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- PDB-4pht: ATPase GspE in complex with the cytoplasmic domain of GspL from t... -

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Basic information

Entry
Database: PDB / ID: 4pht
TitleATPase GspE in complex with the cytoplasmic domain of GspL from the Vibrio vulnificus type II Secretion system
Components
  • General secretory pathway protein E
  • Type II secretion system protein L
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


Gram-negative-bacterium-type cell wall / protein secretion by the type II secretion system / type II protein secretion system complex / membrane => GO:0016020 / nucleotide binding / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Type II secretion system, protein E, N-terminal domain / GspL cytoplasmic domain, C-terminal subdomain / Nucleotidyltransferase; domain 5 - #380 / : / Type II secretion system protein GspE / Type II secretion system protein GspL / GspL, cytoplasmic actin-ATPase-like domain / GspL periplasmic domain / Type II secretion system (T2SS), protein L / GspL periplasmic domain ...Type II secretion system, protein E, N-terminal domain / GspL cytoplasmic domain, C-terminal subdomain / Nucleotidyltransferase; domain 5 - #380 / : / Type II secretion system protein GspE / Type II secretion system protein GspL / GspL, cytoplasmic actin-ATPase-like domain / GspL periplasmic domain / Type II secretion system (T2SS), protein L / GspL periplasmic domain / Beta-Lactamase - #90 / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / GMP Synthetase; Chain A, domain 3 / Beta-Lactamase / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Type II secretion system protein L / Type II secretion system protein E / Type II secretion system protein E / Type II secretion system protein L
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.83 Å
AuthorsLu, C. / Korotkov, K. / Hol, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Crystal structure of the full-length ATPase GspE from the Vibrio vulnificus type II secretion system in complex with the cytoplasmic domain of GspL.
Authors: Lu, C. / Korotkov, K.V. / Hol, W.G.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Type II secretion system protein L
A: General secretory pathway protein E
Y: Type II secretion system protein L
B: General secretory pathway protein E
Z: Type II secretion system protein L
C: General secretory pathway protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,31215
Polymers250,5246
Non-polymers1,7889
Water28816
1
X: Type II secretion system protein L
A: General secretory pathway protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1045
Polymers83,5082
Non-polymers5963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-18 kcal/mol
Surface area31270 Å2
MethodPISA
2
Y: Type II secretion system protein L
B: General secretory pathway protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1045
Polymers83,5082
Non-polymers5963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-17 kcal/mol
Surface area31510 Å2
MethodPISA
3
Z: Type II secretion system protein L
C: General secretory pathway protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1045
Polymers83,5082
Non-polymers5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-17 kcal/mol
Surface area31220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.430, 133.900, 93.490
Angle α, β, γ (deg.)90.00, 91.41, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13X
23Y
14X
24Z
15A
25B
16A
26C
17B
27C
18Y
28Z
19B
29C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYSAB96 - 49797 - 498
21ASPASPLYSLYSBD96 - 49797 - 498
12ASPASPLYSLYSAB96 - 49797 - 498
22ASPASPLYSLYSCF96 - 49797 - 498
13SERSERPROPROXA2 - 2353 - 236
23SERSERPROPROYC2 - 2353 - 236
14SERSERPROPROXA2 - 2353 - 236
24SERSERPROPROZE2 - 2353 - 236
15ARGARGALAALAAB13 - 7614 - 77
25ARGARGALAALABD13 - 7614 - 77
16ARGARGALAALAAB13 - 7614 - 77
26ARGARGALAALACF13 - 7614 - 77
17ASPASPLYSLYSBD96 - 49797 - 498
27ASPASPLYSLYSCF96 - 49797 - 498
18SERSERPROPROYC2 - 2353 - 236
28SERSERPROPROZE2 - 2353 - 236
19ARGARGGLNGLNBD12 - 7813 - 79
29ARGARGGLNGLNCF12 - 7813 - 79

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

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Protein , 2 types, 6 molecules XYZABC

#1: Protein Type II secretion system protein L / T2SS protein L


Mass: 27451.859 Da / Num. of mol.: 3 / Fragment: UNP residues 5-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: gspL, VV1_0869 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DDT8, UniProt: A0A3Q0L2T9*PLUS
#2: Protein General secretory pathway protein E


Mass: 56056.238 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: gspE, VV1_0876 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DDT1, UniProt: A0A3Q0L2V2*PLUS

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Non-polymers , 4 types, 25 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.69→43.22 Å / Num. obs: 72192 / % possible obs: 95.2 % / Redundancy: 1.96 % / Net I/σ(I): 10.41

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementResolution: 2.83→43.22 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.875 / SU B: 18.491 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R: 5.386 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27977 3317 5.1 %RANDOM
Rwork0.24763 ---
obs0.24923 62082 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.909 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å20 Å20.04 Å2
2--2.37 Å20 Å2
3----5.46 Å2
Refinement stepCycle: 1 / Resolution: 2.83→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15337 0 99 16 15452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01915690
X-RAY DIFFRACTIONr_bond_other_d0.0050.0215176
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.97321285
X-RAY DIFFRACTIONr_angle_other_deg1.106334832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.28251970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52724.072663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.711152681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.84915114
X-RAY DIFFRACTIONr_chiral_restr0.050.22504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117648
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023380
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_it3.4055.7227961
X-RAY DIFFRACTIONr_mcbond_other3.4035.7217960
X-RAY DIFFRACTIONr_mcangle_it5.4468.5699904
X-RAY DIFFRACTIONr_mcangle_other5.4468.579905
X-RAY DIFFRACTIONr_scbond_it3.6066.0437729
X-RAY DIFFRACTIONr_scbond_other3.6066.0437730
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9118.90811381
X-RAY DIFFRACTIONr_long_range_B_refined10.21753.12461196
X-RAY DIFFRACTIONr_long_range_B_other10.21753.11661187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A229520.08
12B229520.08
21A228350.09
22C228350.09
31X126590.1
32Y126590.1
41X124570.1
42Z124570.1
51A32240.05
52B32240.05
61A32450.06
62C32450.06
71B232940.07
72C232940.07
81Y129870.07
82Z129870.07
91B33370.08
92C33370.08
LS refinement shellResolution: 2.83→2.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 227 -
Rwork0.333 4628 -
obs--99.35 %

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