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- PDB-5o0w: Crystal structure of the complex between Nb474 and Trypanosoma co... -

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Basic information

Entry
Database: PDB / ID: 5o0w
TitleCrystal structure of the complex between Nb474 and Trypanosoma congolense fructose-1,6-bisphosphate aldolase
Components
  • Fructose-bisphosphate aldolase
  • Nb474
KeywordsLYASE / complex / Nanobody / aldolase / diagnosis
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesTrypanosoma congolense (eukaryote)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsPinto, J. / Magez, S. / Sterckx, Y.
Funding support Belgium, 2items
OrganizationGrant numberCountry
VUBVUB-SRP3 Belgium
IUAP Belgium
CitationJournal: PLoS Negl Trop Dis / Year: 2017
Title: Structural basis for the high specificity of a Trypanosoma congolense immunoassay targeting glycosomal aldolase.
Authors: Pinto, J. / Odongo, S. / Lee, F. / Gaspariunaite, V. / Muyldermans, S. / Magez, S. / Sterckx, Y.G.
History
DepositionMay 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
C: Fructose-bisphosphate aldolase
D: Fructose-bisphosphate aldolase
E: Nb474
F: Nb474
G: Nb474
H: Nb474
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,58714
Polymers234,0358
Non-polymers5536
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20370 Å2
ΔGint-54 kcal/mol
Surface area68340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.820, 188.870, 126.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 through 3 and (name N...
21(chain B and ((resid 2 through 3 and (name N...
31(chain C and ((resid 2 through 3 and (name N...
41(chain D and (resid 2 through 18 or (resid 19...
12(chain E and (resid 2 through 4 or (resid 5...
22(chain F and (resid 2 through 18 or (resid 19...
32(chain G and (resid 2 through 10 or (resid 11...
42(chain H and (resid 2 through 10 or (resid 11...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERARGARG(chain A and ((resid 2 through 3 and (name N...AA2 - 32 - 3
121SERSERASPASP(chain A and ((resid 2 through 3 and (name N...AA2 - 3612 - 361
131SERSERASPASP(chain A and ((resid 2 through 3 and (name N...AA2 - 3612 - 361
141SERSERASPASP(chain A and ((resid 2 through 3 and (name N...AA2 - 3612 - 361
151SERSERASPASP(chain A and ((resid 2 through 3 and (name N...AA2 - 3612 - 361
211SERSERARGARG(chain B and ((resid 2 through 3 and (name N...BB2 - 32 - 3
221SERSERASPASP(chain B and ((resid 2 through 3 and (name N...BB2 - 3592 - 359
231SERSERASPASP(chain B and ((resid 2 through 3 and (name N...BB2 - 3592 - 359
241SERSERASPASP(chain B and ((resid 2 through 3 and (name N...BB2 - 3592 - 359
251SERSERASPASP(chain B and ((resid 2 through 3 and (name N...BB2 - 3592 - 359
311SERSERARGARG(chain C and ((resid 2 through 3 and (name N...CC2 - 32 - 3
321SERSERASPASP(chain C and ((resid 2 through 3 and (name N...CC2 - 3612 - 361
331SERSERASPASP(chain C and ((resid 2 through 3 and (name N...CC2 - 3612 - 361
341SERSERASPASP(chain C and ((resid 2 through 3 and (name N...CC2 - 3612 - 361
351SERSERASPASP(chain C and ((resid 2 through 3 and (name N...CC2 - 3612 - 361
411SERSERLEULEU(chain D and (resid 2 through 18 or (resid 19...DD2 - 182 - 18
421LYSLYSLYSLYS(chain D and (resid 2 through 18 or (resid 19...DD1919
431SERSERLYSLYS(chain D and (resid 2 through 18 or (resid 19...DD2 - 3602 - 360
441SERSERLYSLYS(chain D and (resid 2 through 18 or (resid 19...DD2 - 3602 - 360
451SERSERLYSLYS(chain D and (resid 2 through 18 or (resid 19...DD2 - 3602 - 360
461SERSERLYSLYS(chain D and (resid 2 through 18 or (resid 19...DD2 - 3602 - 360
112VALVALLEULEU(chain E and (resid 2 through 4 or (resid 5...EE2 - 42 - 4
122GLNGLNGLNGLN(chain E and (resid 2 through 4 or (resid 5...EE55
132VALVALHISHIS(chain E and (resid 2 through 4 or (resid 5...EE2 - 1382 - 138
142VALVALHISHIS(chain E and (resid 2 through 4 or (resid 5...EE2 - 1382 - 138
152VALVALHISHIS(chain E and (resid 2 through 4 or (resid 5...EE2 - 1382 - 138
162VALVALHISHIS(chain E and (resid 2 through 4 or (resid 5...EE2 - 1382 - 138
212VALVALLEULEU(chain F and (resid 2 through 18 or (resid 19...FF2 - 182 - 18
222ARGARGARGARG(chain F and (resid 2 through 18 or (resid 19...FF1919
232VALVALHISHIS(chain F and (resid 2 through 18 or (resid 19...FF2 - 1382 - 138
242VALVALHISHIS(chain F and (resid 2 through 18 or (resid 19...FF2 - 1382 - 138
252VALVALHISHIS(chain F and (resid 2 through 18 or (resid 19...FF2 - 1382 - 138
262VALVALHISHIS(chain F and (resid 2 through 18 or (resid 19...FF2 - 1382 - 138
272VALVALHISHIS(chain F and (resid 2 through 18 or (resid 19...FF2 - 1382 - 138
282VALVALHISHIS(chain F and (resid 2 through 18 or (resid 19...FF2 - 1382 - 138
312VALVALGLYGLY(chain G and (resid 2 through 10 or (resid 11...GG2 - 102 - 10
322LEULEULEULEU(chain G and (resid 2 through 10 or (resid 11...GG1111
332VALVALHISHIS(chain G and (resid 2 through 10 or (resid 11...GG2 - 1392 - 139
342VALVALHISHIS(chain G and (resid 2 through 10 or (resid 11...GG2 - 1392 - 139
352VALVALHISHIS(chain G and (resid 2 through 10 or (resid 11...GG2 - 1392 - 139
362VALVALHISHIS(chain G and (resid 2 through 10 or (resid 11...GG2 - 1392 - 139
412VALVALGLYGLY(chain H and (resid 2 through 10 or (resid 11...HH2 - 102 - 10
422LEULEULEULEU(chain H and (resid 2 through 10 or (resid 11...HH1111
432VALVALSERSER(chain H and (resid 2 through 10 or (resid 11...HH2 - 1372 - 137
442VALVALSERSER(chain H and (resid 2 through 10 or (resid 11...HH2 - 1372 - 137
452VALVALSERSER(chain H and (resid 2 through 10 or (resid 11...HH2 - 1372 - 137
462VALVALSERSER(chain H and (resid 2 through 10 or (resid 11...HH2 - 1372 - 137

