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- PDB-2pil: Crystallographic Structure of Phosphorylated Pilin from Neisseria... -

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Basic information

Entry
Database: PDB / ID: 2pil
TitleCrystallographic Structure of Phosphorylated Pilin from Neisseria: Phosphoserine Sites Modify Type IV Pilus Surface Chemistry
ComponentsTYPE 4 PILIN
KeywordsCELL ADHESION / TYPE IV PILIN / FIBER-FORMING PROTEIN / MEMBRANE PROTEIN / DNA INDING PROTEIN / CONTRACTILE PROTEIN
Function / homology
Function and homology information


pilus / cell adhesion / membrane
Similarity search - Function
Glycoprotein, Type 4 Pilin / Glycoprotein, Type 4 Pilin / Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HEPTANE-1,2,3-TRIOL / : / Type IV major pilin protein PilE1
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsForest, K.T. / Dunham, S.A. / Koomey, M. / Tainer, J.A.
Citation
Journal: Mol.Microbiol. / Year: 1999
Title: Crystallographic structure reveals phosphorylated pilin from Neisseria: phosphoserine sites modify type IV pilus surface chemistry and fibre morphology.
Authors: Forest, K.T. / Dunham, S.A. / Koomey, M. / Tainer, J.A.
#1: Journal: Nature / Year: 1995
Title: Structure of the Fibre-Forming Protein Pilin at 2.6 A Resolution
Authors: Parge, H.E. / Forest, K.T. / Hickey, M.J. / Christensen, D.A. / Getzoff, E.D. / Tainer, J.A.
History
DepositionMar 2, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / software / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYPE 4 PILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0134
Polymers17,2861
Non-polymers7273
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.580, 121.080, 26.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-200-

PT

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Components

#1: Protein TYPE 4 PILIN / FIMBRIAE


Mass: 17286.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neisseria gonorrhoeae (bacteria) / Cellular location: EXTRACELLULAR / Organelle: PILUS / Strain: MS11 / References: UniProt: P02974
#2: Polysaccharide alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][b-D-GlcpNAc]{[(3+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#4: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 60 %
Crystal growpH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 60% PEG400, 50 MM CHESS, PH 8.0, 1% BETA-OCTYL GLUCOSIDE, 0.6% 1,2,3-HEPTANETRIOL.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 %(w/v)protein1drop
21-1.5 %BOG1drop
3100 mMTris-HCl1drop
420 mM1dropNaCl
51 mMdithiothreitol1drop
60.02 %1dropNaN3
836-45 %PEG4001reservoir
9100 mMTris-HCl1reservoir
7reservoir1drop
100.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1993 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.6→24 Å / Num. obs: 6565 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.081 / Net I/σ(I): 6.7
Reflection shellResolution: 2.6→2.78 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.307 / % possible all: 80.2
Reflection
*PLUS
Rmerge(I) obs: 0.054

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
X-PLOR3.8model building
X-PLOR3.8refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
Details: FITTING BEGAN WITH PDB MODEL 1AY2. PHOSPHOSERINE 68 WAS ADDED AND A BULK SOLVENT CORRECTION WAS APPLIED. THE EXPECTED N-TERMINAL METHYL-PHE WAS VERIFIED BY N-TERMINAL SEQUENCING BUT WAS NOT ...Details: FITTING BEGAN WITH PDB MODEL 1AY2. PHOSPHOSERINE 68 WAS ADDED AND A BULK SOLVENT CORRECTION WAS APPLIED. THE EXPECTED N-TERMINAL METHYL-PHE WAS VERIFIED BY N-TERMINAL SEQUENCING BUT WAS NOT INCLUDED IN THE MODEL BECAUSE IT IS NOT APPARENT IN ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rwork0.187 --
obs0.187 6565 95 %
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.731 Å20 Å20 Å2
2--18.443 Å20 Å2
3----0.639 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 36 127 1375
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.961.5
X-RAY DIFFRACTIONx_mcangle_it4.662
X-RAY DIFFRACTIONx_scbond_it5.262
X-RAY DIFFRACTIONx_scangle_it8.082.5
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rwork0.312 743
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X_PO4G3P.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH3.CHO
X-RAY DIFFRACTION3HEPT123.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36
LS refinement shell
*PLUS
Rfactor obs: 0.312

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