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- PDB-4p33: Crystal structure of E. coli LptB-E163Q in complex with ATP-sodium -

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Basic information

Entry
Database: PDB / ID: 4p33
TitleCrystal structure of E. coli LptB-E163Q in complex with ATP-sodium
ComponentsLipopolysaccharide export system ATP-binding protein LptB
KeywordsHYDROLASE / ABC transporter / nucleotide-binding domain / ATPase / ATP binding
Function / homology
Function and homology information


Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities ...Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Lipopolysaccharide export system ATP-binding protein LptB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSherman, D.J. / Lazarus, M.B. / Murphy, L. / Liu, C. / Walker, S. / Ruiz, N. / Kahne, D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081059 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066174 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094263 United States
Harvard University United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Decoupling catalytic activity from biological function of the ATPase that powers lipopolysaccharide transport.
Authors: Sherman, D.J. / Lazarus, M.B. / Murphy, L. / Liu, C. / Walker, S. / Ruiz, N. / Kahne, D.
History
DepositionMar 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipopolysaccharide export system ATP-binding protein LptB
B: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,40011
Polymers55,8802
Non-polymers1,5219
Water2,684149
1
A: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules

A: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,49212
Polymers55,8802
Non-polymers1,61310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5650 Å2
ΔGint-35 kcal/mol
Surface area20020 Å2
2
B: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules

B: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,30810
Polymers55,8802
Non-polymers1,4298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5250 Å2
ΔGint-36 kcal/mol
Surface area19510 Å2
3
A: Lipopolysaccharide export system ATP-binding protein LptB
B: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules

A: Lipopolysaccharide export system ATP-binding protein LptB
B: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,80122
Polymers111,7594
Non-polymers3,04218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area15650 Å2
ΔGint-76 kcal/mol
Surface area34790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.620, 138.360, 101.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsBased on comparisons to nucleotide-binding domain structures deposited in the PDB and current literature in the ABC transporter field, we believe that the biologically relevant assembly of LptB-E163Q is a dimer formed by one polypeptide in the asymmetric unit and its symmetry mate.

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Components

#1: Protein Lipopolysaccharide export system ATP-binding protein LptB


Mass: 27939.775 Da / Num. of mol.: 2 / Mutation: E163Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lptB, yhbG, b3201, JW3168 / Plasmid: pET22/42 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX
References: UniProt: P0A9V1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.6 M sodium chloride, 0.1 M MES pH 7.0, 26.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.65→69.18 Å / Num. obs: 56025 / % possible obs: 99.2 % / Redundancy: 7.9 % / Biso Wilson estimate: 19.9 Å2 / Rpim(I) all: 0.053 / Rrim(I) all: 0.149 / Rsym value: 0.139 / Net I/av σ(I): 2.495 / Net I/σ(I): 9.2 / Num. measured all: 442034
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.65-1.7480.8060.96445080570.2990.8062.898.5
1.74-1.848.10.5021.56146476300.1860.5024.298.8
1.84-1.9780.3072.35788872050.1140.3076.499.2
1.97-2.1380.213.35415267420.0780.218.799.3
2.13-2.3380.1593.84966262300.0590.15910.999.6
2.33-2.617.90.1394.24473556560.0520.13912.499.7
2.61-3.017.80.124.53918950260.0450.1213.899.9
3.01-3.697.60.1144.33250643030.0440.11415.1100
3.69-5.227.30.1074.62415533250.0420.10715.899.4
5.22-40.8627.50.114.51383318510.0430.1115.895.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
CNSrefinement
SCALA3.3.16data scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
iMOSFLMdata reduction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P32

