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- PDB-4p31: Crystal structure of a selenomethionine derivative of E. coli Lpt... -

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Basic information

Entry
Database: PDB / ID: 4p31
TitleCrystal structure of a selenomethionine derivative of E. coli LptB in complex with ADP-Magensium
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 / MIRAS / Resolution: 2.05 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
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 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_struct_conn_angle / refine_hist / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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)57,1606
Polymers56,2572
Non-polymers9034
Water1,910106
1
A: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5803
Polymers28,1281
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5803
Polymers28,1281
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)192.600, 35.880, 64.340
Angle α, β, γ (deg.)90.000, 95.830, 90.000
Int Tables number5
Space group name H-MC121
DetailsComparison to nucleotide-binding domain structures deposited in the PDB and biochemical characterization of this class of proteins, we believe that the biologically relevant unit is a monomer (one polypeptide from the asymmetric unit).

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Components

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


Mass: 28128.342 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.: 106 / 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: 1.97 Å3/Da / Density % sol: 37.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 31% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2011
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.05→95.802 Å / Num. obs: 27803 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.63 Å2 / Rpim(I) all: 0.065 / Rrim(I) all: 0.12 / Rsym value: 0.074 / Net I/av σ(I): 7.417 / Net I/σ(I): 8.7 / Num. measured all: 90833
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.163.20.4981.21276239780.3980.4982.397.8
2.16-2.293.30.31221237737710.2480.3123.598.7
2.29-2.453.30.2113.11186335660.170.2114.799.2
2.45-2.653.30.1464.61116433400.120.1466.199.5
2.65-2.93.30.09771034930970.0810.0978.499.6
2.9-3.243.30.06510.5934628280.0570.06511.499.8
3.24-3.743.30.04213.3820124800.0390.04215.499.8
3.74-4.583.20.04113.1678721410.0380.04118.199.9
4.58-6.4830.04412.2495916530.0470.04417.199.6
6.48-32.0043.20.02619.430259490.0350.02618.798.8

