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- PDB-9yu2: Crystal structure of evolved dirhodium artificial metalloenzyme 6... -

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Basic information

Entry
Database: PDB / ID: 9yu2
TitleCrystal structure of evolved dirhodium artificial metalloenzyme 6A from Pfu POP for selective NH insertion
ComponentsEngineered Metalloenzyme 6A
KeywordsHYDROLASE / artificial metalloenzyme / dirhodium / NH insertion / prolyl oligopeptidase / direct evolution
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytosol
Similarity search - Function
: / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / : / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
prolyl oligopeptidase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSaha, P. / Gonzalez-Gutierrez, G. / Lewis, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF CHE-2154726 United States
CitationJournal: To Be Published
Title: Crystal structure of evolved dirhodium artificial metalloenzyme 6A from Pfu POP for selective NH insertion.
Authors: Saha, P. / Gonzalez-Gutierrez, G. / Lewis, J.C.
History
DepositionOct 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 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: Engineered Metalloenzyme 6A
B: Engineered Metalloenzyme 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,6185
Polymers143,5242
Non-polymers943
Water9,350519
1
A: Engineered Metalloenzyme 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8213
Polymers71,7621
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Engineered Metalloenzyme 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7982
Polymers71,7621
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.517, 67.879, 187.468
Angle α, β, γ (deg.)90.000, 105.490, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Engineered Metalloenzyme 6A


