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- PDB-4nd9: The putative substrate binding domain of ABC-type transporter fro... -

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Basic information

Entry
Database: PDB / ID: 4nd9
TitleThe putative substrate binding domain of ABC-type transporter from Agrobacterium tumefaciens in open conformation
ComponentsABC transporter, substrate binding protein (Proline/glycine/betaine)
KeywordsTRANSPORT PROTEIN / putative ABC-type transporter / Structural Genomics / PSI-Biology / 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: 2.3 Å
AuthorsNicholls, 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)
CitationJournal: To be Published
Title: The putative substrate binding domain of ABC-type transporter from Agrobacterium tumefaciens in open conformation
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 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter, substrate binding protein (Proline/glycine/betaine)


Theoretical massNumber of molelcules
Total (without water)30,6091
Polymers30,6091
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.702, 64.155, 101.123
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 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: PEG8000 20%, NaCl 0.2M, phosphate-citrate, pH 4.2, 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: MIRROR
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: 2.3→50 Å / Num. obs: 12333 / % possible obs: 85.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.3-2.34188.1
6.24-50186.9
4.95-6.24189.3
4.33-4.95184.5
3.93-4.33178.2
3.65-3.93182.4
3.44-3.65184.2
3.26-3.44185
3.12-3.26184.5
3-3.12185
2.9-3185.6
2.81-2.9186.3
2.73-2.81185.7
2.66-2.73186.5
2.59-2.66186.7
2.53-2.59186.2
2.48-2.53185.7
2.43-2.48186.1
2.38-2.43187.2
2.34-2.38185.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXSphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.861 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25282 597 4.9 %RANDOM
Rwork0.19963 ---
obs0.2022 11658 89.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.94 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å20 Å20 Å2
2---2.55 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 0 111 2181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222119
X-RAY DIFFRACTIONr_bond_other_d0.0010.021347
X-RAY DIFFRACTIONr_angle_refined_deg0.9611.9572897
X-RAY DIFFRACTIONr_angle_other_deg0.82233336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0575285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72525.97682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38615330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.29155
X-RAY DIFFRACTIONr_chiral_restr0.0490.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3261.51400
X-RAY DIFFRACTIONr_mcbond_other0.051.5570
X-RAY DIFFRACTIONr_mcangle_it0.63622245
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1193719
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8474.5649
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 44 -
Rwork0.247 867 -
obs--92.39 %

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