309 2161 -
all-2283 -
obs--96.98 %
Refinement TLS params.Method: refined / Origin x: 5.2479 Å / Origin y: 34.2901 Å / Origin z: 19.3299 Å
111213212223313233
T0.0277 Å20.0152 Å20.0004 Å2-0.035 Å2-0.0005 Å2--0.0202 Å2
L0.652 °2-0.0582 °20.0908 °2-0.306 °20.0436 °2--0.2433 °2
S-0.0374 Å °0.0119 Å °-0.0088 Å °0.0554 Å °0.0883 Å °-0.0215 Å °0.0322 Å °-0.0117 Å °-0.0509 Å °

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