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- PDB-9o4d: GutD in complex with guanine and cWW -

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Basic information

Entry
Database: PDB / ID: 9o4d
TitleGutD in complex with guanine and cWW
ComponentsCytochrome P450 121
KeywordsBIOSYNTHETIC PROTEIN / P450 / dimerase / cyclic dipeptide / guanine
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
GUANINE / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Chem-UYM / Cytochrome P450 121
Similarity search - Component
Biological speciesStreptomyces purpureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGering, H.E. / Makris, T.M. / Phan, H.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135315 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127588 United States
Citation
Journal: To Be Published
Title: Alternative Oxidative Pathways for Guanitrypmycin Assembly
Authors: Gering, H.E. / Karandikar, S. / Phan, H.N. / Chang, W. / Makris, T.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 121
B: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,51570
Polymers91,1572
Non-polymers6,35868
Water7,242402
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17970 Å2
ΔGint58 kcal/mol
Surface area30930 Å2
Unit cell
Length a, b, c (Å)67.292, 101.319, 121.421
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 8 through 47 or resid 49...
d_2ens_1(chain "B" and (resid 8 through 47 or resid 49...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11THRTHRVALVALAA8 - 479 - 48
d_12SERSERALAALAAA49 - 6850 - 69
d_13GLUGLUASNASNAA70 - 9071 - 91
d_14ASNASNLEULEUAA92 - 10493 - 105
d_15PROPROGLUGLUAA106 - 224107 - 225
d_16LEULEUGLUGLUAA226 - 378227 - 379
d_17LEULEUARGARGAA380 - 402381 - 403
d_18GUNGUNGUNGUNAD502
d_19EDOEDOEDOEDOAE503
d_110EDOEDOEDOEDOAF504
d_111EDOEDOEDOEDOAG505
d_112EDOEDOEDOEDOAH506
d_113EDOEDOEDOEDOAI507
d_114EDOEDOEDOEDOAJ508
d_115EDOEDOEDOEDOAK509
d_116EDOEDOEDOEDOAL510
d_117EDOEDOEDOEDOAM511
d_118EDOEDOEDOEDOAP514
d_119PEGPEGPEGPEGAQ515
d_120PEGPEGPEGPEGAR516
d_121EDOEDOEDOEDOAT518
d_122EDOEDOEDOEDOAU519
d_123EDOEDOEDOEDOAV520
d_124EDOEDOEDOEDOAW521
d_125EDOEDOEDOEDOAX522
d_126EDOEDOEDOEDOAAA525
d_127EDOEDOEDOEDOABA526
d_128EDOEDOEDOEDOACA527
d_129EDOEDOEDOEDOADA528
d_21THRTHRVALVALBB8 - 479 - 48
d_22SERSERALAALABB49 - 6850 - 69
d_23GLUGLUASNASNBB70 - 9071 - 91
d_24ASNASNLEULEUBB92 - 10493 - 105
d_25PROPROARGARGBB106 - 216107 - 217
d_26ALAALAGLUGLUBB219 - 224220 - 225
d_27LEULEUGLUGLUBB226 - 378227 - 379
d_28LEULEUARGARGBB380 - 402381 - 403
d_29GUNGUNGUNGUNBPA503
d_210EDOEDOEDOEDOBQA504
d_211EDOEDOEDOEDOBRA505
d_212EDOEDOEDOEDOBSA506
d_213EDOEDOEDOEDOBTA507
d_214EDOEDOEDOEDOBUA508
d_215EDOEDOEDOEDOBVA509
d_216EDOEDOEDOEDOBWA510
d_217EDOEDOEDOEDOBXA511
d_218EDOEDOEDOEDOBYA512
d_219EDOEDOEDOEDOBBB515
d_220PEGPEGPEGPEGBCB516
d_221PEGPEGPEGPEGBDB517
d_222EDOEDOEDOEDOBGB520
d_223EDOEDOEDOEDOBHB521
d_224EDOEDOEDOEDOBIB522
d_225EDOEDOEDOEDOBJB523
d_226EDOEDOEDOEDOBKB524
d_227EDOEDOEDOEDOBNB527
d_228EDOEDOEDOEDOBOB528
d_229EDOEDOEDOEDOBPB529
d_230EDOEDOEDOEDOBQB530

