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- PDB-5bra: Crystal Structure of a putative Periplasmic Solute binding protei... -

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Basic information

Entry
Database: PDB / ID: 5bra
TitleCrystal Structure of a putative Periplasmic Solute binding protein (IPR025997) from Ochrobactrum Anthropi ATCC49188 (Oant_2843, TARGET EFI-511085)
ComponentsPutative periplasmic binding protein with substrate ribose
KeywordsSOLUTE-BINDING PROTEIN / Periplasmic solute binding Protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


amino acid transport / periplasmic space
Similarity search - Function
: / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Periplasmic binding protein with substrate ribose
Similarity search - Component
Biological speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.971 Å
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. ...Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal Structure of a putative Periplasmic Solute binding protein (IPR025997) from Ochrobactrum Anthropi ATCC49188(Oant_2843, TARGET EFI-511085)
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, ...Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMay 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative periplasmic binding protein with substrate ribose


Theoretical massNumber of molelcules
Total (without water)38,5381
Polymers38,5381
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.204, 81.204, 103.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein Putative periplasmic binding protein with substrate ribose


Mass: 38538.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (strain ATCC 49188 / DSM 6882 / NCTC 12168) (bacteria)
Strain: ATCC 49188 / DSM 6882 / NCTC 12168 / Gene: Oant_2843 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6X2U7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.22 Å3/Da / Density % sol: 44.51 % / Description: pyramid
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (20 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-ribulose); Reservoir (2.5M Ammonium sulphate, 0.1M TRIS, pH 8.5); Cryoprotection (80% Lithium sulfate, 20% Reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 18, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.97→23.8 Å / Num. obs: 7605 / % possible obs: 100 % / Redundancy: 28.3 % / Biso Wilson estimate: 58.6 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.02 / Rrim(I) all: 0.109 / Χ2: 0.98 / Net I/av σ(I): 38.729 / Net I/σ(I): 11.3 / Num. measured all: 215050
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
2.97-3.0229.10.9823750.9580.1840.9990.881
3.02-3.0829.20.7653660.9650.1430.7780.893
3.08-3.1328.90.6793730.9610.1270.6910.885
3.13-3.229.20.4933520.9830.0920.5020.854
3.2-3.2729.10.3853780.9810.0720.3920.878
3.27-3.34290.3113610.9910.0580.3160.892
3.34-3.4328.90.2433800.9920.0460.2470.86
3.43-3.52290.2173680.9940.0410.2210.875
3.52-3.6228.80.2173750.9920.0410.2210.963
3.62-3.7428.70.1323700.9960.0250.1351.185
3.74-3.8728.40.1093880.9970.0210.1110.816
3.87-4.03290.1013700.9970.0190.1030.851
4.03-4.2128.50.0823660.9980.0150.0830.796
4.21-4.4328.40.0763850.9970.0140.0780.839
4.43-4.7128.30.0743860.9980.0140.0750.866
4.71-5.0728.10.0863860.9990.0160.0881.229
5.07-5.5727.70.1033770.9970.020.1051.657
5.57-6.3627.30.0993990.9960.0190.1011.614
6.36-7.9626.80.0624070.9980.0120.0630.844
7.96-23.824.20.0734430.9970.0140.0740.942

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D02

3d02


Resolution: 2.971→23.615 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2951 354 4.7 %
Rwork0.179 7173 -
obs0.1843 7527 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.76 Å2 / Biso mean: 42.4013 Å2 / Biso min: 12.55 Å2
Refinement stepCycle: final / Resolution: 2.971→23.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 0 1 2372
Biso mean---21.37 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012413
X-RAY DIFFRACTIONf_angle_d1.3863274
X-RAY DIFFRACTIONf_chiral_restr0.055371
X-RAY DIFFRACTIONf_plane_restr0.005425
X-RAY DIFFRACTIONf_dihedral_angle_d15.221864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9709-3.39970.3617940.218923522446100
3.3997-4.27910.29881260.17532334246098
4.2791-23.61560.2721340.166724872621100
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)
10.29250.1424-0.02940.29120.02070.24920.1068-0.140.2108-0.0343-0.0350.0008-0.0442-0.00440.00430.1423-0.01580.00640.2846-0.10580.2373-23.50230.3253-9.1828
20.1052-0.03820.11540.1744-0.04020.17220.0309-0.147-0.2681-0.02310.01250.12880.1456-0.1061-0.00090.2164-0.0291-0.03180.2434-0.01690.2486-16.56667.4377-12.6852
30.4213-0.18-0.22240.07940.09840.12780.0888-0.22940.4265-0.02880.08-0.3327-0.14650.1640.35780.0228-0.19120.06640.3575-0.21020.3445-13.198932.6219-4.2965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 162 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 282 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 283 through 344 )A0

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