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- PDB-1t92: Crystal structure of N-terminal truncated pseudopilin PulG -

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Basic information

Entry
Database: PDB / ID: 1t92
TitleCrystal structure of N-terminal truncated pseudopilin PulG
ComponentsGeneral secretion pathway protein G
KeywordsPROTEIN TRANSPORT / domain-swapping / zinc / pseudopilin
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Type II secretion system protein GspG / Type II secretion system protein GspG, C-terminal / Type II secretion system (T2SS), protein G / Glycoprotein, Type 4 Pilin / Bacterial general secretion pathway protein G-type pilin / Glycoprotein, Type 4 Pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II secretion system core protein G
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsKoehler, R. / Schaefer, K. / Mueller, S. / Vignon, G. / Diederichs, K. / Philippsen, A. / Ringler, P. / Pugsley, A.P. / Engel, A. / Welte, W.
CitationJournal: Mol.Microbiol. / Year: 2004
Title: Structure and assembly of the pseudopilin PulG.
Authors: Koehler, R. / Schaefer, K. / Mueller, S. / Vignon, G. / Diederichs, K. / Philippsen, A. / Ringler, P. / Pugsley, A.P. / Engel, A. / Welte, W.
History
DepositionMay 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_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.value / _struct_conn.pdbx_dist_value / _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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: General secretion pathway protein G
B: General secretion pathway protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9223
Polymers25,8562
Non-polymers651
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-56 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.395, 85.395, 145.7205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
32A
42B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNARGARG1AA27 - 333 - 9
211ASNASNARGARG1BB27 - 333 - 9
112GLNGLNGLYGLY1AA34 - 6310 - 39
212GLNGLNGLYGLY1BB34 - 6310 - 39
322PROPROPHEPHE1AA90 - 13366 - 109
422PROPROPHEPHE1BB90 - 13366 - 109
113ALAALALEULEU4AA66 - 8942 - 65
213ALAALALEULEU4BB66 - 8942 - 65

NCS ensembles :
ID
1
2
3

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Components

#1: Protein General secretion pathway protein G / Pullulanase secretion protein pulG


Mass: 12928.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: PULG / Plasmid: pCHAP7013 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15746
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.97 Å3/Da / Density % sol: 58.3 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.2
Details: HEPES, ammonium sulfate, isopropanol, sodium azide, pH 7.2, VAPOR DIFFUSION, HANGING DROP, SEEDING, temperature 100.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODESCHNEIDER11.5418
SYNCHROTRONSLS X06SA20.9196
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATESep 27, 2002
MARRESEARCH2CCDNov 14, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.91961
ReflectionResolution: 1.6→50 Å / Num. all: 42126 / Num. obs: 40533 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 25.14 % / Biso Wilson estimate: 28.98 Å2 / Rsym value: 0.128 / Net I/σ(I): 19.27
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 3644 / Rsym value: 0.52 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.486 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2037 5 %RANDOM
Rwork0.167 ---
all0.169 42126 --
obs0.169 40533 96.2 %-
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: 29.427 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.11 Å20 Å2
2---0.21 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 1 257 1944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211728
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.962349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355214
X-RAY DIFFRACTIONr_chiral_restr0.1050.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021386
X-RAY DIFFRACTIONr_nbd_refined0.1980.2775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2204
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.223
X-RAY DIFFRACTIONr_mcbond_it3.74341072
X-RAY DIFFRACTIONr_mcangle_it5.23361723
X-RAY DIFFRACTIONr_scbond_it2.1422656
X-RAY DIFFRACTIONr_scangle_it3.0763626
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
159tight positional0.030.05
2575tight positional0.040.05
3186medium positional0.340.5
159tight thermal0.110.5
2575tight thermal0.290.5
3186medium thermal1.722
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.22 152
Rwork0.203 2894
obs-3046

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