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- PDB-4ljs: The crystal structure of a periplasmic binding protein from Veill... -

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Basic information

Entry
Database: PDB / ID: 4ljs
TitleThe crystal structure of a periplasmic binding protein from Veillonella parvula DSM 2008
ComponentsPeriplasmic binding protein
KeywordsTRANSPORT PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION / Periplasmic binding protein
Function and homology information
Biological speciesVeillonella parvula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.321 Å
AuthorsTan, K. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a periplasmic binding protein from Veillonella parvula DSM 2008
Authors: Tan, K. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionJul 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3113
Polymers37,1241
Non-polymers1872
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.994, 82.994, 110.419
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsExperimentally unknown. It is predicted to a monomer.

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Components

#1: Protein Periplasmic binding protein


Mass: 37123.527 Da / Num. of mol.: 1 / Fragment: UNP residues 20-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: DSM 2008 / Gene: Vpar_0062 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1BQD8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8M Potassium sodium tartrate, 0.1M Tris:HCl, 0.5%(w/v) PEG MME 5000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2013 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.32→30.2 Å / Num. all: 18692 / Num. obs: 18692 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 7.5 % / Biso Wilson estimate: 42.77 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 38.3
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 5 / Num. unique all: 938 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.321→30.119 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 953 5.11 %random
Rwork0.1538 ---
obs0.1564 18656 99.91 %-
all-18656 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.321→30.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 11 101 2620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062583
X-RAY DIFFRACTIONf_angle_d0.9153513
X-RAY DIFFRACTIONf_dihedral_angle_d14.184965
X-RAY DIFFRACTIONf_chiral_restr0.061394
X-RAY DIFFRACTIONf_plane_restr0.003454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3211-2.44340.25431510.18782496X-RAY DIFFRACTION100
2.4434-2.59640.2291360.18072531X-RAY DIFFRACTION100
2.5964-2.79680.24921310.18622513X-RAY DIFFRACTION100
2.7968-3.0780.29461370.19252545X-RAY DIFFRACTION100
3.078-3.52280.23021430.17582492X-RAY DIFFRACTION100
3.5228-4.43610.18321240.13392558X-RAY DIFFRACTION100
4.4361-30.12130.16411310.12772568X-RAY DIFFRACTION100
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)
14.25340.2483-0.23323.40340.20494.5993-0.0736-0.0470.04060.20520.0144-0.39560.08870.33490.06650.31510.0259-0.00080.3139-0.07420.327736.661525.448321.2532
23.52752.33710.33315.52230.23152.25090.055-0.117-0.09710.4157-0.16080.04770.3726-0.00890.0920.331-0.0030.02530.288-0.01530.190325.007321.070727.2582
31.94920.27931.2536.02765.67397.8988-0.13040.08080.0974-0.21620.042-0.1087-0.22970.09430.10770.2423-0.050.03460.2040.02110.23231.929632.991917.045
42.99762.60063.94093.45254.57728.38820.07120.0937-0.33380.14810.1246-0.37580.51090.5055-0.24870.28810.06180.09040.3616-0.02070.36936.277913.23298.003
56.8876-0.0527-0.44083.2545-0.13433.5882-0.19860.38780.2592-0.6057-0.22170.8041-0.489-0.38750.36470.35590.0448-0.10920.3213-0.07810.37515.824618.2629-2.803
65.7838-0.00761.75924.87320.10174.6996-0.56230.47320.7619-1.1597-0.11571.5532-0.9311-0.70750.57520.49930.1962-0.2250.5433-0.24790.93487.263118.114-3.3804
77.40891.20072.37112.27082.12295.23180.2716-1.38760.91570.5111-0.46151.1854-0.541-1.18490.30710.5670.06780.15461.0117-0.29160.82785.926916.744213.2096
83.82860.2863-0.09173.58851.09344.6352-0.157-0.0271-0.2236-0.274-0.25780.57230.1395-0.49890.31960.28550.02080.03080.3124-0.11090.386114.41879.95664.4485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 170 )
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 205 )
5X-RAY DIFFRACTION5chain 'A' and (resid 206 through 248 )
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 268 )
7X-RAY DIFFRACTION7chain 'A' and (resid 269 through 282 )
8X-RAY DIFFRACTION8chain 'A' and (resid 283 through 339 )

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