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- PDB-4ecf: Crystal structure of an ABC-type phosphate transport system, peri... -

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Basic information

Entry
Database: PDB / ID: 4ecf
TitleCrystal structure of an ABC-type phosphate transport system, periplasmic component (LVIS_0633) from Lactobacillus brevis ATCC 367 at 1.55 A resolution
ComponentsABC-type phosphate transport system, periplasmic component
KeywordsPHOSPHATE-BINDING PROTEIN / ABC transporter / phosphate transport receptor / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


phosphate ion transport / phosphate ion binding / plasma membrane
Similarity search - Function
Phosphate binding protein / : / PBP domain / PBP superfamily domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Phosphate-binding protein
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an ABC-type phosphate transport system, periplasmic component (LVIS_0633) from Lactobacillus brevis ATCC 367 at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 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 1.4Oct 16, 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: ABC-type phosphate transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,89512
Polymers28,1821
Non-polymers71311
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.204, 43.752, 71.475
Angle α, β, γ (deg.)90.000, 102.570, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein ABC-type phosphate transport system, periplasmic component


Mass: 28182.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Strain: ATCC 367 / Gene: LVIS_0633 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q03SP4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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 31-293 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium acetate, 20.0% 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: BL12-2 / Wavelength: 0.9116,0.9795,0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91161
20.97951
30.97931
ReflectionResolution: 1.55→27.274 Å / Num. obs: 38657 / % possible obs: 88.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.587 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.55-1.610.4441.810264681980.2
1.61-1.670.3512.510384642087.4
1.67-1.750.2723.112220742689.2
1.75-1.840.1884.411091687089.4
1.84-1.950.1355.810428657286.4
1.95-2.10.0838.511980717990.1
2.1-2.310.0591111794720090.5
2.31-2.650.04513.511586720189.5
2.65-3.330.03817.311957728792
3.330.02820.911996736392.1

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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: 1.55→27.274 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.963 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.079
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. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. ACETATE (ACT) FROM CRYSTALLIZATION SOLUTION, 1,2-ETHANEDIOL (EDO) FROM CRYOPROTECTION AND PHOSPHATE (PO4) FROM THE PURIFICATION SOLUTIONS ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 1928 5 %RANDOM
Rwork0.1622 ---
obs0.1639 38643 94.97 %-
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: 94.61 Å2 / Biso mean: 26.1055 Å2 / Biso min: 13.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-0.21 Å2
2---0.02 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 45 312 2319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022059
X-RAY DIFFRACTIONr_bond_other_d0.0010.021350
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9412789
X-RAY DIFFRACTIONr_angle_other_deg0.94233316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7085271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29925.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85815335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.367159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 125 -
Rwork0.245 2514 -
all-2639 -
obs--90.63 %
Refinement TLS params.Method: refined / Origin x: 28.979 Å / Origin y: 26.143 Å / Origin z: 19.038 Å
111213212223313233
T0.0738 Å2-0.0038 Å20.015 Å2-0.1373 Å2-0.0161 Å2--0.0068 Å2
L0.9522 °2-0.141 °2-0.3123 °2-0.0397 °20.0122 °2--0.2029 °2
S-0.012 Å °0.0143 Å °-0.0132 Å °-0.0021 Å °0.0161 Å °0.0031 Å °0.0215 Å °0.0286 Å °-0.0041 Å °

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