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- PDB-9w5t: The complex structure of wild-type P450 enzyme with cww -

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Basic information

Entry
Database: PDB / ID: 9w5t
TitleThe complex structure of wild-type P450 enzyme with cww
ComponentsTtpB1-CWW
KeywordsBIOSYNTHETIC PROTEIN / Cytochrome P450 enzyme / Complex.
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / Chem-UYM
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDu, Y.Q. / Qu, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82404485 China
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: P450-Mediated Dual Cyclization Mechanisms for Pyrroloindoline Unit Formation in Bispyrrolidinoindoline Diketopiperazine Alkaloid Biosynthesis.
Authors: Du, Y. / Wei, G. / Zhou, T.P. / Dai, Y. / Tian, W. / Tang, M. / Deng, Z. / Wang, B. / Qu, X.
History
DepositionAug 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TtpB1-CWW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4955
Polymers44,4611
Non-polymers1,0354
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, by gel filtration chromatography with a SuperdexTM 200 Increase column (GE Healthcare)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.840, 89.840, 267.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein TtpB1-CWW


Mass: 44460.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: trans-cinnamate 4-monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UYM / (3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione


Mass: 372.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M ammonium acetate, 25% PEG3350.PH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.962 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.962 Å / Relative weight: 1
ReflectionResolution: 2.5→31.64 Å / Num. obs: 23092 / % possible obs: 100 % / Redundancy: 38.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 29.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 39.8 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 5 / Num. unique obs: 2501 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→31.46 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2957 1160 5.04 %
Rwork0.2551 --
obs0.2572 23005 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 2 39 3221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093286
X-RAY DIFFRACTIONf_angle_d1.1834517
X-RAY DIFFRACTIONf_dihedral_angle_d18.002477
X-RAY DIFFRACTIONf_chiral_restr0.058485
X-RAY DIFFRACTIONf_plane_restr0.008597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.610.39741560.37212612X-RAY DIFFRACTION100
2.61-2.750.43831500.36722655X-RAY DIFFRACTION100
2.75-2.920.47361500.36172664X-RAY DIFFRACTION100
2.92-3.150.38431400.34922685X-RAY DIFFRACTION100
3.15-3.470.3611330.31722726X-RAY DIFFRACTION100
3.47-3.970.2891310.25612745X-RAY DIFFRACTION100
3.97-4.990.2231280.19942809X-RAY DIFFRACTION100
5-31.460.24661720.20532949X-RAY DIFFRACTION100

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