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- PDB-6tu6: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Tra... -

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Database: PDB / ID: 6tu6
TitleKemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
ComponentsKemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
KeywordsDE NOVO PROTEIN / Kemp Eliminase / Enzyme / Protein Design
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 6-NITROBENZOTRIAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsBloch, J.S. / Hilvert, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Acs Catalysis / Year: 2020
Title: Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiencyproficiency
Authors: Kries, H. / Bloch, J.S. / Bunzel, H.A. / Hilvert, D.
History
DepositionJan 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 18, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
B: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
C: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
D: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
E: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
F: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
G: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
H: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
I: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
J: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
K: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
L: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
M: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
N: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
O: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
P: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)554,15956
Polymers549,22816
Non-polymers4,93140
Water117,2966511
1
A: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5873
Polymers34,3271
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5873
Polymers34,3271
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7795
Polymers34,3271
Non-polymers4524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


  • defined by author
  • 34.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)34,7795
Polymers34,3271
Non-polymers4524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6834
Polymers34,3271
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5873
Polymers34,3271
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


  • defined by author
  • 34.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)34,4912
Polymers34,3271
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6834
Polymers34,3271
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6834
Polymers34,3271
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5873
Polymers34,3271
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4912
Polymers34,3271
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5873
Polymers34,3271
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6834
Polymers34,3271
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6834
Polymers34,3271
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5873
Polymers34,3271
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6834
Polymers34,3271
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.370, 108.690, 108.720
Angle α, β, γ (deg.)88.527, 90.155, 89.818
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole


Mass: 34326.742 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical
ChemComp-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6511 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 1.1 M ammonium sulfate, 100 mM sodium acetate, pH 5.9, seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.05→49.18 Å / Num. obs: 2004388 / % possible obs: 95.28 % / Redundancy: 1.05 % / Biso Wilson estimate: 8.65 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.41
Reflection shellResolution: 1.05→1.088 Å / Num. unique obs: 194912 / CC1/2: 0.639

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BS0

4bs0


Resolution: 1.05→49.18 Å / SU ML: 0.1366 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.3355
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 1975 10 %
Rwork0.1958 2001182 -
obs0.1958 2003157 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.51 Å2
Refinement stepCycle: LAST / Resolution: 1.05→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36478 0 312 6511 43301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007540514
X-RAY DIFFRACTIONf_angle_d0.971455722
X-RAY DIFFRACTIONf_chiral_restr0.07236073
X-RAY DIFFRACTIONf_plane_restr0.0077470
X-RAY DIFFRACTIONf_dihedral_angle_d12.990314613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.080.30451360.298139005X-RAY DIFFRACTION92.58
1.08-1.110.28611340.272139449X-RAY DIFFRACTION92.97
1.11-1.140.28781470.257139914X-RAY DIFFRACTION93.34
1.14-1.170.27531320.2448140669X-RAY DIFFRACTION93.71
1.17-1.220.24931210.2406141056X-RAY DIFFRACTION94.07
1.22-1.270.3281470.2272142079X-RAY DIFFRACTION94.62
1.27-1.320.26711440.2164142333X-RAY DIFFRACTION94.9
1.32-1.390.22821340.2076143225X-RAY DIFFRACTION95.45
1.39-1.480.21021410.1973143762X-RAY DIFFRACTION95.9
1.48-1.590.27281600.1868144701X-RAY DIFFRACTION96.41
1.59-1.750.2481350.1885145152X-RAY DIFFRACTION96.68
1.75-2.010.23581470.1815146098X-RAY DIFFRACTION97.42
2.01-2.530.22571510.1725146840X-RAY DIFFRACTION97.88
2.53-49.180.17091460.1706146899X-RAY DIFFRACTION97.96

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