4p32


Resolution: 1.65→40.862 Å / FOM work R set: 0.8727 / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2844 5.08 %Random selection
Rwork0.1881 53160 --
obs0.1892 56004 98.97 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.985 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 70.84 Å2 / Biso mean: 25.9 Å2 / Biso min: 8.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.5336 Å2-0 Å20 Å2
2---2.9211 Å2-0 Å2
3---1.3875 Å2
Refinement stepCycle: final / Resolution: 1.65→40.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 94 149 3901
Biso mean--18.37 29.15 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073873
X-RAY DIFFRACTIONf_angle_d0.9655278
X-RAY DIFFRACTIONf_chiral_restr0.056610
X-RAY DIFFRACTIONf_plane_restr0.004674
X-RAY DIFFRACTIONf_dihedral_angle_d12.2951481
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.67850.33841340.31712624275898
1.6785-1.7090.29061530.27852605275898
1.709-1.74180.3111270.25472622274998
1.7418-1.77740.24351340.23832618275298
1.7774-1.81610.28041460.21122616276299
1.8161-1.85830.21911390.19292612275199
1.8583-1.90480.20341670.17812611277899
1.9048-1.95630.21311590.17222636279599
1.9563-2.01380.20771300.17142642277299
2.0138-2.07880.20731300.17852659278999
2.0788-2.15310.20121630.17352618278199
2.1531-2.23930.20551370.174126652802100
2.2393-2.34120.17361390.17692654279399
2.3412-2.46470.19511340.185226992833100
2.4647-2.6190.24111260.187526752801100
2.619-2.82120.2221490.191827062855100
2.8212-3.1050.21031390.198126992838100
3.105-3.55410.20361390.181627232862100
3.5541-4.47690.18941430.16592714285799
4.4769-40.87480.19881560.19422762291897
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)
10.9243-0.01581.13941.9361-0.02461.9494-0.2421-0.4549-0.19380.4030.0964-0.06730.18750.02980.0990.21340.0884-0.00210.24830.08020.156712.639-40.529544.061
28.64883.18110.23445.9117-0.89091.7621-0.2876-0.43470.27180.16920.0510.0055-0.01820.04540.2180.15390.0698-0.00120.14910.00790.11548.5165-36.336539.793
31.72690.35780.35510.6680.22391.0377-0.0623-0.13060.18680.17080.0418-0.47110.03230.4032-0.03390.15050.0868-0.10030.31590.05220.310722.2454-32.639640.7296
40.59080.03830.85542.8377-4.05227.1905-0.16760.00670.23760.35230.33320.4224-0.8922-0.5139-0.17760.20740.03380.0250.12790.03950.21097.2823-30.520224.5031
52.52870.01470.42581.0259-0.28561.4194-0.09860.2761-0.1406-0.2053-0.233-0.63160.25460.62710.15780.1810.03680.11620.3020.09560.395121.3367-31.221815.4935
64.6381-0.54792.93062.2557-1.30085.4191-0.16880.15670.0356-0.23090.0359-0.20680.15920.16780.12040.15920.00030.05490.09180.01470.167611.8825-34.873617.1633
75.48390.1833.62421.22870.57694.1256-0.04260.2517-0.42120.0108-0.0411-0.15020.4060.28430.0670.19780.04390.06870.11670.03480.22813.7557-46.247523.861
82.0839-0.9390.18360.8766-0.72411.8825-0.1235-0.1134-0.64050.13110.02540.14630.45740.05550.07320.22050.0690.08050.13880.08370.30458.1784-51.866137.1004
90.70890.8264-0.50954.2738-1.81163.4655-0.0281-0.5998-0.76980.75-0.14460.1110.50290.0008-0.28910.404-0.0090.12060.29510.20170.5577-0.5857-55.444842.1589
101.5975-0.49540.07531.26760.17972.4446-0.01640.1221-0.0116-0.18190.0064-0.06870.09320.10640.00060.1402-0.01180.02220.0710.00790.06639.5895-5.93297.2787
113.1996-1.83551.03093.14860.43594.94470.02630.0085-0.0081-0.2628-0.0061-0.28020.16080.472-0.01220.18110.01270.06490.13410.01710.148317.3784-14.31447.0881
123.8262-0.2923-0.92443.4393-0.13654.7607-0.19330.3669-0.0164-0.18470.1661-0.05770.3869-0.11880.02740.10550.00270.02480.0965-0.00850.099912.778-15.411921.3081
130.63330.1473-1.02172.6954-0.58833.4157-0.0441-0.27010.07830.2002-0.1484-0.7869-0.28191.0851-0.21270.0951-0.0206-0.09460.27530.06470.234920.3267-15.2335.0339
146.90012.2345-5.92732.4288-2.70998.523-0.1532-0.0436-0.20650.0835-0.0282-0.2231-0.04960.2020.15160.0947-0.0012-0.01450.0819-0.00650.10712.2506-11.908329.3874
154.0986-0.5248-3.00991.34540.39093.17410.0769-0.24070.15830.02180.0032-0.2442-0.21630.3017-0.04980.1225-0.042-0.00470.13030.01640.111113.7163-0.665525.534
163.0080.75630.06612.5583-0.28342.1331-0.0706-0.19580.25940.07250.05660.0318-0.3255-0.00220.00630.1867-0.012-00.0847-0.01940.09245.12076.401912.4246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:34)A2 - 34
2X-RAY DIFFRACTION2(chain A and resid 35:55)A35 - 55
3X-RAY DIFFRACTION3(chain A and resid 56:82)A56 - 82
4X-RAY DIFFRACTION4(chain A and resid 83:91)A83 - 91
5X-RAY DIFFRACTION5(chain A and resid 92:126)A92 - 126
6X-RAY DIFFRACTION6(chain A and resid 127:158)A127 - 158
7X-RAY DIFFRACTION7(chain A and resid 159:191)A159 - 191
8X-RAY DIFFRACTION8(chain A and resid 192:226)A192 - 226
9X-RAY DIFFRACTION9(chain A and resid 227:236)A227 - 236
10X-RAY DIFFRACTION10(chain B and resid 2:45)B2 - 45
11X-RAY DIFFRACTION11(chain B and resid 46:76)B46 - 76
12X-RAY DIFFRACTION12(chain B and resid 77:91)B77 - 91
13X-RAY DIFFRACTION13(chain B and resid 92:132)B92 - 132
14X-RAY DIFFRACTION14(chain B and resid 133:159)B133 - 159
15X-RAY DIFFRACTION15(chain B and resid 160:193)B160 - 193
16X-RAY DIFFRACTION16(chain B and resid 194:236)B194 - 236

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