[English] 日本語
Yorodumi
- PDB-7uor: Crystal structure of cytochrome P450 enzyme CYP119 in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uor
TitleCrystal structure of cytochrome P450 enzyme CYP119 in complex with methyliridium(III) mesoporphyrin.
ComponentsCytochrome
KeywordsOXIDOREDUCTASE / Cytochrome P450 Iridium
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
methyliridium(III) mesoporphyrin / NICKEL (II) ION / Cytochrome
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsPereira, J.H. / Bloomer, B.J. / Hartwig, J.F. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Nat Catal / Year: 2023
Title: Mechanistic and structural characterization of an iridium-containing cytochrome reveals kinetically relevant cofactor dynamics
Authors: Bloomer, B.J. / Natoli, S.N. / Garcia-Borras, M. / Pereira, J.H. / Hu, D.B. / Adams, P.D. / Houk, K.N. / Clark, D.S. / Hartwig, J.F.
History
DepositionApr 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome
B: Cytochrome
C: Cytochrome
D: Cytochrome
E: Cytochrome
F: Cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,35320
Polymers270,2956
Non-polymers6,05814
Water00
1
A: Cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0984
Polymers45,0491
Non-polymers1,0493
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0393
Polymers45,0491
Non-polymers9902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0393
Polymers45,0491
Non-polymers9902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0984
Polymers45,0491
Non-polymers1,0493
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0393
Polymers45,0491
Non-polymers9902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0393
Polymers45,0491
Non-polymers9902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.213, 190.213, 266.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISASNA1 - 379
d_12ens_1HIRHIRB
d_13ens_1BTBBTBC
d_21ens_1HISASND1 - 379
d_22ens_1HIRHIRE
d_23ens_1BTBBTBF
d_31ens_1HISASNG1 - 379
d_32ens_1HIRHIRH
d_33ens_1BTBBTBI
d_41ens_1HISASNJ1 - 379
d_42ens_1HIRHIRK
d_43ens_1BTBBTBL
d_51ens_1HISASNM1 - 379
d_52ens_1HIRHIRN
d_53ens_1BTBBTBO
d_61ens_1HISASNP1 - 379
d_62ens_1HIRHIRQ
d_63ens_1BTBBTBR

NCS oper:
IDCodeMatrixVector
1given(-0.514049514978, -0.57558760388, 0.635965412905), (0.382472069799, 0.509828729497, 0.770577564171), (-0.76776833223, 0.639354030909, -0.0419310289132)-27.0297376666, -32.6997663471, 44.6899301911
2given(-0.487282678765, 0.40326990578, -0.774550820842), (-0.584486343032, 0.508378926632, 0.63239748716), (0.648792189984, 0.760870718354, -0.0120184927128)34.0308011882, -27.1897510973, 44.0474619193
3given(0.487698656087, 0.602876808931, 0.63141869952), (-0.409925296778, -0.480432500062, 0.775335968433), (0.770786138895, -0.636964807613, 0.0128281702013)67.4433534123, -129.019423939, -88.811669536
4given(-0.186973904217, 0.982118432919, -0.0220032466445), (0.982202304753, 0.187303539091, 0.014000599377), (0.0178715326881, -0.0189938928394, -0.99965986233)95.1616191024, -95.485046792, -45.5619489099
5given(-0.490659644342, 0.41998322611, 0.763457401038), (-0.578603865975, 0.498083013743, -0.645856700592), (-0.651514143893, -0.758635222756, -0.001385316104)61.6729737843, -67.062313653, -87.8846624437

-
Components

#1: Protein
Cytochrome


Mass: 45049.219 Da / Num. of mol.: 6 / Mutation: L155W, T213G, V254L, C317G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: ATY89_07675, ATZ20_10695 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U3HD14
#2: Chemical
ChemComp-HIR / methyliridium(III) mesoporphyrin


Mass: 780.869 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C35H32IrN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate 0.1 M Bis-TRIS pH 6.5 25 % Pentaerythritol propoxylate (5/4 PO/OH)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.159→60.15 Å / Num. obs: 80832 / % possible obs: 99.88 % / Redundancy: 9.2 % / Biso Wilson estimate: 83.69 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.2178 / Net I/σ(I): 7.86
Reflection shellResolution: 3.159→3.272 Å / Num. unique obs: 8034 / CC1/2: 0.406

-
Processing

Software
NameVersionClassification
PHENIX1.20_4444refinement
PHENIX1.20_4444refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BV5

