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- PDB-4mo9: Crystal Structure of TroA-like Periplasmic Binding Protein FepB f... -

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Basic information

Entry
Database: PDB / ID: 4mo9
TitleCrystal Structure of TroA-like Periplasmic Binding Protein FepB from Veillonella parvula
ComponentsPeriplasmic binding protein
KeywordsSOLUTE-BINDING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / periplasmic binding protein / solute binding protein-fold / PROTEIN BINDING
Function / homologyABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / trimethylamine oxide / Periplasmic binding protein
Function and homology information
Biological speciesVeillonella parvula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.925 Å
AuthorsKim, Y. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of TroA-like Periplasmic Binding Protein FepB from Veillonella parvula
Authors: Kim, Y. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8393
Polymers41,6711
Non-polymers1672
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.402, 75.999, 125.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Periplasmic binding protein


Mass: 41671.336 Da / Num. of mol.: 1 / Fragment: UNP residues 25-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: DSM 2008 / Gene: Vpar_0195 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D1BQR9
#2: Chemical ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Trimethylamine N-oxide, 0.1 M Tris pH 8.5, 20 %(w/v) PEGMME2000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97987 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 29285 / Num. obs: 29285 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 32.75 Å2 / Rsym value: 0.103 / Net I/σ(I): 9.9
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 1450 / Rsym value: 0.792 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
PHENIX(phenix.refine: dev_1367)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.925→36.361 Å / SU ML: 0.19 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1484 5.08 %random
Rwork0.166 ---
all0.168 29206 --
obs0.168 29206 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.5 Å2
Refinement stepCycle: LAST / Resolution: 1.925→36.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 11 198 2964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082833
X-RAY DIFFRACTIONf_angle_d1.0353834
X-RAY DIFFRACTIONf_dihedral_angle_d13.1971047
X-RAY DIFFRACTIONf_chiral_restr0.071416
X-RAY DIFFRACTIONf_plane_restr0.005490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9254-1.98750.30961430.25732417256097
1.9875-2.05860.25241290.216724662595100
2.0586-2.1410.22021210.195724972618100
2.141-2.23840.24731200.179225162636100
2.2384-2.35640.24791400.178224712611100
2.3564-2.5040.21281290.185725252654100
2.504-2.69730.2571310.177425112642100
2.6973-2.96860.22831500.18325172667100
2.9686-3.39790.1931460.165525292675100
3.3979-4.27990.16691350.142125882723100
4.2799-36.36770.16251400.14912685282599
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)
10.83630.3230.63291.5129-0.15141.7027-0.062-0.03320.2630.00380.01240.0206-0.3547-0.13330.01380.25950.05030.00620.2499-0.05230.310425.877878.6188-2.6985
21.47460.28020.38951.41210.2591.970.0267-0.2306-0.0530.080.0145-0.12470.0710.0342-0.03550.23890.0350.00110.27950.00010.262524.65864.7287-3.0453
31.39690.1561-0.12341.8370.46132.0629-0.14250.31450.0391-0.41870.0959-0.1358-0.00680.08960.0520.3754-0.00630.01680.36320.02020.270822.940464.7997-27.6638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 114 )
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 366 )

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