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- PDB-7xvj: Crystal structure of CdpNPT in complex with harmol -

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Basic information

Entry
Database: PDB / ID: 7xvj
TitleCrystal structure of CdpNPT in complex with harmol
ComponentsCyclic dipeptide N-prenyltransferase
KeywordsTRANSFERASE / prenyltransferases / cyclic dipeptide N-prenyltransferase
Function / homology
Function and homology information


tryptophanyl aminopeptidase / alkaloid metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / aminopeptidase activity / proteolysis
Similarity search - Function
Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase
Similarity search - Domain/homology
1-methyl-9~{H}-pyrido[3,4-b]indol-7-ol / PHOSPHATE ION / Cyclic dipeptide prenyltransferase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNakashima, Y. / Morita, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02777 Japan
Japan Society for the Promotion of Science (JSPS)22K15303 Japan
CitationJournal: J Nat Med / Year: 2022
Title: Enzymatic formation of a prenyl beta-carboline by a fungal indole prenyltransferase.
Authors: Hamdy, S.A. / Kodama, T. / Nakashima, Y. / Han, X. / Matsui, T. / Morita, H.
History
DepositionMay 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic dipeptide N-prenyltransferase
B: Cyclic dipeptide N-prenyltransferase
C: Cyclic dipeptide N-prenyltransferase
D: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,42513
Polymers184,4674
Non-polymers9589
Water13,908772
1
A: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3073
Polymers46,1171
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-6 kcal/mol
Surface area17180 Å2
MethodPISA
2
B: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3073
Polymers46,1171
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-7 kcal/mol
Surface area17230 Å2
MethodPISA
3
C: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3073
Polymers46,1171
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-16 kcal/mol
Surface area16980 Å2
MethodPISA
4
D: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5054
Polymers46,1171
Non-polymers3883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-6 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.265, 158.669, 161.432
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
Cyclic dipeptide N-prenyltransferase


Mass: 46116.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: cdpNPT / Production host: Escherichia coli (E. coli) / References: UniProt: D1D8L6
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HFI / 1-methyl-9~{H}-pyrido[3,4-b]indol-7-ol / harmol


Mass: 198.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M ammonium phosphate dibasic, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.052 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.052 Å / Relative weight: 1
ReflectionResolution: 2.4→46.97 Å / Num. obs: 163438 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.207 / Rrim(I) all: 0.223 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.229 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 63798 / CC1/2: 0.788 / Rrim(I) all: 1.322 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E0U