5bv5


Resolution: 3.16→60.15 Å / SU ML: 0.4495 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2294 4000 4.95 %
Rwork0.181 76764 -
obs0.1834 80764 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.88 Å2
Refinement stepCycle: LAST / Resolution: 3.16→60.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18798 0 356 0 19154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011619626
X-RAY DIFFRACTIONf_angle_d1.752226622
X-RAY DIFFRACTIONf_chiral_restr0.0912820
X-RAY DIFFRACTIONf_plane_restr0.01263390
X-RAY DIFFRACTIONf_dihedral_angle_d14.08547416
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.680420182644
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.620378791099
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.664435126684
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.595334763546
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.646288782579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.20.39151950.34832548X-RAY DIFFRACTION99.13
3.2-3.240.34781090.33042625X-RAY DIFFRACTION99.93
3.24-3.280.29711420.29732664X-RAY DIFFRACTION100
3.28-3.320.36281510.28192643X-RAY DIFFRACTION100
3.32-3.360.32531380.26282612X-RAY DIFFRACTION99.89
3.36-3.410.31051220.25482655X-RAY DIFFRACTION99.93
3.41-3.460.2768900.2462724X-RAY DIFFRACTION99.96
3.46-3.520.29881280.23832660X-RAY DIFFRACTION99.89
3.52-3.580.30911470.2452634X-RAY DIFFRACTION99.93
3.58-3.640.30951650.25092594X-RAY DIFFRACTION99.93
3.64-3.70.31941530.25762636X-RAY DIFFRACTION99.93
3.7-3.770.2711310.23672655X-RAY DIFFRACTION100
3.77-3.850.24921190.18642650X-RAY DIFFRACTION99.96
3.85-3.940.22291350.17872656X-RAY DIFFRACTION99.96
3.94-4.030.23251160.17772657X-RAY DIFFRACTION99.93
4.03-4.130.22041360.15782653X-RAY DIFFRACTION99.96
4.13-4.240.2088990.16752662X-RAY DIFFRACTION100
4.24-4.360.2031610.14922635X-RAY DIFFRACTION99.96
4.36-4.50.20631530.14352646X-RAY DIFFRACTION100
4.5-4.670.18561740.14032606X-RAY DIFFRACTION100
4.67-4.850.18511240.13592689X-RAY DIFFRACTION100
4.85-5.070.18961310.13552638X-RAY DIFFRACTION100
5.07-5.340.18371640.14362621X-RAY DIFFRACTION100
5.34-5.670.1851440.16652663X-RAY DIFFRACTION100
5.67-6.110.22541710.16522645X-RAY DIFFRACTION100
6.11-6.730.22441340.17782643X-RAY DIFFRACTION100
6.73-7.70.2287990.16722701X-RAY DIFFRACTION100
7.7-9.690.1952980.13372717X-RAY DIFFRACTION99.96
9.71-60.150.18431710.16042632X-RAY DIFFRACTION98.59
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)
11.12612082093-0.795836685833-0.3917380719941.093132290590.6488249384970.814154808291-0.131537920143-0.102825669557-0.08848773379550.0633741094140.08934423359720.00172415735872-0.00455360563060.14694039998-0.005981917717350.2228332222110.0008781896575390.05159447572710.312436598187-0.05343148245560.31104088586529.3143886253-51.69844379825.05860440474
21.01968621543-0.1598219460140.3637178168690.3480676679490.506469001481.186971462120.1048920625690.139693874771-0.0818781244339-0.05300013296380.03367049369370.0601836870242-0.1711015597430.08136950512520.009989481691550.2889499382520.0471679608966-0.08995053898630.380203092993-0.08714120450560.302055288711-9.12868293211-43.9477535105-11.0850949898
30.71796523360.3614554386490.1404377806451.44896538402-0.4081820232830.637304731279-0.189321732596-0.120630848713-0.1328110011540.09934306055150.263411914380.46829498715-0.03583793747340.1194290999230.02973854978660.2442834287-0.0616756308229-0.02882547211290.07213682438460.02734507635570.45559754585-5.0211053715-67.410674771623.6691888262
40.854768417513-0.164607172246-0.3675054399330.714233813444-0.4104634098561.311825952420.0335706716926-0.140489670855-0.1441444847670.0485778165970.0574170322432-0.15335273877-0.231246352873-0.01801221585410.006423581448310.445672177239-0.02717854109360.0879710229220.3498945008270.07542212475220.26715283682653.7656607354-112.278398012-33.2176737905
50.622994889062-0.376287238115-0.7661101532070.9391530635761.253023638670.7006895109740.07160925052270.140126379634-0.07502360269890.369773894147-1.0186225156-0.530273593854-0.588165061030.678393429246-0.2587676931650.1586732490170.3578766913740.238562857748-0.0504270404635-0.6992735460980.0094009089570838.795274353-76.3025249139-49.1117034872
61.70400889717-0.3693030253010.6035106114471.247285359970.02934618332650.8880190583720.192432917461-0.1371954387480.0157092889801-0.0477115022751-0.0795652453952-0.1076527861280.40657339241-0.3560497616270.06374084351330.513088328372-0.2097296125950.02036307220180.526388437193-0.03076059612980.23126554383729.4350384778-113.040264755-67.7707334741
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: -11 - 367 / Label seq-ID: 1 - 379

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and ( resid -11:390 ) )AA
22(chain 'B' and ( resid -11:390 ) )BD
33(chain 'C' and ( resid -11:390 ) )CG
44(chain 'D' and ( resid -11:390 ) )DJ
55(chain 'E' and ( resid -11:390 ) )EM
66(chain 'F' and ( resid -11:390 ) )FP

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more