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- PDB-7eu6: Structural and mechanistic studies of a novel non-heme iron epime... -

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Basic information

Entry
Database: PDB / ID: 7eu6
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 / : / PHOSPHITE ION / Cupin domain-containing protein
Function and homology information
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05010806519 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 16, 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)27,8545
Polymers27,6642
Non-polymers1913
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-57 kcal/mol
Surface area10140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.033, 67.033, 117.183
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
Components on special symmetry positions
IDModelComponents
11B-334-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: VAL / End label comp-ID: VAL

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALA(chain 'A' and (resid 12 through 24 or resid 30 through 56 or resid 58 through 128))AA12 - 2412 - 24
12PROPRO(chain 'A' and (resid 12 through 24 or resid 30 through 56 or resid 58 through 128))AA30 - 5630 - 56
13LYSLYS(chain 'A' and (resid 12 through 24 or resid 30 through 56 or resid 58 through 128))AA58 - 12758 - 127
24ALAALAchain 'B'BB12 - 2412 - 24
25PROPROchain 'B'BB30 - 5630 - 56
26LYSLYSchain 'B'BB58 - 12758 - 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, G3260_000576 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 19687 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 29.1066472483 Å2 / Rsym value: 0.052 / Net I/σ(I): 21.15
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.708 / Num. unique obs: 1913

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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: 2.05010806519→26.1541485906 Å / SU ML: 0.247947966559 / Cross valid method: NONE / σ(F): 1.34434588892 / Phase error: 22.7243337717
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.230186270007 985 5.00635324015 %
Rwork0.189419686879 18690 -
obs0.191435303009 19675 99.7212366954 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.0813185145 Å2
Refinement stepCycle: LAST / Resolution: 2.05010806519→26.1541485906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 6 107 1825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007804047473791761
X-RAY DIFFRACTIONf_angle_d1.024103800312407
X-RAY DIFFRACTIONf_chiral_restr0.0719085327409282
X-RAY DIFFRACTIONf_plane_restr0.00587519219337312
X-RAY DIFFRACTIONf_dihedral_angle_d13.97054261771037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0502-2.15810.2969972272711380.2331525737882627X-RAY DIFFRACTION99.7834716709
2.1581-2.29330.2541067273691380.2082699924632631X-RAY DIFFRACTION100
2.2933-2.47020.2745815812791410.2171235952362647X-RAY DIFFRACTION100
2.4702-2.71860.2733886298981380.2112694323152638X-RAY DIFFRACTION100
2.7186-3.11140.2498370954521400.2145285029472666X-RAY DIFFRACTION99.9287749288
3.1114-3.91790.2297885352041430.1796942067282693X-RAY DIFFRACTION99.8240056318
3.9179-26.15410.1832958177871470.1602196772762788X-RAY DIFFRACTION98.589183742

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