Mass: 71762.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: engineered from prolyl oligopeptidase / Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q51714, prolyl oligopeptidase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 and 1.4 M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.96→57.39 Å / Num. obs: 54039 / % possible obs: 92 % / Redundancy: 2.7 % / Biso Wilson estimate: 25.64 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.083 / Rrim(I) all: 0.145 / Rsym value: 0.119 / Net I/σ(I): 6.9
Reflection shellResolution: 1.96→2.19 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2702 / CC1/2: 0.511 / Rpim(I) all: 0.472 / Rrim(I) all: 0.744 / Rsym value: 0.571 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→57.39 Å / Cross valid method: FREE R-VALUE / σ(F): 95.29 / Phase error: 29.697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2598 2677 4.95 %
Rwork0.2219 50982 -
obs0.2254 54039 55.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.29 Å2
Refinement stepCycle: LAST / Resolution: 1.96→57.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10001 0 3 519 10523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005810250
X-RAY DIFFRACTIONf_angle_d0.8713832
X-RAY DIFFRACTIONf_chiral_restr0.05091464
X-RAY DIFFRACTIONf_plane_restr0.01711771
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-20.337570.2797110X-RAY DIFFRACTION2.15
2-2.030.3747100.2849233X-RAY DIFFRACTION4.59
2.03-2.080.3377180.2768429X-RAY DIFFRACTION8.53
2.08-2.120.4108290.2749625X-RAY DIFFRACTION12.25
2.12-2.170.2349410.2814802X-RAY DIFFRACTION15.83
2.17-2.230.3133450.26121150X-RAY DIFFRACTION22.67
2.23-2.290.3287750.25671529X-RAY DIFFRACTION30.21
2.29-2.350.3217990.25881921X-RAY DIFFRACTION37.51
2.35-2.430.28571160.25642306X-RAY DIFFRACTION44.99
2.43-2.520.35771570.25492783X-RAY DIFFRACTION54.65
2.52-2.620.28431770.25183305X-RAY DIFFRACTION65.05
2.62-2.730.28182040.24273736X-RAY DIFFRACTION73.67
2.74-2.880.282140.22964466X-RAY DIFFRACTION87.69
2.88-3.060.27952600.22784685X-RAY DIFFRACTION91.43
3.06-3.30.27462180.22384662X-RAY DIFFRACTION91.11
3.3-3.630.2732470.21644722X-RAY DIFFRACTION91.69
3.63-4.150.24552520.20134649X-RAY DIFFRACTION90.91
4.15-5.230.22192450.19124595X-RAY DIFFRACTION89.19
5.23-57.390.24232630.23794654X-RAY DIFFRACTION87.7
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.369488713520.7858498739680.6307870156762.237891665581.729499107124.137637822920.067925275236-0.196019502931-0.182590255749-0.0809795028565-0.1168627237560.2960961360950.40934290929-0.1108681659890.03479175032960.178918301350.02328742031280.01059530663250.09104268613550.04206259842710.331556523015-11.1096591922-14.292511667477.9950832072
22.263769601571.951424361140.6155571474622.52943094339-0.3756017822411.509008939820.0983701996224-0.4649607089540.2176137360880.1192198766390.01258948646210.513934232964-0.108493653493-0.2915132849320.04621659283210.1443771278970.048640687660.07600620409780.386104434027-0.07309959014430.490813988353-23.592352087316.629345234679.7055094401
31.16904858480.663096007972-0.6950919594041.95371190573-0.8876650130352.76109778667-0.0571755158427-0.1975769943140.0487209984905-0.1081745042550.004290393910650.3756131490510.05890135983230.04358629170710.05548005118720.1806362504040.0286281437939-0.05213300109940.252732415145-0.06520489866950.321431260654-26.646393460415.631382568259.9690516613
41.934696405910.3670541265340.733157026191.45327177470.1766355973521.42037993294-0.0281049880610.1498697064960.153219005466-0.23065219613-0.0803201639478-0.0953281299793-0.1058049965850.02016412112740.1403948584930.208221620310.006191604867280.03057158564980.1724518469060.03125505246380.116472305889-4.6284295305926.801621177958.1386410111
50.3263755814270.1036810202060.257951112831.854454946980.1972495042430.928302653440.01312092241880.0359110448594-0.0310854249672-0.074537918324-0.00155499851553-0.0976807572085-0.05798293243690.0970611189846-0.01152050885370.07094927302020.006475600371760.02404787487510.1222118869570.01008665766620.1510318328072.962307896899.1687504344475.9088133836
60.8972199674290.05041547889350.3108271791471.68777837942-0.03347158180631.27464059805-0.02985561686970.233366548432-0.344054129109-0.470488415930.120967399491-0.1502659300620.0008027242181970.159613139582-0.03048451750.2079406180160.003761210843250.04176599901490.168126227614-0.04222968523730.2133820440070.353070069351-9.5246246156461.3192758899
71.560983434090.2974736582830.4874681827891.854005652441.010525509823.30136307036-0.03144988027320.116159612270.1529353109860.00938076042448-0.008808943868710.084045105842-0.1355656268-0.2519071784850.05554966681550.0737447203734-0.0116509157905-0.005838300868310.1190238474470.05559338713090.190737972758-6.58294642755-9.5176932309179.0906174964
80.762558352652-0.033610715687-0.1994328073793.11911891771.313440239982.40577584574-0.02351544755620.06536836246640.284345887020.24899024209-0.02906887624510.184092183572-0.236596278511-0.189040541118-0.006257536713650.1618237483250.0626550733181-0.03148006859040.1937160136950.008919147523180.470558616048-39.317040022528.006351743414.6697151703
91.08327612023-0.733991838962-1.152959650071.32837626553-0.372418612414.86129109954-0.0755034550089-0.0004977282680850.1068035346950.1299904185280.1489732388960.4208771220940.0454537688144-0.412230406234-0.131038781370.313412447733-0.000851957583369-0.0004176078375320.4817884714290.01715447553130.445622566708-52.3365672502-1.4970606246124.1498706096
100.725644541420.09837851473950.2388061631.02691738488-1.229636175491.59455214113-0.0500664362077-0.169106673971-0.007026499382540.068024852642-0.00252343655340.04240401113250.154177495808-0.1574298271030.04463605178390.2837425470060.00115548099347-0.002691709399190.208971550095-0.05716856397980.202747094511-32.7294366311-10.470104993928.0637212896
110.764702532436-0.2360835973530.2763955442082.08215011154-0.0861199239652.3296073826-0.0267225993159-0.02339993582370.0651138217951-0.0182591622209-0.0364426443779-0.066998931937-0.237568679207-0.06149179488120.07243070597250.130470728524-0.00293655256664-0.01667602670940.1305022996240.01630875606650.157652454078-25.591701557917.353600906717.8921246129
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 46 )AA1 - 461 - 46
22chain 'A' and (resid 47 through 108 )AA47 - 10847 - 108
33chain 'A' and (resid 109 through 204 )AA109 - 204109 - 204
44chain 'A' and (resid 205 through 317 )AA205 - 317205 - 317
55chain 'A' and (resid 318 through 489 )AA318 - 489318 - 489
66chain 'A' and (resid 490 through 550 )AA490 - 550490 - 550
77chain 'A' and (resid 551 through 623 )AA551 - 623551 - 619
88chain 'B' and (resid 1 through 46 )BB1 - 461 - 46
99chain 'B' and (resid 47 through 176 )BB47 - 17647 - 171
1010chain 'B' and (resid 177 through 367 )BB177 - 367172 - 362
1111chain 'B' and (resid 368 through 623 )BB368 - 623363 - 612

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