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- PDB-10ym: Crystal structure of a computationally designed protein bound to ... -

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Basic information

Entry
Database: PDB / ID: 10ym
TitleCrystal structure of a computationally designed protein bound to a Mn-containing cofactor (L1-dnMSBP)
ComponentsL1-dnMSBP
KeywordsDE NOVO PROTEIN / Artificial Metalloenzyme
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWang, J.-X. / Lu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: De Novo Design and Structural Optimization of Mn(salen)-Based Artificial Metalloenzymes for Asymmetric Sulfoxidation.
Authors: Wang, J.X. / Deng, Y. / Kalvet, I. / Haque, A. / Dai, H. / Baker, D. / Lu, Y.
History
DepositionFeb 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L1-dnMSBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9642
Polymers24,3291
Non-polymers6351
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.651, 50.176, 84.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein L1-dnMSBP


Mass: 24329.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-A1C87 / chlorido[2,2'-{(1R,2R)-cyclohexane-1,2-diylbis[(azanylylidene-kappaN)methanylylidene]}bis(4,6-di-tert-butylphenolato-kappaO)]manganate / (R,R)-Jacobsen's catalyst


Mass: 635.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H52ClMnN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.04 Å3/Da / Density % sol: 39.75 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 700 uM L1-dnMSBP in 25 mM Tris buffer at pH 8 containing 300 mM NaCl was mixed with 20 mM ammonium phosphate monobasic buffer at pH 4.0 with 11-16% w/v PEG 3350 at a 1.5 uL : 1.5 uL mixing ...Details: 700 uM L1-dnMSBP in 25 mM Tris buffer at pH 8 containing 300 mM NaCl was mixed with 20 mM ammonium phosphate monobasic buffer at pH 4.0 with 11-16% w/v PEG 3350 at a 1.5 uL : 1.5 uL mixing ratio under room temperature.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→43.19 Å / Num. obs: 32611 / % possible obs: 99.84 % / Redundancy: 6.3 % / Biso Wilson estimate: 18.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0713 / Rpim(I) all: 0.03046 / Rrim(I) all: 0.07772 / Net I/σ(I): 11.44
Reflection shellResolution: 1.5→1.554 Å / Rmerge(I) obs: 0.3799 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 3213 / CC1/2: 0.918 / Rpim(I) all: 0.1656 / Rrim(I) all: 0.4153

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Processing

Software
NameVersionClassification
BOSdata collection
xia2data scaling
xia2data reduction
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→43.19 Å / SU ML: 0.1725 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1979 2965 4.84 %
Rwork0.1629 58257 -
obs0.1645 32594 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.11 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 41 263 1981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01141838
X-RAY DIFFRACTIONf_angle_d1.16342522
X-RAY DIFFRACTIONf_chiral_restr0.0613324
X-RAY DIFFRACTIONf_plane_restr0.0088300
X-RAY DIFFRACTIONf_dihedral_angle_d6.9874270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.28721550.2692733X-RAY DIFFRACTION98
1.52-1.550.27391340.26452735X-RAY DIFFRACTION97.25
1.55-1.580.31211310.25812696X-RAY DIFFRACTION96.09
1.58-1.610.28441320.23742768X-RAY DIFFRACTION99.15
1.61-1.640.25831520.22852759X-RAY DIFFRACTION99.52
1.64-1.680.28631410.22362828X-RAY DIFFRACTION99.7
1.68-1.720.20431270.21892754X-RAY DIFFRACTION99.52
1.72-1.760.29751450.22412809X-RAY DIFFRACTION99.49
1.76-1.810.27871700.21452713X-RAY DIFFRACTION99.14
1.81-1.860.24311670.1962784X-RAY DIFFRACTION99.39
1.86-1.920.1651280.16542750X-RAY DIFFRACTION99.9
1.92-1.990.21691690.16622769X-RAY DIFFRACTION99.86
1.99-2.070.21041320.14832808X-RAY DIFFRACTION99.93
2.07-2.160.18911130.15482797X-RAY DIFFRACTION99.83
2.16-2.280.20341670.13842786X-RAY DIFFRACTION99.76
2.28-2.420.18021470.14832779X-RAY DIFFRACTION99.52
2.42-2.610.16591550.13842772X-RAY DIFFRACTION99.93
2.61-2.870.1661420.14972781X-RAY DIFFRACTION99.97
2.87-3.280.17461040.14542830X-RAY DIFFRACTION99.8
3.28-4.140.15091210.1342800X-RAY DIFFRACTION99.76
4.14-43.190.19251330.1612806X-RAY DIFFRACTION99.76

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