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- PDB-5khn: Crystal structures of the Burkholderia multivorans hopanoid trans... -

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Basic information

Entry
Database: PDB / ID: 5khn
TitleCrystal structures of the Burkholderia multivorans hopanoid transporter HpnN
ComponentsRND transporter
KeywordsMEMBRANE PROTEIN / transmembrane helices
Function / homology:
Function and homology information
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.445 Å
AuthorsSu, C.-C. / Yu, E.W.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Crystal structures of the Burkholderia multivorans hopanoid transporter HpnN.
Authors: Kumar, N. / Su, C.C. / Chou, T.H. / Radhakrishnan, A. / Delmar, J.A. / Rajashankar, K.R. / Yu, E.W.
History
DepositionJun 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Mar 6, 2024Group: 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: RND transporter
A: RND transporter


Theoretical massNumber of molelcules
Total (without water)187,0032
Polymers187,0032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-61 kcal/mol
Surface area71940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.914, 129.546, 111.728
Angle α, β, γ (deg.)90.000, 114.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RND transporter


Mass: 93501.477 Da / Num. of mol.: 2 / Mutation: R362A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (bacteria) / Gene: WM33_10510 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B4TSD3

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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: 4 Å3/Da / Density % sol: 69.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 3.5 / Details: 18% PEG2000, and 0.2M LiSo4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 27, 2016
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.45→100 Å / Num. obs: 38588 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 126.04 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.051 / Rrim(I) all: 0.132 / Χ2: 1.227 / Net I/σ(I): 7.3 / Num. measured all: 424764
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.45-3.5710.738460.6730.7120.91799.9
3.57-3.7210.338380.7690.520.95299.9
3.72-3.899.838300.8350.3831.00299.9
3.89-4.0911.638290.9610.211.0681000.6910.723
4.09-4.3511.638550.9770.1411.2011000.4640.485
4.35-4.6811.338700.9890.0881.35599.90.2860.3
4.68-5.1510.538170.9920.0681.32399.90.210.221
5.15-5.91239090.9940.0591.2321000.1970.206
5.9-7.4311.138520.9940.0411.34899.90.1320.139
7.43-10011.239420.9950.0261.899.90.080.084

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.445→93.803 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.319 1927 5 %
Rwork0.2831 36585 -
obs0.2848 38512 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217.92 Å2 / Biso mean: 127.5209 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.445→93.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12612 0 0 0 12612
Num. residues----1696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312872
X-RAY DIFFRACTIONf_angle_d0.60417607
X-RAY DIFFRACTIONf_chiral_restr0.0392175
X-RAY DIFFRACTIONf_plane_restr0.0052232
X-RAY DIFFRACTIONf_dihedral_angle_d14.3967726
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4445-3.53070.47271510.42362489264097
3.5307-3.62610.43591550.396426232778100
3.6261-3.73280.39141200.351126182738100
3.7328-3.85330.35921190.345626192738100
3.8533-3.99110.36921490.331326092758100
3.9911-4.15090.36651280.293726072735100
4.1509-4.33980.30141130.288726292742100
4.3398-4.56860.32691450.271325972742100
4.5686-4.85480.30061330.281126362769100
4.8548-5.22960.34281490.266725852734100
5.2296-5.75580.28831690.291525902759100
5.7558-6.58850.31481300.319226612791100
6.5885-8.30.29351360.256926242760100
8.3-93.83740.28431300.2452698282899

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