4e0u


Resolution: 2.4→46.97 Å / Cross valid method: FREE R-VALUE / σ(F): 1.85 / Phase error: 23.7364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.223 8501 5.2 %
Rwork0.1842 154937 -
obs0.1866 163438 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12634 0 30 772 13436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002913099
X-RAY DIFFRACTIONf_angle_d0.541317808
X-RAY DIFFRACTIONf_chiral_restr0.04031948
X-RAY DIFFRACTIONf_plane_restr0.00372282
X-RAY DIFFRACTIONf_dihedral_angle_d20.33154749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.31843760.28457774X-RAY DIFFRACTION95.27
2.44-2.490.32264440.27497760X-RAY DIFFRACTION94.54
2.49-2.540.30934590.26917670X-RAY DIFFRACTION94.28
2.54-2.590.30434420.26147713X-RAY DIFFRACTION94.51
2.59-2.640.31244260.26457800X-RAY DIFFRACTION94.78
2.64-2.70.29824360.24817658X-RAY DIFFRACTION94.57
2.7-2.770.26934440.24037724X-RAY DIFFRACTION94.52
2.77-2.850.26184140.22827772X-RAY DIFFRACTION94.88
2.85-2.930.26633740.22017819X-RAY DIFFRACTION95.42
2.93-3.020.25344130.2087725X-RAY DIFFRACTION94.9
3.02-3.140.26074300.19547787X-RAY DIFFRACTION94.77
3.14-3.260.23113970.18677768X-RAY DIFFRACTION95.14
3.26-3.430.22434420.17877703X-RAY DIFFRACTION94.56
3.43-3.580.22484300.16917745X-RAY DIFFRACTION94.73
3.58-3.840.20593920.16377797X-RAY DIFFRACTION95.21
3.84-4.10.17424740.15067704X-RAY DIFFRACTION94.2
4.1-4.640.16733920.13167770X-RAY DIFFRACTION95.2
4.64-5.170.1644070.13287754X-RAY DIFFRACTION95
5.17-5.70.17463550.16587839X-RAY DIFFRACTION95.67
5.7-46.970.22164690.18167694X-RAY DIFFRACTION94.21
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)
10.0166321338380.0368038395689-0.03459409375990.0849194015226-0.01415693984410.0847143930579-0.01160378616530.03047689138980.0185712033135-0.01018776186830.008100840295180.0455720213971-0.04113151216830.03524330466640.04564848029350.112294182257-0.026088569436-0.01226109673480.2003579378550.01327062670660.105409281487-18.990318491913.2728696962-22.0692618506
20.05704908687540.0245701824571-0.01751147940420.0421357030702-0.03234759874820.02374927309350.0751487660957-0.05311294179970.06344681423390.0735338178846-0.0422496233006-0.0712722596396-0.1199804249040.134339961002-4.49504674627E-60.211317222659-0.0798157333440.001304890601320.245887731449-0.01366716245310.170468049341-5.2253381047229.3733129841-17.5724620105
30.0231576001928-0.01016142297140.02191866638130.1554466549960.01331498704280.0276443289293-0.03688452185230.02498800580160.0384601244136-0.1511818010320.04992301429120.00836736212716-0.05210153177580.1019003148920.00990571006050.168014471974-0.0655261751812-0.0005101836312630.2742389645120.02920416731890.132379091968-6.7819446955725.4671092221-34.7764272391
40.132292747720.03626491021150.02543118185960.0234522187560.02231161273740.0446353155864-0.0169731099474-0.006466584111090.05843695432590.0189947825791-0.0327676128042-0.0377017957549-0.0297858094562-0.0728561899107-0.03503025596010.00513345735555-0.00715726089446-0.009800384325640.2818345357130.00353082783960.12107722557237.1404177673-1.97308828633-24.3081295556
50.13755916019-0.0352713593013-0.06229429152130.0965859449063-0.004614593711870.0250993523671-0.02189130259040.286157127689-0.08992776054910.03863832479430.0409537619980.04490687961490.10111904616-0.151631877371-0.0138597333152-0.074260611495-0.04216959875880.01615537103290.4701261379-0.06876637224090.18193401400418.6015216133-12.0900180701-33.1091826053
60.096523678779-0.0258648773390.04636947465070.0537895888799-0.02397934086880.0909108337765-0.07642903977890.01570727785450.09714325891880.009199942426730.0136324514131-0.031383726537-0.037970614658-0.0825559528656-0.005232338778380.09606486349790.00538662106105-0.02107835935420.311652049883-0.001986527467510.20138766432216.1803298353.57666823559-23.8968733701
70.107252342515-0.104697616396-0.003491672399130.0937551042510.01865835927730.09484738373760.0162867607573-0.0274217658002-0.02354487323880.0048307633941-0.02644288858590.0371740709720.08226704655240.0212888807224-0.001427432884190.1189679800610.000337308358897-0.001847118632980.1946233646060.008134965900950.13312790018-25.1053775494-20.3417321342-22.8089091785
80.0467270465813-0.0494714165694-0.02913229038630.04140402153270.04351781982560.08807128487620.001844839410820.103213630377-0.216802123176-0.0898038008428-0.08267659983030.1490582451540.0647478563774-0.0172848919278-0.004022149883030.1499509258930.00316977196752-0.003474554670520.191883679488-0.07380317182870.271143975735-28.9636244507-38.2124121235-36.4196678514
90.0264744975772-0.0442846284106-0.01823406139760.1172707747660.01116140436230.0466717061162-0.0494460060928-0.0355642885681-0.140236432804-0.0104388989914-0.0281940631876-0.09328284464570.0926569526184-0.00943138704371-8.64906373775E-60.230400706170.0626733852246-0.003079243930350.291120413797-0.01111791364340.225843697955-11.936067018-35.5622622389-30.2463222204
100.04431560125240.0123620320116-0.07021081052690.0523268080133-0.03188303972670.09910563337440.0107076119521-0.05016236135260.0227076690549-0.0174972466498-0.0314347816961-0.000695230623593-0.01401638859530.0275302157672-0.01868151656440.128371418215-0.02729967084730.0006245364538830.2537765238590.001231195368530.0958612650981-15.5496854499-0.43817877035-77.9157632145
110.102174499669-0.0948818964134-0.03642633540970.08153089135020.00178889518830.260102404478-0.0403782948171-0.0833297942290.0422192393551-0.0375972061630.0197304538019-0.02480873302490.115642001019-0.0191042045420.001658170884010.154133182832-0.0258563017837-0.01386756081170.3070039533580.01138688450570.118863825252-17.705477996-8.02968614452-58.0537993742
120.0311361168054-0.0465288228371-0.04110160979150.155451451310.08769514723660.06223007666630.002330035624570.000936696822780.005816456638480.0002866682944790.0003238526838890.00755630511020.0001469825899940.0004936518856220.0003841736180921.02339649064-0.01372150491910.1028621508771.008008897170.001405889202990.909139152856-12.427383303911.0438623319-69.6650247194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 199 )
2X-RAY DIFFRACTION2chain 'A' and (resid 200 through 328 )
3X-RAY DIFFRACTION3chain 'A' and (resid 329 through 440 )
4X-RAY DIFFRACTION4chain 'B' and (resid 37 through 210 )
5X-RAY DIFFRACTION5chain 'B' and (resid 211 through 328 )
6X-RAY DIFFRACTION6chain 'B' and (resid 329 through 440 )
7X-RAY DIFFRACTION7chain 'C' and (resid 37 through 210 )
8X-RAY DIFFRACTION8chain 'C' and (resid 211 through 328 )
9X-RAY DIFFRACTION9chain 'C' and (resid 329 through 440 )
10X-RAY DIFFRACTION10chain 'D' and (resid 37 through 216 )
11X-RAY DIFFRACTION11chain 'D' and (resid 217 through 437 )
12X-RAY DIFFRACTION12chain 'D' and (resid 438 through 439 )

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