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- PDB-1uyo: Translocator domain of autotransporter NalP from Neisseria mening... -

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Basic information

Entry
Database: PDB / ID: 1uyo
TitleTranslocator domain of autotransporter NalP from Neisseria meningitidis
ComponentsNALPNLRP
KeywordsMEMBRANE PROTEIN / AUTOTRANSPORTER / TRANSLOCATOR DOMAIN / OUTER MEMBRANE / BETA-DOMAIN / BETA-BARREL
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / serine-type endopeptidase activity / intracellular membrane-bounded organelle / cell surface / proteolysis / extracellular region
Similarity search - Function
Autotransporter serine protease peptidase domain / Autotransporter-associated beta strand repeat / Passenger-associated-transport-repeat / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Serine proteases, subtilase family, serine active site. ...Autotransporter serine protease peptidase domain / Autotransporter-associated beta strand repeat / Passenger-associated-transport-repeat / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PENTAETHYLENE GLYCOL MONODECYL ETHER / Neisserial autotransporter lipoprotein NalP
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsOomen, C.J. / Van Ulsen, P. / Van Gelder, P. / Feijen, M. / Tommassen, J. / Gros, P.
CitationJournal: Embo J. / Year: 2004
Title: Structure of the Translocator Domain of a Bacterial Autotransporter
Authors: Oomen, C.J. / Van Ulsen, P. / Van Gelder, P. / Feijen, M. / Tommassen, J. / Gros, P.
History
DepositionMar 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: NALP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4602
Polymers32,0821
Non-polymers3791
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.430, 84.893, 122.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein NALP / NLRP / OUTER MEMBRANE PROTEIN


Mass: 32081.588 Da / Num. of mol.: 1
Fragment: OUTER MEMBRANE TRANSLOCATOR DOMAIN, RESIDUES 776-1083
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Strain: H44/76 / Description: OUTER MEMBRANE. REFOLDED PROTEIN / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8GKS5
#2: Chemical ChemComp-CXE / PENTAETHYLENE GLYCOL MONODECYL ETHER


Mass: 378.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O6

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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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growpH: 7.5
Details: 88 MM TRIS-HCL, PH 7.0, 9% PEG2000MME 18% MPD. PROTEIN WAS CRYSTALLISED IN THE PRESENSE OF 0.06%, N-DECYLPENTAOXYETHYLENE AND 0.5% HEPTYL-B-GLUCOPYRANOSIDE AND 10 MM DTT
Crystal grow
*PLUS
Temperature: 28 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18.5 mg/mlSe-Met NalP~beta1drop
210 mMTris-HCl1droppH7.5
30.06 %(w/v)1dropC10E5
40.5 %(w/v)heptyl-beta-glucopyranoside1drop
588 mMTris-HCl1reservoirpH7.0
69 %(w/v)PEG2000 MME1reservoir
718 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811
DetectorDate: Jun 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 5100 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.206 / Net I/σ(I): 9.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3 / % possible all: 94.8
Reflection
*PLUS
Highest resolution: 3.2 Å / Num. measured all: 45309 / Rmerge(I) obs: 0.15
Reflection shell
*PLUS
% possible obs: 94.8 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.82 / SU B: 26.01 / SU ML: 0.461 / Cross valid method: THROUGHOUT / ESU R Free: 0.668 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.298 208 4.4 %RANDOM
Rwork0.215 ---
obs0.219 4470 90.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20 Å20 Å2
2--1.53 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 10 0 1968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212001
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.9522691
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4295272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021511
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2790.2756
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.50.21
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.405 10
Rwork0.236 230
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.92

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