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- PDB-4lw9: Crystal structure of Vibrio cholera major pseudopilin EpsG -

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Basic information

Entry
Database: PDB / ID: 4lw9
TitleCrystal structure of Vibrio cholera major pseudopilin EpsG
ComponentsType II secretion system protein G
KeywordsTRANSPORT PROTEIN / TYPE II SECRETION SYSTEM / PSEUDOPILUS
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / 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 / Pilin-like ...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 / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Type II secretion system core protein G
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsVago, F.S. / Raghunathan, K. / Jens, J.C. / Wedemeyer, W.J. / Bagdasarian, M. / Brunzelle, J.S. / Arvidson, D.N.
CitationJournal: To be Published
Title: Crystal structure of Vibrio cholera major pseudopilin EpsG
Authors: Vago, F.S. / Raghunathan, K. / Jens, J.C. / Wedemeyer, W.J. / Bagdasarian, M. / Brunzelle, J.S. / Arvidson, D.N.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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.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_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

Downloads & links

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Assembly

Deposited unit
A: Type II secretion system protein G
B: Type II secretion system protein G
C: Type II secretion system protein G
D: Type II secretion system protein G
E: Type II secretion system protein G
F: Type II secretion system protein G
I: Type II secretion system protein G
J: Type II secretion system protein G
K: Type II secretion system protein G
L: Type II secretion system protein G
Q: Type II secretion system protein G
R: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,49599
Polymers160,69812
Non-polymers6,79787
Water11,962664
1
A: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,00010
Polymers13,3921
Non-polymers6099
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8939
Polymers13,3921
Non-polymers5018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9197
Polymers13,3921
Non-polymers5276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,07310
Polymers13,3921
Non-polymers6829
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,05510
Polymers13,3921
Non-polymers6649
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8947
Polymers13,3921
Non-polymers5026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
I: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0158
Polymers13,3921
Non-polymers6247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
J: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8546
Polymers13,3921
Non-polymers4625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
K: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,11610
Polymers13,3921
Non-polymers7249
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
L: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8587
Polymers13,3921
Non-polymers4676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
Q: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9598
Polymers13,3921
Non-polymers5687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
R: Type II secretion system protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8597
Polymers13,3921
Non-polymers4686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.610, 70.015, 131.544
Angle α, β, γ (deg.)90.00, 103.29, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein , 1 types, 12 molecules ABCDEFIJKLQR

#1: Protein
Type II secretion system protein G / T2SS protein G / Cholera toxin secretion protein EpsG / General secretion pathway protein G


Mass: 13391.531 Da / Num. of mol.: 12 / Fragment: UNP residues 35-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961, O1 biovar / Gene: epsG, VC_2730 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45773

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Non-polymers , 7 types, 751 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Pt
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 6 mM zinc sulfate, 60 mM MES pH 6.5, 15% PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0712 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0712 Å / Relative weight: 1
ReflectionResolution: 1.9→29.54 Å / Num. obs: 117230

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.379 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24527 6178 5 %RANDOM
Rwork0.20249 ---
obs0.20468 117230 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.656 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10913 0 143 664 11720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02111431
X-RAY DIFFRACTIONr_bond_other_d0.0010.027319
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.94915318
X-RAY DIFFRACTIONr_angle_other_deg0.862317927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22851404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02726.078589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.777151691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.851528
X-RAY DIFFRACTIONr_chiral_restr0.0850.21579
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022120
X-RAY DIFFRACTIONr_nbd_refined0.2120.32519
X-RAY DIFFRACTIONr_nbd_other0.1860.37304
X-RAY DIFFRACTIONr_nbtor_refined0.1830.55637
X-RAY DIFFRACTIONr_nbtor_other0.0960.55512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.51013
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.53
X-RAY DIFFRACTIONr_metal_ion_refined0.1820.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3520.370
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.397
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2920.534
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2060.512
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.45427050
X-RAY DIFFRACTIONr_mcbond_other0.30322896
X-RAY DIFFRACTIONr_mcangle_it2.352311132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.52524556
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.16834185
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 450 -
Rwork0.232 8612 -
obs--99.68 %

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