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- PDB-10yr: Crystal structure of Q40A mutant of a computationally designed pr... -

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Basic information

Entry
Database: PDB / ID: 10yr
TitleCrystal structure of Q40A mutant of a computationally designed protein bound to a Mn-containing cofactor (L1-Q40A-dnMSBP)
ComponentsL1-Q40A-dnMSBP
KeywordsDE NOVO PROTEIN / Artificial Metalloenzyme
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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

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Assembly

Deposited unit
A: L1-Q40A-dnMSBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9072
Polymers24,2721
Non-polymers6351
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.925, 50.517, 84.771
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-Q40A-dnMSBP


Mass: 24272.242 Da / Num. of mol.: 1 / Mutation: Q40A
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.: 283 / 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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 700 uM L1-Q40A-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 ...Details: 700 uM L1-Q40A-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: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.62→43.4 Å / Num. obs: 26287 / % possible obs: 99.98 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.36 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1172 / Rpim(I) all: 0.05049 / Rrim(I) all: 0.1279 / Net I/σ(I): 8.46
Reflection shellResolution: 1.62→1.678 Å / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 2558 / CC1/2: 0.721 / Rpim(I) all: 0.2968 / Rrim(I) all: 0.7623

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
xia2data scaling
xia2data reduction
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→43.4 Å / SU ML: 0.2222 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.7251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 2363 4.78 %
Rwork0.1792 47029 -
obs0.1812 26284 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.38 Å2
Refinement stepCycle: LAST / Resolution: 1.62→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 41 283 2001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461745
X-RAY DIFFRACTIONf_angle_d0.7482390
X-RAY DIFFRACTIONf_chiral_restr0.0379311
X-RAY DIFFRACTIONf_plane_restr0.0074281
X-RAY DIFFRACTIONf_dihedral_angle_d6.1058253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.650.29611420.29422693X-RAY DIFFRACTION99.72
1.65-1.690.32341510.282785X-RAY DIFFRACTION99.59
1.69-1.730.30791640.2742744X-RAY DIFFRACTION99.83
1.73-1.770.29821430.25722741X-RAY DIFFRACTION99.93
1.77-1.820.23041390.23762812X-RAY DIFFRACTION99.86
1.82-1.870.25661510.21972752X-RAY DIFFRACTION99.97
1.87-1.930.24881270.19792760X-RAY DIFFRACTION99.83
1.93-20.26141390.19682760X-RAY DIFFRACTION99.9
2-2.080.23031320.19292753X-RAY DIFFRACTION99.83
2.08-2.180.2581410.16692787X-RAY DIFFRACTION100
2.18-2.290.20961170.16852797X-RAY DIFFRACTION99.93
2.29-2.440.23091190.17322798X-RAY DIFFRACTION99.97
2.44-2.620.21841340.16662773X-RAY DIFFRACTION100
2.62-2.890.19231410.16382759X-RAY DIFFRACTION99.9
2.89-3.310.21781610.16382763X-RAY DIFFRACTION99.9
3.31-4.160.18021310.14642772X-RAY DIFFRACTION99.9
4.17-43.40.20231310.16622780X-RAY DIFFRACTION99.97

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