NCS oper: (Code: givenMatrix: (-0.153955513973, -0.704000685856, 0.693311426439), (-0.696404517398, -0.420456618309, -0.581581447665), (0.700941115833, -0.572362880028, -0.425537643106)Vector: 29. ...NCS oper: (Code: given
Matrix: (-0.153955513973, -0.704000685856, 0.693311426439), (-0.696404517398, -0.420456618309, -0.581581447665), (0.700941115833, -0.572362880028, -0.425537643106)
Vector: 29.6129478835, 16.349805683, -19.5837490923)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450 121


Mass: 45578.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces purpureus (bacteria) / Gene: cyp121, GCM10014713_29760 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A918H2T3

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Non-polymers , 8 types, 470 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-UYM / (3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione


Mass: 372.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H20N4O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES 30%PEG400 0.1M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.3→17.18 Å / Num. obs: 36397 / % possible obs: 97 % / Redundancy: 2 % / Biso Wilson estimate: 27.82 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.05318 / Rrim(I) all: 0.07521 / Net I/σ(I): 3.03
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.1874 / Num. unique obs: 3568 / CC1/2: 0.909 / % possible all: 96.33

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrysalisProdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→17.18 Å / SU ML: 0.2515 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0775
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 1330 3.66 %
Rwork0.1993 35038 -
obs0.2007 36368 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→17.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6107 0 424 402 6933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326677
X-RAY DIFFRACTIONf_angle_d0.78128997
X-RAY DIFFRACTIONf_chiral_restr0.0454977
X-RAY DIFFRACTIONf_plane_restr0.0111147
X-RAY DIFFRACTIONf_dihedral_angle_d15.9522476
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 5.01144262683 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.28771300.23843438X-RAY DIFFRACTION96.41
2.38-2.480.24061310.22993444X-RAY DIFFRACTION96.6
2.48-2.590.29521320.24323474X-RAY DIFFRACTION96.78
2.59-2.730.28991310.24093459X-RAY DIFFRACTION97.71
2.73-2.90.32631320.25783470X-RAY DIFFRACTION96.75
2.9-3.120.28211320.24193504X-RAY DIFFRACTION97.69
3.12-3.430.24351340.1983517X-RAY DIFFRACTION97.91
3.43-3.920.2071360.1653564X-RAY DIFFRACTION97.99
3.92-4.920.17621360.15213601X-RAY DIFFRACTION98.03
4.92-17.180.2251360.18463567X-RAY DIFFRACTION93.79
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)
11.675519305742.0595146669-1.192767941982.99413063439-1.237148038513.12698147862-0.13735367460.2290345180610.163350592471-0.1889503141460.1446535957280.274840858888-0.159457485024-0.257053317222-0.01854038473160.2796166762430.0567841859469-0.06444620075660.266276857460.01524780163820.247308544296-6.8969553825836.4853686203-55.6539488897
21.501024972810.5856144414860.1619923667611.606300118820.2420791580770.7962499834050.02716212187480.0461806968126-0.000645231089717-0.0905512106496-0.0155203572957-0.123251463054-0.03034427074280.2351391252540.004345514461570.2216869057540.0117889581631-0.01107370467650.231311771507-0.009959709670860.1555971432647.3206331071925.7094302485-36.7575343323
36.471610322262.745448908230.1222854703697.283246206251.716965688017.81385896929-0.219349470059-0.373581405138-0.4949640604750.1882088438430.0781798366305-1.251263654650.4731343728561.229380021290.2138074830270.3331824030460.1044493950260.05708030015310.639960302981-0.00892842439550.34938380519827.2123031424.4439345546-36.5916957759
41.445556784090.0425832115988-0.2966196274891.3694978788-0.01483027315121.006525409620.005133515183690.328851347178-0.128951273875-0.1946471112080.03848455654690.1080534166980.110740800106-0.0702721632163-0.03900014145160.2073248497950.0183083979245-0.02142009048810.239224985252-0.02792863890720.165475028465-4.8605725076321.0527571998-47.7512150723
