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- PDB-4e0u: Crystal structure of CdpNPT in complex with thiolodiphosphate and... -

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Basic information

Entry
Database: PDB / ID: 4e0u
TitleCrystal structure of CdpNPT in complex with thiolodiphosphate and (S)-benzodiazependione
ComponentsCyclic dipeptide N-prenyltransferase
KeywordsTRANSFERASE / PT-fold / C(3)b-prenyltransferase
Function / homology
Function and homology information


tryptophanyl aminopeptidase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / alkaloid metabolic process / aminopeptidase activity / proteolysis
Similarity search - Function
Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase
Similarity search - Domain/homology
Chem-0MV / IMIDAZOLE / TRIHYDROGEN THIODIPHOSPHATE / Cyclic dipeptide prenyltransferase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchuller, J.M. / Zocher, G. / Stehle, T.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structure and catalytic mechanism of a cyclic dipeptide prenyltransferase with broad substrate promiscuity.
Authors: Schuller, J.M. / Zocher, G. / Liebhold, M. / Xie, X. / Stahl, M. / Li, S.M. / Stehle, T.
History
DepositionMar 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,92713
Polymers97,5212
Non-polymers1,40611
Water84747
1
A: Cyclic dipeptide N-prenyltransferase
hetero molecules

A: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,95014
Polymers97,5212
Non-polymers1,42912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4120 Å2
ΔGint-5 kcal/mol
Surface area33370 Å2
MethodPISA
2
B: Cyclic dipeptide N-prenyltransferase
hetero molecules

B: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,90412
Polymers97,5212
Non-polymers1,38310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4140 Å2
ΔGint-2 kcal/mol
Surface area33220 Å2
MethodPISA
3
A: Cyclic dipeptide N-prenyltransferase
B: Cyclic dipeptide N-prenyltransferase
hetero molecules

A: Cyclic dipeptide N-prenyltransferase
B: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,85526
Polymers195,0434
Non-polymers2,81222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14900 Å2
ΔGint-28 kcal/mol
Surface area59940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.730, 137.730, 170.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cyclic dipeptide N-prenyltransferase


Mass: 48760.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: cdpNPT / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: D1D8L6

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Non-polymers , 6 types, 58 molecules

#2: Chemical ChemComp-0MV / (3S)-3-(1H-indol-3-ylmethyl)-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione


Mass: 305.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H15N3O2
#3: Chemical ChemComp-PIS / TRIHYDROGEN THIODIPHOSPHATE / THIOPYROPHOSPHATE


Mass: 193.033 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3O6P2S
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 4.15 Å3/Da / Density % sol: 70.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2011
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 51035 / Num. obs: 50027 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.6→2.67 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O2K

3o2k


Resolution: 2.6→29.83 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 16.288 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22888 2502 5 %RANDOM
Rwork0.19629 ---
obs0.19792 47521 100 %-
all-50027 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 79.311 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2--2.06 Å20 Å2
3----4.11 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6485 0 91 47 6623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226748
X-RAY DIFFRACTIONr_bond_other_d0.0020.024519
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9729165
X-RAY DIFFRACTIONr_angle_other_deg0.8623.00211000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86624.091308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.278151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9251532
X-RAY DIFFRACTIONr_chiral_restr0.070.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021398
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3013.54086
X-RAY DIFFRACTIONr_mcbond_other0.3183.51644
X-RAY DIFFRACTIONr_mcangle_it2.17646583
X-RAY DIFFRACTIONr_scbond_it2.04752662
X-RAY DIFFRACTIONr_scangle_it2.80852582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 181 -
Rwork0.3 3429 -
obs--100 %
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)
12.8306-0.14050.46210.85270.19242.0822-0.02730.5909-0.1442-0.2673-0.1771-0.22790.17090.59670.20440.15440.02440.02120.4390.24980.256911.1923-19.9431-14.1924
21.86880.23540.68750.91920.12782.7484-0.05890.21150.0845-0.4516-0.0370.2026-0.0851-0.00790.09590.2769-0.0023-0.20670.04270.04090.2149-32.3141-22.3889-25.2187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 440
2X-RAY DIFFRACTION2B33 - 440

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