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- PDB-7euz: Structural and mechanistic studies of a novel non-heme iron epime... -

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Basic information

Entry
Database: PDB / ID: 7euz
TitleStructural and mechanistic studies of a novel non-heme iron epimerase/lyase and its utilization in chemoselective synthesis.
ComponentsCupin domain-containing protein
KeywordsISOMERASE / non-heme iron epimerase/lyase
Function / homologyRmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / : / (2S,3R)-2-azanyl-3-(1H-indol-3-yl)butanoic acid / PHOSPHITE ION / Cupin domain-containing protein
Function and homology information
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91028166603 Å
AuthorsLi, T.L. / Li, Y.S. / Chen, M.H.
CitationJournal: Acs Catalysis / Year: 2022
Title: Structural and Mechanistic Bases for StnK3 and Its Mutant-Mediated Lewis-Acid-Dependent Epimerization and Retro-Aldol Reactions.
Authors: Chen, M.H. / Li, Y.S. / Hsu, N.S. / Lin, K.H. / Wang, Y.L. / Wang, Z.C. / Chang, C.F. / Lin, J.P. / Chang, C.Y. / Li, T.L.
History
DepositionMay 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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
A: Cupin domain-containing protein
B: Cupin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0736
Polymers27,6642
Non-polymers4094
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-43 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.834, 66.834, 116.742
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVAL(chain 'A' and (resid 12 through 24 or resid 26...AA12 - 2412 - 24
12GLYGLYVALVAL(chain 'A' and (resid 12 through 24 or resid 26...AA26 - 5626 - 56
13LYSLYSLEULEU(chain 'A' and (resid 12 through 24 or resid 26...AA58 - 11458 - 114
14ALAALAVALVAL(chain 'A' and (resid 12 through 24 or resid 26...AA116 - 127116 - 127
25ALAALAVALVAL(chain 'B' and (resid 12 through 114 or resid 116 through 128))BB12 - 2412 - 24
26GLYGLYVALVAL(chain 'B' and (resid 12 through 114 or resid 116 through 128))BB26 - 5626 - 56
27LYSLYSLEULEU(chain 'B' and (resid 12 through 114 or resid 116 through 128))BB58 - 11458 - 114
28ALAALAVALVAL(chain 'B' and (resid 12 through 114 or resid 116 through 128))BB116 - 127116 - 127

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Components

#1: Protein Cupin domain-containing protein


Mass: 13831.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus (bacteria) / Gene: stnK3 / Production host: Escherichia coli (E. coli) / References: UniProt: L7PIL3
#2: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-JD3 / (2S,3R)-2-azanyl-3-(1H-indol-3-yl)butanoic acid


Mass: 218.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.2 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic, pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→30 Å / Num. obs: 24066 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 34.4892209598 Å2 / Rsym value: 0.032 / Net I/σ(I): 46.99
Reflection shellResolution: 1.91→1.98 Å / Num. unique obs: 2352 / Rsym value: 0.716

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Processing

Software
NameVersionClassification
PHENIXv1.11.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXv1.11.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J4C

6j4c


Resolution: 1.91028166603→26.0599360487 Å / SU ML: 0.211623634292 / Cross valid method: NONE / σ(F): 1.33793730719 / Phase error: 21.40877158
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216540553297 1200 4.99625281039 %
Rwork0.189210590329 22818 -
obs0.190608641498 24018 99.9375858195 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.5055080751 Å2
Refinement stepCycle: LAST / Resolution: 1.91028166603→26.0599360487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 18 113 1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007517522312421812
X-RAY DIFFRACTIONf_angle_d1.00603344822479
X-RAY DIFFRACTIONf_chiral_restr0.06595544195287
X-RAY DIFFRACTIONf_plane_restr0.0062630774956322
X-RAY DIFFRACTIONf_dihedral_angle_d13.14873704221246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9103-1.98670.2840135938331310.2504620060552475X-RAY DIFFRACTION99.9616417338
1.9867-2.07710.2408799999951360.2236774686332506X-RAY DIFFRACTION100
2.0771-2.18660.2612904807581280.2099276618382473X-RAY DIFFRACTION99.8847926267
2.1866-2.32350.264767240051340.2025601880592521X-RAY DIFFRACTION100
2.3235-2.50280.2204907999961310.2138812241622510X-RAY DIFFRACTION99.9621498864
2.5028-2.75440.2545807243581330.2122511541362527X-RAY DIFFRACTION100
2.7544-3.15240.2257602914321340.2055330418882538X-RAY DIFFRACTION100
3.1524-3.96940.1879943621781320.180822816112579X-RAY DIFFRACTION100
3.9694-26.05980.1961942111331410.1631005339462689X-RAY DIFFRACTION99.7532604864

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