53.164283514240.929667177256-0.7647637893332.1317870143-0.08671994790740.7960201223360.04989065429250.01855979272270.132849785107-0.0302831038027-0.06410548847920.237723499042-0.00801119415333-0.2435683310430.008134468066590.1862954003750.0116196380834-0.04449763473360.316144757371-0.02076720578210.207917810073-33.455816260838.1677543094-21.7007037774
61.09430713937-1.863947872841.100109644175.29677868775-4.864405762356.19177399473-0.0689409922082-0.0585730591037-0.206325169358-0.0614698211033-0.0558195954940.1574314823030.153613598643-0.4488823797170.05728799208440.193304117737-0.04421574307260.005332171092970.282904564681-0.03272355133190.299637676274-31.584593550120.1992516505-14.9234210342
72.962616753731.84416653966-0.5214532820660.910697968157-0.1570795845650.02670215397520.050538748086-0.508631744251-0.1988619030020.190873119644-0.14319803361-0.107279309028-0.02528162636610.02969367563590.1098728398950.2318304205740.0481154945293-0.02142973181890.2722744875090.04421654624310.20324877899-6.5177248356127.4295045422-8.06370006472
82.71282515110.320066574266-0.452663696722.823544070420.2153037579172.2266316706-0.0757134608042-0.196404130337-0.6810219178740.123561815999-0.0251835883288-0.006875243302820.3376424577730.1204682567320.0785292242140.3056583776340.004089641263020.07023387408020.2205214343630.009703457637270.269524850438-15.633706722213.9669560342-16.9131213105
91.992497532631.69114867441-0.403554492424.28179036109-0.8901599538661.02728099169-0.0251495473343-0.214938160245-0.194973543229-0.00549725143113-0.00676222129047-0.1094666735430.105051708726-0.0761256358580.02842880347240.1713984015180.0236480612230.008348769744220.243465539358-0.003143644212790.193537540276-15.502277229925.7167933617-8.86135898077
107.321134471532.186523608391.308277899721.756467299570.5299611778661.646976812670.0123179084313-0.2083357396280.6232045916660.0173095928177-0.1543973718650.126466511479-0.0746429845875-0.1293913500380.119139093890.1940027615670.00689023689161-0.01690831175310.1733285088890.001835796551790.181452591052-24.267929220940.0942230997-11.9624285426
116.789693406232.167046527790.4708342217622.459294205780.4184882180372.6860058424-0.03689940816890.3013473672260.706465760796-0.161264075850.01039494780270.356507938463-0.131405798365-0.01577039655250.07917028787360.2037050210270.0458968311758-0.0168869270430.231199821455-0.01163420118380.280466820935-32.99533038143.6738268509-17.1482166074
126.663207473821.50660655709-0.9685972408982.01916258745-0.6838257531891.32749162866-0.0829099739725-0.1711423385040.00656215118520.04599562468470.02329772589220.2230012474870.103733083902-0.138431763640.05540142451580.197812051419-0.0142402848919-0.01729271909720.186073618468-0.03093916561560.122459524036-16.475499651839.185799255-7.33343392036
135.413967712063.19165314472-0.5950050577674.68115681582-0.2032767819953.60159005081-0.2137584232030.1633132950060.288894882538-0.1583870019630.0799898554767-0.0481316829265-0.1577259789260.1395569432130.07982681059750.1952416278660.04845273618930.04136219953610.07428591194540.004031894974470.158197295972-5.3462825314738.2440189656-24.434649344
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 68 )AA8 - 681 - 61
22chain 'A' and (resid 69 through 196 )AA69 - 19662 - 189
33chain 'A' and (resid 197 through 222 )AA197 - 222190 - 213
44chain 'A' and (resid 223 through 402 )AA223 - 402214 - 393
55chain 'B' and (resid 8 through 68 )BB8 - 681 - 61
66chain 'B' and (resid 69 through 94 )BB69 - 9462 - 87
77chain 'B' and (resid 95 through 155 )BB95 - 15588 - 148
88chain 'B' and (resid 156 through 203 )BB156 - 203149 - 196
99chain 'B' and (resid 204 through 264 )BB204 - 264197 - 257
1010chain 'B' and (resid 265 through 297 )BB265 - 297258 - 290
1111chain 'B' and (resid 298 through 327 )BB298 - 327291 - 320
1212chain 'B' and (resid 328 through 367 )BB328 - 367321 - 360
1313chain 'B' and (resid 368 through 402 )BB368 - 402361 - 395

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