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- PDB-4beg: Structure of Rv2140c, a phosphatidyl-ethanolamine binding protein... -

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Basic information

Entry
Database: PDB / ID: 4beg
TitleStructure of Rv2140c, a phosphatidyl-ethanolamine binding protein from Mycobacterium tuberculosis in complex with sulphate
ComponentsPHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / PEBP / RKIP
Function / homology
Function and homology information


extracellular region / identical protein binding / plasma membrane
Similarity search - Function
YbhB/YbcL / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
UPF0098 protein Rv2140c / UPF0098 protein Rv2140c
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsHolton, S.J. / Williams, M.
CitationJournal: FEBS Lett. / Year: 2013
Title: Structural and Biochemical Characterization of Rv2140C, a Phosphatidylethanolamine-Binding Protein from Mycobacterium Tuberculosis.
Authors: Eulenburg, G. / Higman, V.A. / Diehl, A. / Wilmanns, M. / Holton, S.J.
History
DepositionMar 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
B: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,30110
Polymers37,5562
Non-polymers7458
Water6,215345
1
A: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
B: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
hetero molecules

A: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
B: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,60120
Polymers75,1124
Non-polymers1,48916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area10160 Å2
ΔGint-140.7 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.118, 62.118, 181.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN / UPF0098 PROTEIN RV2140C/MT2198


Mass: 18777.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P67226, UniProt: P9WFN1*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growDetails: 0.1M TRIS PH 8.0, 2.4 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.41→28.01 Å / Num. obs: 67729 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 5.32 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.86
Reflection shellResolution: 1.41→1.49 Å / Redundancy: 5.23 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.81 / % possible all: 87.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BEF

4bef
PDB Unreleased entry


Resolution: 1.42→27.248 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.691 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 3427 5.15 %RANDOM
Rwork0.1491 ---
obs0.151 67658 99.189 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.055 Å2
Baniso -1Baniso -2Baniso -3
1-0.457 Å20 Å20 Å2
2--0.457 Å20 Å2
3----0.913 Å2
Refinement stepCycle: LAST / Resolution: 1.42→27.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 46 345 3028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192830
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.9753890
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5625369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.35623.153111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07815369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.221516
X-RAY DIFFRACTIONr_chiral_restr0.1480.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0222242
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.08232830
X-RAY DIFFRACTIONr_sphericity_free23.0275119
X-RAY DIFFRACTIONr_sphericity_bonded9.08252972
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 229 -
Rwork0.236 4418 -
obs--94.3 %

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