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- PDB-4ne4: Crystal structure of ABC transporter substrate binding protein Pr... -

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Basic information

Entry
Database: PDB / ID: 4ne4
TitleCrystal structure of ABC transporter substrate binding protein ProX from Agrobacterium tumefaciens cocrystalized with BTB
ComponentsABC transporter, substrate binding protein (Proline/glycine/betaine)
KeywordsTRANSPORT PROTEIN / putative ABC-type transporter / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


response to stress / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Osmoprotection protein (prox); domain 2 / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter, substrate binding protein (Proline/glycine/betaine)
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.73 Å
AuthorsTkaczuk, K.L. / Nicholls, R. / Kagan, O. / Chruszcz, M. / Domagalski, M.J. / Savchenko, A. / Joachimiak, A. / Murshudov, G. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of ABC transporter substrate binding protein ProX from Agrobacterium tumefaciens cocrystalized with BTB
Authors: Nicholls, R. / Tkaczuk, K.L. / Kagan, O. / Chruszcz, M. / Domagalski, M.J. / Savchenko, A. / Joachimiak, A. / Murshudov, G. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: ABC transporter, substrate binding protein (Proline/glycine/betaine)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8543
Polymers30,6091
Non-polymers2452
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.888, 64.388, 100.746
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter, substrate binding protein (Proline/glycine/betaine)


Mass: 30609.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (bacteria) / Strain: C58 / Gene: Atu0199 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CKK7
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG3350 25%, Li-Sulfate 0.2M, Bis-Tris 0.1M, pH 5.5, vapor diffusion, sitting drop, temperature 293K

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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: Mar 19, 2010 / Details: mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 31774 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.083 / Χ2: 1.765 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.73-1.766.50.45915670.8461100
1.76-1.797.80.40415520.8531100
1.79-1.838.10.3415680.9121100
1.83-1.868.10.28715430.9731100
1.86-1.980.24715941.0021100
1.9-1.958.10.19715441.0461100
1.95-28.10.16615851.1211100
2-2.058.10.14115361.1211100
2.05-2.1180.12715731.2571100
2.11-2.188.10.11115911.3131100
2.18-2.268.10.115611.4081100
2.26-2.3580.09415831.5211100
2.35-2.458.10.08915861.6371100
2.45-2.5880.08315791.8251100
2.58-2.7580.07715832.0341100
2.75-2.9680.07116152.351100
2.96-3.267.90.06816052.9621100
3.26-3.737.70.06616203.7941100
3.73-4.697.50.05216463.2191100
4.69-507.30.05417433.947199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.73→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1786 / WRfactor Rwork: 0.1451 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9176 / SU R Cruickshank DPI: 0.098 / SU Rfree: 0.0972 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.097
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1865 1602 5.1 %RANDOM
Rwork0.1516 ---
obs0.1533 31715 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.79 Å2 / Biso mean: 16.9227 Å2 / Biso min: 6.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---0.48 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 15 435 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022248
X-RAY DIFFRACTIONr_bond_other_d00.021450
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.973089
X-RAY DIFFRACTIONr_angle_other_deg4.29233611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3825312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18826.48994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07415358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.134155
X-RAY DIFFRACTIONr_chiral_restr0.2890.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212568
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02409
LS refinement shellResolution: 1.733→1.778 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 113 -
Rwork0.227 2160 -
all-2273 -
obs--97.72 %

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