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
ADSC Quantumdata collection
SCALA3.3.16data scaling
SHARPphasing
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX1.7_650refinement
CNSrefinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.05→32.004 Å / FOM work R set: 0.8391 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1392 5.01 %Random selection
Rwork0.1845 26394 --
obs0.1873 27786 99.09 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.91 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 146.02 Å2 / Biso mean: 35.8 Å2 / Biso min: 9.79 Å2
Baniso -1Baniso -2Baniso -3
1--4.2994 Å20 Å2-4.2869 Å2
2--6.4716 Å20 Å2
3----2.1721 Å2
Refinement stepCycle: final / Resolution: 2.05→32.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 56 106 3774
Biso mean--31.34 36.47 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063750
X-RAY DIFFRACTIONf_angle_d0.9155102
X-RAY DIFFRACTIONf_chiral_restr0.053590
X-RAY DIFFRACTIONf_plane_restr0.003657
X-RAY DIFFRACTIONf_dihedral_angle_d14.5851422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.12330.28851300.23982570270097
2.1233-2.20830.25181190.20092593271299
2.2083-2.30870.27561140.19342621273599
2.3087-2.43040.29111360.18852606274299
2.4304-2.58260.24991450.18722632277799
2.5826-2.78190.26791320.183526412773100
2.7819-3.06170.24151460.181426612807100
3.0617-3.50430.23461470.177926562803100
3.5043-4.41320.21641680.164226542822100
4.4132-32.00750.21721550.19182760291599
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)
10.24990.07830.05430.0638-0.19120.6052-0.0340.18990.0191-0.09870.0510.25870.0513-0.6774-0.10460.02810.0537-0.03640.38750.03060.104451.791928.00915.2189
20.10280.0938-0.07740.0934-0.07370.0667-0.13510.1195-0.0441-0.0153-0.13830.0553-0.0010.02290.13170.3807-0.1361-0.06720.52420.05420.543752.513911.163614.7525
30.305-0.3965-0.0540.55790.12330.0807-0.0092-0.34660.03350.02840.1129-0.10430.0201-0.19470.05980.1618-0.0188-0.01480.34190.07140.067960.77522.315722.7037
40.2216-0.18430.04840.2835-0.42661.10990.0415-0.018-0.15580.3002-0.00030.0407-0.2371-0.11150.0340.088-0.0206-0.0090.05990.0310.224777.466420.794127.8245
50.77260.5099-0.22780.4105-0.18540.51480.04860.1147-0.1137-0.1727-0.044-0.2099-0.048-0.0192-0.01210.1615-0.0104-0.01590.11050.00970.165480.043427.334619.8471
60.33440.12770.18020.11870.01780.3815-0.05490.1815-0.03130.0753-0.0231-0.0376-0.09080.0380.02050.17670.0054-0.03290.27560.02420.149269.038429.33339.2133
70.5334-0.3121-0.12250.3690.13010.06810.1510.42230.4442-0.4096-0.0001-0.188-0.0428-0.31480.04080.23210.1197-0.06250.55870.08930.049655.263232.99620.8958
80.1736-0.1735-0.0390.17480.03840.00830.1210.0491-0.0135-0.34280.1436-0.10070.26830.4009-0.08380.34380.0876-0.07480.68310.05340.201750.592243.4505-0.5371
90.4982-0.18250.13860.0584-0.01310.1268-0.0123-0.02270.18460.0682-0.0133-0.1197-0.08480.0234-0.00550.17820.0120.00130.0760.0130.196984.67834.173747.2524
100.14990.02430.16370.2806-0.01190.240.1403-0.005-0.23090.02310.1021-0.02970.07810.0303-0.10660.19180.00860.00550.0832-0.01040.167891.724328.964443.5703
110.3547-0.0885-0.07770.35530.08780.030.1682-0.1338-0.18660.22340.064-0.24290.1997-0.07050.03760.2095-0.0279-0.1020.11780.13550.408288.977917.866947.6277
120.9213-0.27460.03780.57690.14250.267-0.02140.42770.12440.1930.05560.00960.0333-0.0845-0.01610.19830.01230.00890.18650.00810.204279.164625.16439.4962
130.9776-0.19660.30820.31520.3250.6540.0718-0.1783-0.26070.0723-0.17480.1904-0.035-0.49570.07690.1752-0.0380.01270.4143-0.03610.240560.123122.74839.0309
140.3104-0.10360.05930.48230.21740.6319-0.0202-0.0543-0.0211-0.02140.04530.1485-0.0359-0.5639-0.01010.15890.02080.02910.28480.02630.209768.484830.350352.3229
150.459-0.09280.0820.5133-0.09760.1667-0.0043-0.36730.090.36470.09890.1115-0.2696-0.0864-0.05280.26030.00610.01510.2678-0.04110.159680.305436.453158.9439
160.17770.0691-0.03750.09210.06360.10490.2425-0.15230.00050.27990.1121-0.0764-0.01790.1978-0.10760.5402-0.17270.02160.6646-0.23520.381282.664941.944966.3369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:61)A2 - 61
2X-RAY DIFFRACTION2(chain A and resid 62:66)A62 - 66
3X-RAY DIFFRACTION3(chain A and resid 67:89)A67 - 89
4X-RAY DIFFRACTION4(chain A and resid 90:114)A90 - 114
5X-RAY DIFFRACTION5(chain A and resid 115:154)A115 - 154
6X-RAY DIFFRACTION6(chain A and resid 155:198)A155 - 198
7X-RAY DIFFRACTION7(chain A and resid 199:230)A199 - 230
8X-RAY DIFFRACTION8(chain A and resid 231:235)A231 - 235
9X-RAY DIFFRACTION9(chain B and resid 2:54)B2 - 54
10X-RAY DIFFRACTION10(chain B and resid 55:61)B55 - 61
11X-RAY DIFFRACTION11(chain B and resid 62:66)B62 - 66
12X-RAY DIFFRACTION12(chain B and resid 67:88)B67 - 88
13X-RAY DIFFRACTION13(chain B and resid 89:153)B89 - 153
14X-RAY DIFFRACTION14(chain B and resid 154:198)B154 - 198
15X-RAY DIFFRACTION15(chain B and resid 199:222)B199 - 222
16X-RAY DIFFRACTION16(chain B and resid 223:231)B223 - 231

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