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

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Basic information

Entry
Database: PDB / ID: 1uyn
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 / MAD / Resolution: 2.6 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 18, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL.

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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)32,4184
Polymers31,8471
Non-polymers5713
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.970, 57.970, 346.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein NALP / NLRP / OUTER MEMBRANE PROTEIN


Mass: 31847.115 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): BL21(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
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growpH: 4
Details: 200 MM LI2SO4, 100 MM NA CIT BUFFER, PH 4.0, 9% PEG 1000. PROTEIN WAS CRYSTALLISED IN THE PRESENCE OF 0.06% N-DECYLPENTAOXYETHYLENE AND 0.5% HEPTYL-B-GLUCOPYRANOSIDE
Crystal grow
*PLUS
Temperature: 28 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
117 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
30.06 %(w/v)1dropC10E5
40.5 %(w/v)heptyl-beta-glucopyranoside1drop
59 %(w/v)PEG10001reservoir
6200 mMlithium sulfate1reservoir
7100 mMsodium citrate1reservoirpH4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDate: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 10715 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 24
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 9.2 / % possible all: 88.7
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. measured all: 97916 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 88.7 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 9.2

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.781 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.567 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 565 5 %RANDOM
Rwork0.228 ---
obs0.231 10715 97.2 %-
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: 24.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20.68 Å20 Å2
2--1.37 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 36 29 2080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212078
X-RAY DIFFRACTIONr_bond_other_d0.0020.021847
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9532794
X-RAY DIFFRACTIONr_angle_other_deg1.06634279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8625276
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_restr0.1430.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022394
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02432
X-RAY DIFFRACTIONr_nbd_refined0.2020.2306
X-RAY DIFFRACTIONr_nbd_other0.2640.22206
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0950.21488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.260
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_it0.8061.51349
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53822097
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4293729
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1024.5697
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: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 41
Rwork0.225 670
Refinement TLS params.Method: refined / Origin x: 9.794 Å / Origin y: 18.893 Å / Origin z: 181.791 Å
111213212223313233
T0.1301 Å20.0139 Å20.0035 Å2-0.1817 Å2-0.1119 Å2--0.07 Å2
L1.8795 °2-0.1156 °2-0.1926 °2-1.3636 °20.5546 °2--3.372 °2
S-0.0006 Å °0.0024 Å °-0.1172 Å °0.0389 Å °-0.0882 Å °0.0422 Å °0.3152 Å °0.2484 Å °0.0888 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X785 - 1084
2X-RAY DIFFRACTION1X2085
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8

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