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- PDB-2v7s: Crystal structure of the putative lipoprotein LppA from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 2v7s
TitleCrystal structure of the putative lipoprotein LppA from Mycobacterium tuberculosis
ComponentsPROBABLE CONSERVED LIPOPROTEIN LPPA
KeywordsUNKNOWN FUNCTION / LIPOPROTEIN / PUTATIVE LIPOPROTEIN
Function / homologyTBP-like - #20 / Putative lipoprotein, pathogenic bacteria / Lipoprotein confined to pathogenic Mycobacterium / TBP-like / 2-Layer Sandwich / plasma membrane / Alpha Beta / Putative lipoprotein LppA / Putative lipoprotein LppA
Function and homology information
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsGrana, M. / Miras, I. / Haouz, A. / Winter, N. / Buschiazzo, A. / Bellinzoni, M. / Alzari, P.M.
CitationJournal: Proteins / Year: 2010
Title: Crystal Structure of Mycobacterium Tuberculosis Lppa, a Lipoprotein Confined to Pathogenic Mycobacteria.
Authors: Grana, M. / Bellinzoni, M. / Bellalou, J. / Haouz, A. / Miras, I. / Buschiazzo, A. / Winter, N. / Alzari, P.M.
History
DepositionAug 1, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 28, 2011Group: Database references / Non-polymer description
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: PROBABLE CONSERVED LIPOPROTEIN LPPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6144
Polymers24,3381
Non-polymers2763
Water1,11762
1
A: PROBABLE CONSERVED LIPOPROTEIN LPPA
hetero molecules

A: PROBABLE CONSERVED LIPOPROTEIN LPPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2288
Polymers48,6752
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2900 Å2
ΔGint-9.87 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.000, 49.820, 42.210
Angle α, β, γ (deg.)90.00, 99.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROBABLE CONSERVED LIPOPROTEIN LPPA / LPPA / LIPOPROTEIN / PUTATIVE


Mass: 24337.549 Da / Num. of mol.: 1 / Fragment: RESIDUES 34-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P95010, UniProt: P9WK81*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RECOMBINANT PROTEIN INCLUDES A N-TERMINAL TAG ( SEQUENCE MSYYHHHHHHLESTSLYKKAGSENLYFQG) FUSED ...THE RECOMBINANT PROTEIN INCLUDES A N-TERMINAL TAG ( SEQUENCE MSYYHHHHHHLESTSLYKKAGSENLYFQG) FUSED TO RESIDUES 34-219 OF THE NP-217059 GENE)

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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: 2.81 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 9 / Details: 20% PEG-3350, BICINE 0.1 M, PH 9, 50 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.96→45 Å / Num. obs: 15229 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.6
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.7 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.96→6 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.91 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 728 5 %RANDOM
Rwork0.19 ---
obs0.192 13939 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å2-0.9 Å2
2--0.64 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.96→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 18 62 1384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9691806
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.724.21964
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76415227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1271512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021010
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2610
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2942
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.091.5874
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49121345
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9823527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4484.5461
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 29
Rwork0.194 715
Refinement TLS params.Method: refined / Origin x: -20.6971 Å / Origin y: -38.7189 Å / Origin z: -12.7807 Å
111213212223313233
T-0.0831 Å2-0.0074 Å2-0.0008 Å2--0.1474 Å2-0.0188 Å2---0.0931 Å2
L3.0697 °2-0.6875 °20.5788 °2-0.7702 °2-0.4196 °2--1.2827 °2
S-0.0807 Å °-0.125 Å °0.0775 Å °0.0312 Å °0.078 Å °-0.0267 Å °-0.1297 Å °0.0035 Å °0.0027 Å °

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