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- PDB-5hnp: The structure of the kdo-capped saccharide binding subunit of the... -

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Basic information

Entry
Database: PDB / ID: 5hnp
TitleThe structure of the kdo-capped saccharide binding subunit of the O-12 specific ABC transporter, Wzt
ComponentsABC transporter
KeywordsTRANSPORT PROTEIN / O antigen export / carbohydrate binding subunit / ABC transporter
Function / homologyabc- transporter (atp binding component) like domain / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta / :
Function and homology information
Biological speciesRaoultella ornithinolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMallette, E. / Mann, E. / Whitfield, C. / Kimber, M.S.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Klebsiella pneumoniae O12 ATP-binding Cassette (ABC) Transporter Recognizes the Terminal Residue of Its O-antigen Polysaccharide Substrate.
Authors: Mann, E. / Mallette, E. / Clarke, B.R. / Kimber, M.S. / Whitfield, C.
History
DepositionJan 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Jul 6, 2016Group: Other
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter
B: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7463
Polymers41,7112
Non-polymers351
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-32 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.780, 104.070, 106.330
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


Mass: 20855.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raoultella ornithinolytica (bacteria) / Gene: TE10_19180 / Plasmid: pWQ284 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pEEM003) / References: UniProt: A0A0B5INH8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.17 Å3/Da / Density % sol: 61.19 % / Description: Prisms up to 600 micrometers in length
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris.Cl pH 8.5, 0.3 M sodium acetate, 20% w/v PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.03321 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27614 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.803 / Rsym value: 0.05 / Net I/σ(I): 20.06
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 7.52 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 2.35 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HNO

5hno


Resolution: 2.2→46.739 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.16 / Details: TLS employed. Hydrogen atoms in riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 1381 5 %Random
Rwork0.1928 ---
obs0.1941 27604 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 1 201 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042547
X-RAY DIFFRACTIONf_angle_d0.8893427
X-RAY DIFFRACTIONf_dihedral_angle_d14.315969
X-RAY DIFFRACTIONf_chiral_restr0.032393
X-RAY DIFFRACTIONf_plane_restr0.003439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.3371360.29312575X-RAY DIFFRACTION100
2.2786-2.36990.25821360.25492584X-RAY DIFFRACTION100
2.3699-2.47770.26081350.23352575X-RAY DIFFRACTION100
2.4777-2.60830.25721370.21382586X-RAY DIFFRACTION100
2.6083-2.77170.24321360.21932587X-RAY DIFFRACTION100
2.7717-2.98570.25911370.22392612X-RAY DIFFRACTION100
2.9857-3.28610.24971370.20232592X-RAY DIFFRACTION100
3.2861-3.76140.20161390.18652644X-RAY DIFFRACTION100
3.7614-4.73830.17581400.1342672X-RAY DIFFRACTION100
4.7383-46.7490.1611480.16252796X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.78850.6671-1.42150.92870.01212.3298-0.39191.18060.3564-1.27060.1010.4619-0.3127-0.6682-0.19110.777-0.1495-0.0370.6330.17960.066821.0418-20.9969-26.1758
20.9988-0.33630.20413.9601-3.98854.4033-0.30410.32070.6707-0.32570.08850.6921-0.5344-0.6663-0.15910.23250.0178-0.15040.29110.02720.39567.2495-19.0089-8.0335
32.90490.6543-0.55082.1093-0.01652.7834-0.23180.40980.1646-0.52090.1109-0.05080.1634-0.1180.11060.2229-0.04230.00780.1730.03120.135823.1706-22.8419-12.2318
43.2001-0.6727-1.96753.4111.62124.4258-0.10450.53090.3161-0.6689-0.0305-0.14-0.1068-0.12820.00920.3243-0.0386-0.01590.27950.12690.242525.0701-17.6035-17.0324
54.99470.6561-1.65162.65181.69014.09030.2006-0.75120.63670.2356-0.17760.6615-0.3388-0.4807-0.05210.17120.01520.01220.3188-0.15530.511719.1682-7.07548.4689
61.6216-0.05770.18413.96641.51783.09570.0055-0.45140.44520.2866-0.12510.0735-0.51460.3511-0.00160.4037-0.1033-0.03970.387-0.21020.400136.70577.109319.2637
74.85280.59731.28534.35241.83227.07010.021-0.9475-0.18230.7975-0.0441-0.00620.01060.09670.04030.28520.01790.02270.2836-0.03190.172335.6653-14.594815.4449
81.1691-0.30730.42362.67581.482.8637-0.0136-0.53040.52250.2329-0.24520.5243-0.4224-0.35610.03610.2865-0.00140.0730.3536-0.2310.467425.54631.160316.0916
90.3198-0.17240.18174.56413.22174.15080.0542-0.6180.21590.6007-0.13520.52980.04150.19360.18570.2557-0.04120.12080.3722-0.15030.290427.7064-6.858716.864
100.67980.50610.02812.77430.5622.87-0.0581-0.10550.5473-0.0688-0.3220.6924-0.9675-0.1512-0.05260.41720.0671-0.0820.2246-0.17430.544228.44746.383111.8137
113.09321.75721.41934.36122.15183.6771-0.0329-0.0581-0.0814-0.0715-0.0044-0.00250.06450.06740.00020.06460.02540.0330.13740.01230.166331.586-18.38951.5435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 276:311 )A276 - 311
2X-RAY DIFFRACTION2( CHAIN A AND RESID 312:322 )A312 - 322
3X-RAY DIFFRACTION3( CHAIN A AND RESID 323:401 )A323 - 401
4X-RAY DIFFRACTION4( CHAIN A AND RESID 402:422 )A402 - 422
5X-RAY DIFFRACTION5( CHAIN A AND RESID 423:438 )A423 - 438
6X-RAY DIFFRACTION6( CHAIN B AND RESID 275:312 )B275 - 312
7X-RAY DIFFRACTION7( CHAIN B AND RESID 313:328 )B313 - 328
8X-RAY DIFFRACTION8( CHAIN B AND RESID 329:375 )B329 - 375
9X-RAY DIFFRACTION9( CHAIN B AND RESID 376:390 )B376 - 390
10X-RAY DIFFRACTION10( CHAIN B AND RESID 391:414 )B391 - 414
11X-RAY DIFFRACTION11( CHAIN B AND RESID 415:440 )B415 - 440

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