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- PDB-2whn: N-terminal domain from the PilC type IV pilus biogenesis protein -

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Basic information

Entry
Database: PDB / ID: 2whn
TitleN-terminal domain from the PilC type IV pilus biogenesis protein
ComponentsPILUS ASSEMBLY PROTEIN PILC
KeywordsPROTEIN TRANSPORT / TRANSPORT / TRANSMEMBRANE / PILUS BIOGENESIS
Function / homology
Function and homology information


protein secretion / plasma membrane
Similarity search - Function
: / Type II secretion system (T2SS), domain F / T2SS_GspF/T4SS_PilC conserved site / Bacterial type II secretion system protein F signature. / Type II secretion system protein F, N-terminal domain / GspF/PilC family / Type II secretion system protein GspF domain / Type II secretion system GspF domain superfamily / Type II secretion system (T2SS), protein F / Receptor-associated Protein ...: / Type II secretion system (T2SS), domain F / T2SS_GspF/T4SS_PilC conserved site / Bacterial type II secretion system protein F signature. / Type II secretion system protein F, N-terminal domain / GspF/PilC family / Type II secretion system protein GspF domain / Type II secretion system GspF domain superfamily / Type II secretion system (T2SS), protein F / Receptor-associated Protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Type IV pilus assembly protein PilC
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.05 Å
AuthorsKaruppiah, V. / Hassan, D. / Saleem, M. / Derrick, J.P.
CitationJournal: Proteins / Year: 2010
Title: Structure and Oligomerization of the Pilc Type Iv Pilus Biogenesis Protein from Thermus Thermophilus.
Authors: Karuppiah, V. / Hassan, D. / Saleem, M. / Derrick, J.P.
History
DepositionMay 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Other / Category: pdbx_database_proc / pdbx_database_status / Item: _pdbx_database_status.recvd_author_approval
Revision 1.3Apr 10, 2019Group: Data collection / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PILUS ASSEMBLY PROTEIN PILC
B: PILUS ASSEMBLY PROTEIN PILC


Theoretical massNumber of molelcules
Total (without water)25,8522
Polymers25,8522
Non-polymers00
Water1,63991
1
A: PILUS ASSEMBLY PROTEIN PILC


Theoretical massNumber of molelcules
Total (without water)12,9261
Polymers12,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PILUS ASSEMBLY PROTEIN PILC


Theoretical massNumber of molelcules
Total (without water)12,9261
Polymers12,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.168, 55.168, 152.078
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 PILUS ASSEMBLY PROTEIN PILC / PILC


Mass: 12926.129 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 53-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): T7 EXPRESS / References: UniProt: Q5SK58
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.29 Å3/Da / Density % sol: 46.25 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9497
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9497 Å / Relative weight: 1
ReflectionResolution: 2.05→76 Å / Num. obs: 14807 / % possible obs: 95.4 % / Observed criterion σ(I): 3 / Redundancy: 11.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.05→15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.949 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26994 728 5 %RANDOM
Rwork0.21638 ---
obs0.21899 13962 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.906 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.05→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 0 91 1742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0221666
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.5212.0072233
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9915211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20722.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80315327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9941518
X-RAY DIFFRACTIONr_chiral_restr0.0380.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021196
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_it0.5891.51048
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08221660
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1533618
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.464.5573
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: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 39 -
Rwork0.251 895 -
obs--86.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.30192.19343.44441.2880.92442.0629-0.0106-0.14150.38260.0421-0.15920.0823-0.04890.00360.16980.0645-0.02790.02370.0746-0.04390.13110.925111.102521.4764
24.20282.40443.18293.90832.33526.1885-0.01290.35650.2164-0.68880.0253-0.2819-0.4610.7041-0.01240.2134-0.00050.10740.14980.0080.1650.62137.198811.3395
30.18791.35810.623710.81314.14712.6505-0.02850.0025-0.0412-0.34460.0215-0.6417-0.11050.24640.0070.0344-0.02590.03980.12830.00430.13687.32193.357316.3696
45.83293.71280.85049.17534.65514.27940.162-0.6229-0.15710.5153-0.0045-0.65560.4230.5428-0.15740.15360.06-0.02430.23520.01730.10633.7937-1.602723.4665
59.78383.25671.81558.80920.21476.446-0.2354-0.3285-0.39930.1670.132-0.2770.3289-0.0520.10340.04850.02810.01950.03880.01340.0251-4.9859-2.872525.1724
66.15272.92881.35149.68432.20785.57520.1635-0.52890.50180.4832-0.20780.4449-0.0482-0.01550.04440.0498-0.04250.03710.0847-0.05790.0534-11.70087.847924.7249
73.955-2.77191.18169.8269-1.50983.95150.103-0.17240.13270.3566-0.01960.0967-0.37130.1741-0.08340.0694-0.04760.0230.0553-0.01050.0135-21.0043-7.115337.0662
86.2846-4.2772-1.855410.77692.27224.6987-0.027-0.3417-0.12720.45490.11440.38920.1599-0.1913-0.08740.0355-0.02210.00860.05160.01930.0236-28.194-12.82238.0269
91.6685-0.6615-0.55949.52336.4476.68450.06830.0710.1370.0343-0.31010.5910.0067-0.58820.24180.00360.00230.010.07980.0210.0827-33.4456-11.147331.2225
107.4917-0.83-3.50468.78051.15431.7155-0.05430.7840.0964-0.37920.05130.3682-0.0383-0.34650.00290.124-0.0351-0.06480.10.03430.0445-28.6215-8.645923.4183
119.2403-1.8096-0.965210.12981.47775.4727-0.12120.3586-0.3-0.1774-0.0104-0.14630.06170.05350.13160.0486-0.04430.00710.0539-0.00720.0184-19.7503-8.35222.9867
122.1057-1.1145-0.204211.70121.74972.56460.1436-0.17550.0007-0.026-0.1908-0.1381-0.14970.20870.04720.0216-0.0293-0.00230.05160.01390.0108-14.1887-2.531832.6725
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 82
2X-RAY DIFFRACTION2A83 - 97
3X-RAY DIFFRACTION3A98 - 115
4X-RAY DIFFRACTION4A116 - 125
5X-RAY DIFFRACTION5A126 - 142
6X-RAY DIFFRACTION6A143 - 162
7X-RAY DIFFRACTION7B62 - 82
8X-RAY DIFFRACTION8B83 - 97
9X-RAY DIFFRACTION9B98 - 115
10X-RAY DIFFRACTION10B116 - 125
11X-RAY DIFFRACTION11B126 - 142
12X-RAY DIFFRACTION12B143 - 162

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