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- PDB-4p32: Crystal structure of E. coli LptB in complex with ADP-magnesium -

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Basic information

Entry
Database: PDB / ID: 4p32
TitleCrystal structure of E. coli LptB in complex with ADP-magnesium
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Lipopolysaccharide export system ATP-binding protein LptB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 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 1.4Dec 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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)56,7856
Polymers55,8822
Non-polymers9034
Water3,027168
1
A: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3923
Polymers27,9411
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-39 kcal/mol
Surface area20330 Å2
MethodPISA
2
B: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3923
Polymers27,9411
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)191.900, 36.020, 64.510
Angle α, β, γ (deg.)90.000, 96.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 27940.760 Da / Num. of mol.: 2
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): BL21(DE3)
References: UniProt: P0A9V1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 30% 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: Apr 29, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.544→95.396 Å / Num. obs: 63324 / % possible obs: 98.6 % / Redundancy: 3.9 % / Rsym value: 0.074 / Net I/σ(I): 9.8

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.7_650)refinement
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P31

4p31


Resolution: 1.55→31.799 Å / FOM work R set: 0.8709 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 3170 5.01 %Random selection
Rwork0.1976 60147 --
obs0.1986 63317 98.39 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.025 Å2 / ksol: 0.427 e/Å3
Displacement parametersBiso max: 105.13 Å2 / Biso mean: 29.75 Å2 / Biso min: 9.96 Å2
Baniso -1Baniso -2Baniso -3
1--3.5344 Å20 Å2-1.5384 Å2
2--1.7332 Å2-0 Å2
3---1.8012 Å2
Refinement stepCycle: final / Resolution: 1.55→31.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 56 168 3836
Biso mean--25.88 32.8 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043812
X-RAY DIFFRACTIONf_angle_d0.955187
X-RAY DIFFRACTIONf_chiral_restr0.055604
X-RAY DIFFRACTIONf_plane_restr0.003673
X-RAY DIFFRACTIONf_dihedral_angle_d12.5721458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.57310.34321400.32512278241886
1.5731-1.59770.32891440.31152416256095
1.5977-1.62390.3181200.29842630275099
1.6239-1.65190.2911380.2652638277699
1.6519-1.68190.25841640.248926162780100
1.6819-1.71430.2611230.227626652788100
1.7143-1.74930.23671340.216926252759100
1.7493-1.78730.23911310.201326432774100
1.7873-1.82890.23991200.19626462766100
1.8289-1.87460.20671320.18626302762100
1.8746-1.92530.22251370.186926552792100
1.9253-1.98190.23731450.180926482793100
1.9819-2.04590.24081490.187426342783100
2.0459-2.1190.19571420.179226642806100
2.119-2.20380.24051190.185326472766100
2.2038-2.30410.21240.186927022826100
2.3041-2.42550.23581340.194726532787100
2.4255-2.57740.2241420.199526792821100
2.5774-2.77630.22221360.200526692805100
2.7763-3.05550.24931450.20812655280099
3.0555-3.49720.19221490.186826602809100
3.4972-4.40420.18961680.1672621278998
4.4042-31.80530.19551340.21482473260788
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)
10.20020.0613-0.19970.0233-0.07070.25920.11870.08090.0493-0.0713-0.02660.1879-0.0718-0.39380.0560.1870.0851-0.0080.525-0.09190.241147.160629.033915.7923
