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- PDB-4e0t: Crystal structure of CdpNPT in its unbound state -

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Basic information

Entry
Database: PDB / ID: 4e0t
TitleCrystal structure of CdpNPT in its unbound state
ComponentsCyclic dipeptide N-prenyltransferase
KeywordsTRANSFERASE / PT-fold / C(3)b-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
DI(HYDROXYETHYL)ETHER / Cyclic dipeptide prenyltransferase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
C: Cyclic dipeptide N-prenyltransferase
D: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,84540
Polymers195,0434
Non-polymers1,80336
Water13,944774
1
A: Cyclic dipeptide N-prenyltransferase
B: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,50721
Polymers97,5212
Non-polymers98519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cyclic dipeptide N-prenyltransferase
D: Cyclic dipeptide N-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,33919
Polymers97,5212
Non-polymers81717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14600 Å2
ΔGint-1 kcal/mol
Surface area59650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.510, 137.020, 172.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cyclic dipeptide N-prenyltransferase


Mass: 48760.645 Da / Num. of mol.: 4
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 , 5 types, 810 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 774 / 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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine HCl, 0.02 M DL-serine 0.1 M MES/imidazole pH 6.5, VAPOR DIFFUSION, ...Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine HCl, 0.02 M DL-serine 0.1 M MES/imidazole pH 6.5, 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: 2.25→50 Å / Num. all: 109011 / Num. obs: 108641 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.45 Å2
Reflection shellResolution: 2.25→2.31 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O2K

3o2k


Resolution: 2.25→29.83 Å / Cor.coef. Fo:Fc: 0.9503 / Cor.coef. Fo:Fc free: 0.9384 / SU B: 13.146 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 5429 5 %RANDOM
Rwork0.1664 ---
obs0.1678 108640 99.72 %-
all-108640 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.83 Å2
Baniso -1Baniso -2Baniso -3
1--4.2739 Å20 Å20 Å2
2---5.1123 Å20 Å2
3---9.3861 Å2
Refine analyzeLuzzati coordinate error obs: 0.292 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12944 0 99 774 13817
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113407HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0418183HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4574SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes325HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1936HARMONIC5
X-RAY DIFFRACTIONt_it13407HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2283 365 4.71 %
Rwork0.2012 7391 -
all0.2025 7756 -
obs--99.72 %
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)
10.9078-0.18120.36411.0848-0.15891.97-0.0266-0.1013-0.04470.1348-0.0018-0.12110.15310.18650.0284-0.1165-0.0015-0.0357-0.1330.064-0.1517-4.8282-10.327348.0388
21.08980.2010.37291.2647-0.19542.34230.02570.2488-0.222-0.38040.055-0.00880.6444-0.0006-0.08080.0842-0.0545-0.0345-0.2413-0.075-0.2512-19.8875-21.3182-0.1503
31.00780.1622-0.10220.8902-0.39262.0139-0.0428-0.09840.01570.01860.06240.2880.1853-0.6832-0.0196-0.2779-0.10950.00240.0540.0117-0.1439-47.6703-2.389840.5026
40.72720.19010.18541.0642-0.0751.7372-0.16420.06880.1164-0.14590.03920.0043-0.2890.16260.125-0.0546-0.0887-0.1052-0.16530.0475-0.1557-15.612321.857.9367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 439
2X-RAY DIFFRACTION2B33 - 439
3X-RAY DIFFRACTION3C33 - 439
4X-RAY DIFFRACTION4D33 - 439

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