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- PDB-4pag: ABC transporter solute binding protein from Sulfurospirillum dele... -

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Basic information

Entry
Database: PDB / ID: 4pag
TitleABC transporter solute binding protein from Sulfurospirillum deleyianum DSM 6946
ComponentsPeriplasmic binding protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ABC transporter / solute binding protein
Function / homology
Function and homology information


Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2180 / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / DI(HYDROXYETHYL)ETHER / Periplasmic binding protein
Similarity search - Component
Biological speciesSulfurospirillum deleyianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsChang, C. / Endres, M. / Li, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of ABC transporter solute binding protein from Sulfurospirillum deleyianum DSM 6946
Authors: Chang, C. / Endres, M. / Li, H. / Joachimiak, A.
History
DepositionApr 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Source and taxonomy
Revision 1.2Mar 22, 2017Group: Source and taxonomy
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic binding protein
B: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7308
Polymers74,7762
Non-polymers9546
Water11,241624
1
A: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8464
Polymers37,3881
Non-polymers4583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8854
Polymers37,3881
Non-polymers4973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint27 kcal/mol
Surface area26370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.055, 50.813, 91.544
Angle α, β, γ (deg.)90.000, 98.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic binding protein


Mass: 37388.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurospirillum deleyianum (bacteria) / Strain: ATCC 51133 / DSM 6946 / 5175 / Gene: Sdel_2069 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1B4R1
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: magnesiun chloride, MES, PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 59912 / Num. obs: 59880 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.119 / Χ2: 0.799 / Net I/av σ(I): 16.769 / Net I/σ(I): 6.8 / Num. measured all: 426232
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.936.20.9629780.91799.9
1.93-1.976.90.86929500.868100
1.97-2.017.20.67329550.842100
2.01-2.057.20.55930040.853100
2.05-2.097.20.52529700.949100
2.09-2.147.20.41229670.856100
2.14-2.197.20.3429790.839100
2.19-2.257.20.29929610.918100
2.25-2.327.20.25630230.835100
2.32-2.397.20.20629400.796100
2.39-2.487.20.1929940.857100
2.48-2.587.20.15429670.804100
2.58-2.77.20.13130030.836100
2.7-2.847.30.10730020.732100
2.84-3.027.20.08429840.654100
3.02-3.257.20.07230060.655100
3.25-3.587.20.06530170.747100
3.58-4.097.10.05930110.756100
4.09-5.1670.04930570.583100
5.16-506.90.05831120.799.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.901→40.21 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.321 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.425 / ESU R Free: 0.128
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 3010 5.1 %RANDOM
Rwork0.1414 56524 --
obs0.1445 59534 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.34 Å2 / Biso mean: 24.137 Å2 / Biso min: 10.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.92 Å2
2---0.47 Å2-0 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 1.901→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 31 624 5875
Biso mean--27.72 36.16 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195528
X-RAY DIFFRACTIONr_bond_other_d0.0010.025317
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9767524
X-RAY DIFFRACTIONr_angle_other_deg0.7493.00112272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2365665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01624.591257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28215917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2871526
X-RAY DIFFRACTIONr_chiral_restr0.0710.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021262
X-RAY DIFFRACTIONr_rigid_bond_restr1.975310845
X-RAY DIFFRACTIONr_sphericity_free35.6985187
X-RAY DIFFRACTIONr_sphericity_bonded9.434511133
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 187 -
Rwork0.174 3885 -
all-4072 -
obs--92.15 %

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