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- PDB-2ych: PilM-PilN type IV pilus biogenesis complex -

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Basic information

Entry
Database: PDB / ID: 2ych
TitlePilM-PilN type IV pilus biogenesis complex
Components
  • COMPETENCE PROTEIN PILM
  • COMPETENCE PROTEIN PILN
KeywordsCELL CYCLE / TYPE IV PILUS ACTIN SECRETION
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
PilN biogenesis protein dimerization domain / PilN biogenesis protein dimerization domain / Dna Ligase; domain 1 - #300 / : / Type IV pilus inner membrane component PilM / Type IV pilus assembly protein PilM; / : / ATPase, nucleotide binding domain / Dna Ligase; domain 1 / ATPase, nucleotide binding domain ...PilN biogenesis protein dimerization domain / PilN biogenesis protein dimerization domain / Dna Ligase; domain 1 - #300 / : / Type IV pilus inner membrane component PilM / Type IV pilus assembly protein PilM; / : / ATPase, nucleotide binding domain / Dna Ligase; domain 1 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Competence protein PilN / Competence protein PilM / Competence protein pilN / Pilus-associated protein pilM
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKaruppiah, V. / Derrick, J.P.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of the Pilm-Piln Inner Membrane Type Iv Pilus Biogenesis Complex from Thermus Thermophilus.
Authors: Karuppiah, V. / Derrick, J.P.
History
DepositionMar 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references / Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_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

Downloads & links

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Assembly

Deposited unit
A: COMPETENCE PROTEIN PILM
B: COMPETENCE PROTEIN PILN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1304
Polymers43,5982
Non-polymers5312
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-26.6 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.780, 50.780, 366.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein COMPETENCE PROTEIN PILM


Mass: 41700.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B843(DE3) / References: UniProt: Q5SIJ0, UniProt: Q72IW8*PLUS
#2: Protein/peptide COMPETENCE PROTEIN PILN


Mass: 1897.406 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-15 / Source method: obtained synthetically / Source: (synth.) THERMUS THERMOPHILUS (bacteria) / References: UniProt: Q5SII9, UniProt: Q72IW7*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsF334L DUE TO PCR ERROR

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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: 2.8 Å3/Da / Density % sol: 0.55 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M TRIS PH 8.0, 0.2M MAGNESIUM CHLORIDE AND 20% (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 4, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.16→91 Å / Num. obs: 27534 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 13.3 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.3
Reflection shellResolution: 2.16→2.21 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXD2006phasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.2→50.3 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.55 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.209
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. OMITTED RESIDUES ARE 1-10 AT THE N-TERMINUS, 250-274. BETWEEN ALPHA7 AND ALPHA8, AND 376-377 AT THE C-TERMINUS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27944 1289 5 %RANDOM
Rwork0.23739 ---
obs0.23947 24500 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.861 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2--1.64 Å20 Å2
3----3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 32 84 2743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222701
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3412.0373676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2355339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01223.495103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.6515466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3311525
X-RAY DIFFRACTIONr_chiral_restr0.1910.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0221970
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
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_it1.4221.51719
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.58322766
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4143982
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.4144.5910
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 84 -
Rwork0.271 1734 -
obs--100 %

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