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- PDB-9w0a: Wild-type P450 enzyme-TtpB1 -

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Basic information

Entry
Database: PDB / ID: 9w0a
TitleWild-type P450 enzyme-TtpB1
ComponentsTtpB1
KeywordsBIOSYNTHETIC PROTEIN / Complex / Cytochrome P450 enzyme / Dimerase
Function / homology: / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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
DepositionJul 24, 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

Downloads & links

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Assembly

Deposited unit
A: TtpB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8284
Polymers44,3291
Non-polymers1,4993
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.860, 89.860, 269.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
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


Mass: 44329.309 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-A1EUF / (3~{S},6~{S})-3,6-bis[(6-chloranyl-1~{H}-indol-3-yl)methyl]piperazine-2,5-dione


Mass: 441.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H18Cl2N4O2
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.55 Å3/Da / Density % sol: 65.33 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium cacodylate trihydrate, 1M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.48→38.91 Å / Num. obs: 43178 / % possible obs: 100 % / Redundancy: 38.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 29.8
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 39.2 % / Rmerge(I) obs: 1.811 / Mean I/σ(I) obs: 3 / Num. unique obs: 2610 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→37.4 Å / SU ML: 0.3418 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.1197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2562 3652 8.46 %
Rwork0.2154 39526 -
obs0.2189 43178 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.24 Å2
Refinement stepCycle: LAST / Resolution: 2.48→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 103 36 3205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353291
X-RAY DIFFRACTIONf_angle_d0.74924540
X-RAY DIFFRACTIONf_chiral_restr0.0482489
X-RAY DIFFRACTIONf_plane_restr0.0058609
X-RAY DIFFRACTIONf_dihedral_angle_d13.5902509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.510.40361320.35311524X-RAY DIFFRACTION100
2.51-2.550.37811350.32721484X-RAY DIFFRACTION100
2.55-2.580.33011420.3051552X-RAY DIFFRACTION99.94
2.58-2.620.40331460.30851507X-RAY DIFFRACTION100
2.62-2.660.38141430.2891515X-RAY DIFFRACTION100
2.66-2.710.30751420.28781548X-RAY DIFFRACTION99.94
2.71-2.750.35041370.28761488X-RAY DIFFRACTION100
2.75-2.80.32571430.28391552X-RAY DIFFRACTION100
2.8-2.860.38061340.29881487X-RAY DIFFRACTION100
2.86-2.920.34231450.27291532X-RAY DIFFRACTION100
2.92-2.980.31241430.27721532X-RAY DIFFRACTION100
2.98-3.050.31161390.28021518X-RAY DIFFRACTION99.94
3.05-3.120.24971350.26771536X-RAY DIFFRACTION100
3.12-3.210.30181410.2661539X-RAY DIFFRACTION100
3.21-3.30.35811370.26421504X-RAY DIFFRACTION100
3.3-3.410.33371360.24751504X-RAY DIFFRACTION100
3.41-3.530.25631440.2581522X-RAY DIFFRACTION100
3.53-3.670.29381350.23791521X-RAY DIFFRACTION100
3.67-3.840.26381400.22221539X-RAY DIFFRACTION100
3.84-4.040.21761430.20151518X-RAY DIFFRACTION100
4.04-4.290.21911410.17781520X-RAY DIFFRACTION100
4.3-4.630.191430.14691512X-RAY DIFFRACTION100
4.63-5.090.20431430.17021516X-RAY DIFFRACTION100
5.09-5.820.24311460.18621515X-RAY DIFFRACTION100
5.83-7.330.22451380.20881532X-RAY DIFFRACTION100
7.33-37.40.20471490.16371509X-RAY DIFFRACTION99.34
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)
12.32738264339-0.646929398729-1.063482720962.586012679930.3413506661860.557454755993-0.217211080502-0.896647791658-0.3862158723250.444112800988-0.50563211965-0.8636958154730.4736690203581.096267770450.4911051590670.508172869420.1616943219720.1084162062551.35266135750.4912617382250.889012556934-7.9151253363926.869864343514.0840594891
22.965477877341.875171804170.3286667374712.20647070934-1.36969790552.96966588634-0.057670648168-1.12506546819-0.09443439474390.168903603944-0.355541911122-0.1136458483450.492501692439-0.4562195013420.362989883730.601287402791-0.04318533581130.1601917488641.087880651670.2601372962620.70085868275-26.232915998624.765778614714.1826636289
34.320342877750.35888171782-2.822824873471.6480842687-0.9451564421753.62827613264-0.5628941679571.347474174470.131688762716-0.4877930598430.3411507561530.1603740153720.542924691091-0.974411356210.1552591271230.502045823872-0.2225854109120.01377841810221.249119843690.1454744191820.59016311305-28.551579464632.1249918626-10.4319094606
44.133888277791.06749388701-1.673737591622.41919168847-0.5540307518353.66526702968-0.5584111773780.422740507108-0.492406784634-0.3040087922050.165835030078-0.2192698463860.904613525312-0.3028179702420.3926518823260.395822500343-0.1208888579650.1413796379830.7735189004330.1248509829130.517487838978-22.089777282826.0131863242-2.49856539831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 400 )

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