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- PDB-4qc2: Crystal structure of lipopolysaccharide transport protein LptB in... -

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Basic information

Entry
Database: PDB / ID: 4qc2
TitleCrystal structure of lipopolysaccharide transport protein LptB in complex with ATP and Magnesium ions
ComponentsABC transporter related protein
KeywordsTRANSPORT PROTEIN / nucleotide-binding domain / Lipopolysaccharide transport / LptFGC
Function / homologyP-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ADENOSINE-5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsWang, Z. / Xiang, Q. / Zhu, X. / Dong, H. / He, C. / Wang, H. / Zhang, Y. / Wang, W. / Dong, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport.
Authors: Wang, Z. / Xiang, Q. / Zhu, X. / Dong, H. / He, C. / Wang, H. / Zhang, Y. / Wang, W. / Dong, C.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.2Nov 8, 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 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,3966
Polymers55,3332
Non-polymers1,0634
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.160, 125.760, 89.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-481-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 2 - 236 / Label seq-ID: 2 - 236

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein ABC transporter related protein


Mass: 27666.551 Da / Num. of mol.: 2 / Fragment: nucleotide-binding protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lptB, EcDH1_0506, ECDH1ME8569_3090 / Plasmid: pACYCDue / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9QY46
#2: 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
#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 / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293.25 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M ammonium fluoride, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.25K

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Data collection

DiffractionMean temperature: 293.25 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2012 / Details: mirros
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→44.81 Å / Num. all: 24034 / Num. obs: 24010 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.056 / Net I/σ(I): 1
Reflection shellResolution: 2.22→2.29 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / Num. unique all: 2362 / Rsym value: 0.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
MLPHAREphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JI0

1ji0


Resolution: 2.22→44.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.447 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24825 1230 5.1 %RANDOM
Rwork0.18067 ---
all0.185 22834 --
obs0.18398 22804 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.239 Å2
Baniso -1Baniso -2Baniso -3
1-9.13 Å20 Å20 Å2
2--3.49 Å20 Å2
3----12.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.034 Å
Luzzati d res low-2.2 Å
Luzzati sigma a0.55 Å0.021 Å
Refinement stepCycle: LAST / Resolution: 2.22→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 64 144 3866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193776
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9945122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32723.068176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62415658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7281542
X-RAY DIFFRACTIONr_chiral_restr0.1250.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212814
Refine LS restraints NCS

Ens-ID: 1 / Number: 3391 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.219→2.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 88 -
Rwork0.25 1598 -
obs--96.56 %
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)
10.1535-0.08930.01490.3171-0.34010.58880.050.05180.0275-0.062-0.056-0.01990.04430.08340.0060.07510.0249-0.010.04380.00440.012747.508945.881653.9219
21.0631-0.1294-0.58810.07040.04010.8241-0.2204-0.0286-0.0826-0.00890.025-0.02220.32170.0940.19550.17330.0550.08750.04630.01570.060155.627613.451261.5712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 236
2X-RAY DIFFRACTION2B3 - 236

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