20.52460.01090.45510.0784-0.13380.68150.10780.0482-0.0515-0.05850.02340.08880.0618-0.47080.02110.17310.0332-0.04010.3723-0.02810.178354.251623.640417.1932
30.55150.14430.27660.4085-0.15490.38310.0468-0.148-0.1191-0.0692-0.12550.1686-0.0542-0.19570.02090.15120.0354-0.04250.2201-0.02660.167165.515226.800822.8095
40.34160.260.08230.3126-0.04160.60110.0353-0.0909-0.13080.143-0.0674-0.2005-0.0257-0.10850.00150.1253-0.0063-0.00650.09410.0090.1677.922920.252827.2621
50.47150.0925-0.01060.48670.02620.55840.04630.0898-0.0292-0.1499-0.02-0.1098-0.1437-0.0014-0.0040.16330.0088-0.01040.13550.00470.138178.465628.683519.5903
60.6112-0.10090.30360.48760.46090.91650.04930.5584-0.0807-0.2774-0.10950.0476-0.18080.12050.02660.20260.0614-0.02340.3672-0.03060.154570.412628.09369.5497
70.7014-0.30470.16240.306-0.07220.0778-0.10160.6880.4345-0.26290.0686-0.2741-0.2065-0.35340.01040.19960.1104-0.04810.57420.01560.092457.306932.24264.2658
80.08030.00990.10550.0852-0.0430.18020.05610.13970.0617-0.06870.0665-0.03850.06220.10940.03410.12390.0158-0.27330.89460.2158-0.043651.53237.1521-3.4975
90.3072-0.0906-0.01980.06270.13460.3081-0.0038-0.03030.05610.06940.07260.10490.080.0095-0.02230.1579-0.00980.02670.13830.04980.18188.155632.738245.8448
100.8017-0.2022-0.0350.1150.11560.49320.0531-0.07090.18670.0703-0.0301-0.0273-0.0820.0385-0.02510.1453-0.00210.02560.11450.00240.152883.04734.705948.0011
110.9160.34930.30330.41740.33360.30270.13150.0961-0.07150.0862-0.0413-0.02890.07560.0575-0.04070.1525-0.00530.00460.14830.01510.145887.175822.91642.2574
120.38020.3077-0.25690.8560.59291.4464-0.03480.1105-0.0787-0.0739-0.0367-0.15760.1744-0.3590.03520.13020.01890.00270.1809-0.00010.174273.088328.194240.951
130.2913-0.09550.05280.1210.13950.39920.1131-0.1397-0.17990.0217-0.19730.2583-0.1295-0.44680.05850.1733-0.1010.01040.5401-0.0310.200560.065919.477838.8644
140.4413-0.34910.11170.44830.03350.4433-0.0077-0.0993-0.0669-0.0127-0.13230.2805-0.1709-0.2960.05880.18770.01-0.00460.5474-0.1190.269160.086728.913441.2489
150.34430.04630.2580.1689-0.08020.5873-0.0598-0.31940.11310.09680.06640.13010.011-0.6381-0.05680.16260.00380.05190.35560.01050.223266.407729.195452.7959
161.3897-0.42940.0720.66050.46780.602-0.0465-0.41880.28350.31380.01390.1006-0.3264-0.13480.02410.27950.00280.03650.2478-0.0390.205777.517837.68456.9042
170.6910.3603-0.01831.00410.34280.15990.2939-0.5401-0.01540.4838-0.0543-0.09420.08020.1647-0.06670.3504-0.07590.00310.5869-0.02870.229981.56639.475566.3024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:24)A2 - 24
2X-RAY DIFFRACTION2(chain A and resid 25:76)A25 - 76
3X-RAY DIFFRACTION3(chain A and resid 77:90)A77 - 90
4X-RAY DIFFRACTION4(chain A and resid 91:119)A91 - 119
5X-RAY DIFFRACTION5(chain A and resid 120:156)A120 - 156
6X-RAY DIFFRACTION6(chain A and resid 157:190)A157 - 190
7X-RAY DIFFRACTION7(chain A and resid 191:221)A191 - 221
8X-RAY DIFFRACTION8(chain A and resid 222:235)A222 - 235
9X-RAY DIFFRACTION9(chain B and resid 2:14)B2 - 14
10X-RAY DIFFRACTION10(chain B and resid 15:55)B15 - 55
11X-RAY DIFFRACTION11(chain B and resid 56:76)B56 - 76
12X-RAY DIFFRACTION12(chain B and resid 77:89)B77 - 89
13X-RAY DIFFRACTION13(chain B and resid 90:130)B90 - 130
14X-RAY DIFFRACTION14(chain B and resid 131:156)B131 - 156
15X-RAY DIFFRACTION15(chain B and resid 157:190)B157 - 190
16X-RAY DIFFRACTION16(chain B and resid 191:217)B191 - 217
17X-RAY DIFFRACTION17(chain B and resid 218:231)B218 - 231

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