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- PDB-1p4t: Crystal structure of Neisserial surface protein A (NspA) -

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Basic information

Entry
Database: PDB / ID: 1p4t
TitleCrystal structure of Neisserial surface protein A (NspA)
Componentsouter membrane protein NspA
KeywordsMEMBRANE PROTEIN / beta barrel / outer membrane protein
Function / homology
Function and homology information


porin activity / cell outer membrane
Similarity search - Function
Porin, opacity type / Opacity family porin protein / Porin - #20 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PENTAETHYLENE GLYCOL MONODECYL ETHER / ETHANOLAMINE / Surface protein A
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsVandeputte-Rutten, L. / Bos, M.P. / Tommassen, J. / Gros, P.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of Neisserial Surface Protein A (NspA), a conserved outer membrane protein with vaccine potential
Authors: Vandeputte-Rutten, L. / Bos, M.P. / Tommassen, J. / Gros, P.
History
DepositionApr 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: outer membrane protein NspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6328
Polymers16,5821
Non-polymers2,0507
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: outer membrane protein NspA
hetero molecules

A: outer membrane protein NspA
hetero molecules

A: outer membrane protein NspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,89724
Polymers49,7473
Non-polymers6,15021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10960 Å2
ΔGint-60 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.372, 97.372, 171.939
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsNspA is a monomer

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Components

#1: Protein outer membrane protein NspA / Neisserial surface protein A / NspA


Mass: 16582.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: nspa / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RP17
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CXE / PENTAETHYLENE GLYCOL MONODECYL ETHER


Mass: 378.544 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H42O6
#4: Chemical ChemComp-ETA / ETHANOLAMINE / Ethanolamine


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.73 Å3/Da / Density % sol: 73.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.06% n-decylpentaoxyethylene (c10e5), 12% (w/v) PEG 3000, 0.1 M lithium sulfate, 0.1 M N-(2-acetamido)iminodiacetic acid (ADA), 2% (v/v) isopropanol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
20.06 %(w/v)C10E51drop
312 %(w/v)PEG30001reservoir
40.1 Mlithium sulfate1reservoir
50.1 MADA1reservoirpH6.6
62 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 4, 2002 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. all: 10503 / Num. obs: 10350 / % possible obs: 98.6 % / Observed criterion σ(F): -3.7 / Observed criterion σ(I): -3.7 / Redundancy: 12.1 % / Biso Wilson estimate: 69.8 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 19
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1029 / Rsym value: 0.375 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 125566 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 1029 / Num. measured obs: 8944

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→30.15 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.572 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.314 / ESU R Free: 0.245 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25791 501 4.8 %RANDOM
Rwork0.22514 ---
obs0.22664 10340 100 %-
all-10340 --
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: 39.103 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 92 9 1262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211326
X-RAY DIFFRACTIONr_bond_other_d0.0020.021265
X-RAY DIFFRACTIONr_angle_refined_deg1.7392.031744
X-RAY DIFFRACTIONr_angle_other_deg0.79632957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3185154
X-RAY DIFFRACTIONr_chiral_restr0.0990.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021371
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02270
X-RAY DIFFRACTIONr_nbd_refined0.20.2171
X-RAY DIFFRACTIONr_nbd_other0.2440.21365
X-RAY DIFFRACTIONr_nbtor_other0.0880.2931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.24
X-RAY DIFFRACTIONr_mcbond_it0.6841.5767
X-RAY DIFFRACTIONr_mcangle_it1.35121216
X-RAY DIFFRACTIONr_scbond_it2.0183559
X-RAY DIFFRACTIONr_scangle_it3.334.5528
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.452 39
Rwork0.236 694
Refinement TLS params.Method: refined / Origin x: 37.149 Å / Origin y: 16.983 Å / Origin z: 33.008 Å
111213212223313233
T0.0567 Å2-0.0422 Å2-0.0747 Å2-0.196 Å2-0.0503 Å2--0.1666 Å2
L3.3852 °21.0316 °2-0.6774 °2-3.8066 °2-0.5308 °2--5.274 °2
S0.1487 Å °-0.1624 Å °-0.1803 Å °0.1476 Å °-0.0737 Å °0.0617 Å °0.2167 Å °-0.2243 Å °-0.075 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1551 - 155
2X-RAY DIFFRACTION1AC - G157 - 500
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.77

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