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- PDB-2qgu: Three-dimensional structure of the phospholipid-binding protein f... -

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Basic information

Entry
Database: PDB / ID: 2qgu
TitleThree-dimensional structure of the phospholipid-binding protein from Ralstonia solanacearum Q8XV73_RALSQ in complex with a phospholipid at the resolution 1.53 A. Northeast Structural Genomics Consortium target RsR89
ComponentsProbable signal peptide protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / RsR89 / Q8XV73 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


phospholipid-binding protein / Toluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Arc Repressor Mutant, subunit A / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Probable signal peptide protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsKuzin, A.P. / Chen, Y. / Jayaraman, S. / Chen, C.X. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Chen, Y. / Jayaraman, S. / Chen, C.X. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Three-dimensional structure of the phospholipid-binding protein from Ralstonia solanacearum Q8XV73_RALSQ in complex with a phospholipid at the resolution 1.53 A.
Authors: Kuzin, A.P. / Chen, Y. / Jayaraman, S. / Chen, C.X. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600 HETEROGEN AUTHORS STATE THAT THERE IS NO CHEMICAL CONFIRMATION WHETHER THE LIGAND PRESENT IN THE ... HETEROGEN AUTHORS STATE THAT THERE IS NO CHEMICAL CONFIRMATION WHETHER THE LIGAND PRESENT IN THE STRUCTURE IS PEA OR PEF. THE LIGAND CAME FROM THE BACTERIAL EXPRESSION AND ITS ASSIGNMENT HAS BEEN MADE BASED ON THE 3-D STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable signal peptide protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8722
Polymers23,1801
Non-polymers6921
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.495, 46.478, 117.508
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 Probable signal peptide protein


Mass: 23179.979 Da / Num. of mol.: 1
Mutation: F10V, M16V, T33A, S50P, S54G, M57L, T103S, V106I, S122A, M154V, A158P, E183D, S192G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Strain: GMI1000 / Gene: RSc2958 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XV73
#2: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL / Phosphatidylethanolamine


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 25% w/v PEG6000, 0.1M Trimethylamine, 10% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 66846 / Num. obs: 34787 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.6
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 7.6 / % possible all: 84.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→29.95 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.01 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21142 1750 5 %RANDOM
Rwork0.18535 ---
obs0.18667 33037 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 47 356 1801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221516
X-RAY DIFFRACTIONr_angle_refined_deg1.021.972051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.65188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07624.65873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05315253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1331512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021160
X-RAY DIFFRACTIONr_nbd_refined0.1910.2720
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0850.2247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.239
X-RAY DIFFRACTIONr_mcbond_it0.5271.5940
X-RAY DIFFRACTIONr_mcangle_it0.88721485
X-RAY DIFFRACTIONr_scbond_it1.5573640
X-RAY DIFFRACTIONr_scangle_it2.5524.5566
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 107 -
Rwork0.163 2073 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 16.538 Å / Origin y: 19.758 Å / Origin z: 72.378 Å
111213212223313233
T-0.0391 Å20.0109 Å20.0029 Å2--0.0574 Å2-0.0036 Å2---0.0285 Å2
L0.7692 °20.1428 °20.3084 °2-0.7277 °2-0.0324 °2--1.5544 °2
S-0.019 Å °-0.0299 Å °0.0607 Å °0.0622 Å °0.0032 Å °-0.0174 Å °-0.067 Å °0.0069 Å °0.0157 Å °

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