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- PDB-1ay2: STRUCTURE OF THE FIBER-FORMING PROTEIN PILIN AT 2.6 ANGSTROMS RES... -

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Basic information

Entry
Database: PDB / ID: 1ay2
TitleSTRUCTURE OF THE FIBER-FORMING PROTEIN PILIN AT 2.6 ANGSTROMS RESOLUTION
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. / Parge, H.E. / Tainer, J.A.
CitationJournal: 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
DepositionNov 13, 1997Processing site: BNL
Revision 1.0Apr 29, 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 / 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_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.conn_type_id / _struct_conn.id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Feb 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_angle / struct_conn
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_atom_id / _atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id

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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)17,9194
Polymers17,1921
Non-polymers7273
Water2,324129
1
A: TYPE 4 PILIN
hetero molecules

A: TYPE 4 PILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8388
Polymers34,3852
Non-polymers1,4536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_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: 17192.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neisseria gonorrhoeae (bacteria) / Cellular location: EXTRACELLULARGlossary of biology / 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 / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 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 / Details: Parge, H.E., (1990) J. Biol. Chem., 265, 2278.
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
736-45 %PEG4001drop
8100 mMTris-HCl1reservoir
9reservoir1drop
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 1, 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: 6494 / % 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: 0.081

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
Details: SOLVENT FLATTENING (WITH 50%) SOLVENT) USING PHASES WAS USED TO IMPROVE PHASES (F.O.M. INCREASED FROM 0.75 - 0.86) FOR FITTING. DATA FROM A PT-SOAKED DERIVATIVE CRYSTAL WAS USED FOR ...Details: SOLVENT FLATTENING (WITH 50%) SOLVENT) USING PHASES WAS USED TO IMPROVE PHASES (F.O.M. INCREASED FROM 0.75 - 0.86) FOR FITTING. DATA FROM A PT-SOAKED DERIVATIVE CRYSTAL WAS USED FOR REFINEMENT BECAUSE IT WAS STRONGER THAN "NATIVE" DATA. THE EXPECTED N-TERMINAL METHYL-PHE WAS VERIFIED BY N-TERMINAL SEQUENCING BUT WAS NOT INCLUDED IN THE MODEL BECAUSE IT WAS NOT APPARENT IN ELECTRON DENSITY. WATERS WERE NOT RESTRAINED DURING REFINEMENT AND TWO WATERS (333 AND 348) MOVED CLOSE TO THE PT SITE.
RfactorNum. reflection% reflection
Rwork0.194 --
obs0.194 6565 95 %
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--4.25 Å20 Å20 Å2
2--8.25 Å20 Å2
3----4 Å2
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 36 129 1373
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_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.359
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rwork0.324 723
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM_AUX.PROTOPH3.CHO
X-RAY DIFFRACTION3PARAM3_MOD.CHOHEPT123.TOP
X-RAY DIFFRACTION4TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.359

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