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- PDB-4p98: ABC transporter system solute-bindng protein from Conexibacter wo... -

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Basic information

Entry
Database: PDB / ID: 4p98
TitleABC transporter system solute-bindng protein from Conexibacter woesei DSM 14684
ComponentsExtracellular solute-binding protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / APC transporter / solute binding protein. reductive methylation
Function / homology
Function and homology information


ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Basic membrane lipoprotein
Similarity search - Component
Biological speciesConexibacter woesei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsChang, C. / Endres, M. / Joachimiak, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: ABC transporter system solute-bindng protein from Conexibacter woesei DSM 14684
Authors: Chang, C. / Endres, M. / Joachimiak, G. / Joachimiak, A.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 11, 2015Group: Source and taxonomy
Revision 1.3Sep 27, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,91923
Polymers33,1611
Non-polymers1,75822
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.091, 79.091, 139.713
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-533-

HOH

21A-578-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Extracellular solute-binding protein


Mass: 33160.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conexibacter woesei (bacteria) / Strain: DSM 14684 / JCM 11494 / NBRC 100937 / ID131577 / Gene: Cwoe_2680 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: D3F9N7
#2: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Br
#3: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.0 M Ammonium Sulfate, 0.1 M Tris-Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91975 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35740 / % possible obs: 99.9 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.071 / Χ2: 0.989 / Net I/av σ(I): 40.184 / Net I/σ(I): 11.8 / Num. measured all: 495004
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.9312.10.8217580.857100
1.93-1.97130.64117560.873100
1.97-2.0114.10.5317350.865100
2.01-2.0514.30.44317520.869100
2.05-2.0914.20.35317670.901100
2.09-2.1414.30.29217620.923100
2.14-2.1914.30.25717490.917100
2.19-2.2514.30.20817740.946100
2.25-2.3214.30.18517670.927100
2.32-2.3914.30.1517670.968100
2.39-2.4814.20.13617720.984100
2.48-2.5814.30.11417490.998100
2.58-2.714.20.09817881100
2.7-2.8414.20.07818001.039100
2.84-3.0214.20.06417831.063100
3.02-3.25140.05118021.137100
3.25-3.5813.80.04418181.254100
3.58-4.0913.60.03918181.21100
4.09-5.1613.30.03518631.0599.9
5.16-50120.03619600.96297.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 1.9→24.68 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.264 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.109
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 1786 5 %RANDOM
Rwork0.1569 33809 --
obs0.1592 35595 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.31 Å2 / Biso mean: 22.785 Å2 / Biso min: 10.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20 Å2
2--0.05 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.9→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 22 280 2534
Biso mean--48.36 33.56 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192346
X-RAY DIFFRACTIONr_bond_other_d0.0010.022239
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.9673202
X-RAY DIFFRACTIONr_angle_other_deg0.74135129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2565315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8123.981108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2315347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4411520
X-RAY DIFFRACTIONr_chiral_restr0.070.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
X-RAY DIFFRACTIONr_rigid_bond_restr2.07634585
X-RAY DIFFRACTIONr_sphericity_free26.188583
X-RAY DIFFRACTIONr_sphericity_bonded8.44254756
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 122 -
Rwork0.201 2415 -
all-2537 -
obs--98.45 %

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