NCS ensembles :
ID
1
2

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Components

#1: Protein
Fructose-bisphosphate aldolase /


Mass: 42708.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma congolense (strain IL3000) (eukaryote)
Gene: TCIL3000_10_4760 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0UWE7, fructose-bisphosphate aldolase
#2: Antibody
Nb474


Mass: 15800.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate pH 6.5, 200 mM magnesium acetate, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.57→47.226 Å / Num. obs: 92520 / % possible obs: 99.56 % / Redundancy: 6.88 % / Biso Wilson estimate: 48.65 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.1805 / Net I/σ(I): 11.25
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 7.11 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 9072 / CC1/2: 0.498 / Rrim(I) all: 1.496 / % possible all: 99.15

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F2J
Resolution: 2.57→47.226 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.99 / Phase error: 23.89
RfactorNum. reflection% reflection
Rfree0.2221 8923 5.02 %
Rwork0.1923 --
obs0.1938 92502 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.76 Å2 / Biso mean: 51.8862 Å2 / Biso min: 25 Å2
Refinement stepCycle: final / Resolution: 2.57→47.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14952 0 36 516 15504
Biso mean--61.82 49.85 -
Num. residues----1985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315278
X-RAY DIFFRACTIONf_angle_d0.65320737
X-RAY DIFFRACTIONf_chiral_restr0.0442316
X-RAY DIFFRACTIONf_plane_restr0.0052695
X-RAY DIFFRACTIONf_dihedral_angle_d10.2879089
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6644X-RAY DIFFRACTION10.837TORSIONAL
12B6644X-RAY DIFFRACTION10.837TORSIONAL
13C6644X-RAY DIFFRACTION10.837TORSIONAL
14D6644X-RAY DIFFRACTION10.837TORSIONAL
21E2387X-RAY DIFFRACTION10.837TORSIONAL
22F2387X-RAY DIFFRACTION10.837TORSIONAL
23G2387X-RAY DIFFRACTION10.837TORSIONAL
24H2387X-RAY DIFFRACTION10.837TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.57-2.59920.37022970.32715595589299
2.5992-2.62980.33482980.32355642594099
2.6298-2.66190.37672850.32335531581699
2.6619-2.69560.3422990.30475652595199
2.6956-2.7310.31652990.302356065905100
2.731-2.76840.30412970.29815602589999
2.7684-2.8080.33922990.2975651595099
2.808-2.84990.33072950.29515575587099
2.8499-2.89440.30212960.29825635593199
2.8944-2.94190.38982920.326155765868100
2.9419-2.99260.35433020.313156585960100
2.9926-3.0470.26722910.25975562585399
3.047-3.10560.26562980.22795689598799
3.1056-3.1690.24892980.226756085906100
3.169-3.23790.25232930.21956025895100
3.2379-3.31320.2343000.208456465946100
3.3132-3.3960.25662980.206456465944100
3.396-3.48780.24643040.206556355939100
3.4878-3.59040.25152920.187756235915100
3.5904-3.70620.19013010.166856365937100
3.7062-3.83860.19583020.156156465948100
3.8386-3.99220.16442960.155656455941100
3.9922-4.17380.2032990.154356715970100
4.1738-4.39370.16122960.138856575953100
4.3937-4.66880.16252950.127456395934100
4.6688-5.02890.14732990.130256475946100
5.0289-5.53430.20553000.153656375937100
5.5343-6.33350.21123070.174856325939100
6.3335-7.97330.17862990.157256475946100
7.9733-47.23410.15052960.1556445940100

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