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- PDB-3nnd: The crystal structure of ABC transporter from Rhodopseudomonas pa... -

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Basic information

Entry
Database: PDB / ID: 3nnd
TitleThe crystal structure of ABC transporter from Rhodopseudomonas palustris
ComponentsPossible substrate binding protein of ABC transporter system
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / ABC transporter / SGX
Function / homologyLeucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Possible substrate binding protein of ABC transporter system
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of ABC transporter from Rhodopseudomonas palustris
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Possible substrate binding protein of ABC transporter system
A: Possible substrate binding protein of ABC transporter system
C: Possible substrate binding protein of ABC transporter system
D: Possible substrate binding protein of ABC transporter system


Theoretical massNumber of molelcules
Total (without water)161,4324
Polymers161,4324
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Possible substrate binding protein of ABC transporter system
A: Possible substrate binding protein of ABC transporter system


Theoretical massNumber of molelcules
Total (without water)80,7162
Polymers80,7162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-47 kcal/mol
Surface area30390 Å2
MethodPISA
3
C: Possible substrate binding protein of ABC transporter system
D: Possible substrate binding protein of ABC transporter system


Theoretical massNumber of molelcules
Total (without water)80,7162
Polymers80,7162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-46 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.742, 118.427, 93.464
Angle α, β, γ (deg.)90.00, 106.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Possible substrate binding protein of ABC transporter system


Mass: 40358.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA4397 / Plasmid: Codon+ril Stratagene / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3) / References: UniProt: Q6N1K8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 291 K / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→118.43 Å / Num. obs: 40725 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 56.58 Å2 / Rmerge(I) obs: 0.111
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.486 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→51.54 Å / SU ML: 0.51 / σ(F): 0.03 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.296 2019 4.96 %
Rwork0.244 --
obs0.246 40725 98.1 %
all-41463 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.84 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.2227 Å2-0 Å23.0359 Å2
2--1.4897 Å2-0 Å2
3---6.733 Å2
Refinement stepCycle: LAST / Resolution: 2.8→51.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10115 0 0 140 10255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710335
X-RAY DIFFRACTIONf_angle_d1.11413974
X-RAY DIFFRACTIONf_dihedral_angle_d19.0583724
X-RAY DIFFRACTIONf_chiral_restr0.0721594
X-RAY DIFFRACTIONf_plane_restr0.0061775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.31911220.26182683X-RAY DIFFRACTION94
2.87-2.94760.3791270.27242640X-RAY DIFFRACTION95
2.9476-3.03430.35031260.27442746X-RAY DIFFRACTION97
3.0343-3.13230.35961460.26922727X-RAY DIFFRACTION98
3.1323-3.24420.32791440.26142747X-RAY DIFFRACTION98
3.2442-3.37410.31051410.24782785X-RAY DIFFRACTION98
3.3741-3.52760.34311420.25232759X-RAY DIFFRACTION99
3.5276-3.71350.28481690.23122762X-RAY DIFFRACTION99
3.7135-3.94610.28131470.21872800X-RAY DIFFRACTION99
3.9461-4.25070.24731560.21892809X-RAY DIFFRACTION99
4.2507-4.67820.24921570.20792766X-RAY DIFFRACTION99
4.6782-5.35450.25181490.21472807X-RAY DIFFRACTION99
5.3545-6.74370.29331440.24792828X-RAY DIFFRACTION99
6.7437-51.54760.28891490.24882847X-RAY DIFFRACTION99

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