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

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Basic information

Entry
Database: PDB / ID: 7eqk
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 / 1-(1~{H}-indol-3-yl)ethanone / : / GLYCOLIC ACID / (E)-3-(1H-indol-3-yl)-2-oxidanyl-but-2-enoic acid / Cupin domain-containing protein
Function and homology information
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04001020299 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 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_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
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)28,2287
Polymers27,6642
Non-polymers5645
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-44 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.782, 66.782, 116.336
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
11ASPASPLEULEU(chain 'A' and (resid 11 through 114 or resid 116 through 128))AA11 - 11411 - 114
12ALAALAVALVAL(chain 'A' and (resid 11 through 114 or resid 116 through 128))AA116 - 127116 - 127
23ASPASPLEULEU(chain 'B' and (resid 11 through 114 or resid 116 through 128))BB11 - 11411 - 114
24ALAALAVALVAL(chain 'B' and (resid 11 through 114 or resid 116 through 128))BB116 - 127116 - 127

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Components

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Protein , 1 types, 2 molecules AB

#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, G3260_000576 / Production host: Escherichia coli (E. coli) / References: UniProt: L7PIL3

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Non-polymers , 5 types, 107 molecules

#2: 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
#3: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-5RN / 1-(1~{H}-indol-3-yl)ethanone


Mass: 159.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-JAX / (E)-3-(1H-indol-3-yl)-2-oxidanyl-but-2-enoic acid


Mass: 217.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.56 %
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: 2.04→30 Å / Num. obs: 19749 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 33.5243086976 Å2 / Rsym value: 0.07 / Net I/σ(I): 32.84
Reflection shellResolution: 2.04→2.11 Å / Rmerge(I) obs: 0.738 / Num. unique obs: 1912

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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: 2.04001020299→28.9588223376 Å / SU ML: 0.25789248673 / Cross valid method: NONE / σ(F): 1.36651513816 / Phase error: 24.8507519835
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244796606859 973 4.93632996804 %
Rwork0.199336969955 18738 -
obs0.201582819044 19711 99.9442247237 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.6291999048 Å2
Refinement stepCycle: LAST / Resolution: 2.04001020299→28.9588223376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 35 103 1894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007498776697571847
X-RAY DIFFRACTIONf_angle_d0.9680562820152530
X-RAY DIFFRACTIONf_chiral_restr0.061482104077288
X-RAY DIFFRACTIONf_plane_restr0.00651007393658332
X-RAY DIFFRACTIONf_dihedral_angle_d13.13898982111262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0401-2.14750.3113754369961420.256775113032610X-RAY DIFFRACTION99.7101449275
2.1475-2.2820.2676155299151360.2307362627592633X-RAY DIFFRACTION99.963898917
2.282-2.45810.2977256767721360.2329654718432639X-RAY DIFFRACTION100
2.4581-2.70540.3116598588141360.2303597554942642X-RAY DIFFRACTION100
2.7054-3.09640.2517267127211390.2322658779792680X-RAY DIFFRACTION100
3.0964-3.89970.2437355388111410.1823677648042700X-RAY DIFFRACTION100
3.8997-28.95880.1943383211991430.1686979296172834X-RAY DIFFRACTION99.9664204164

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