[English] 日本語
Yorodumi
- PDB-5bv5: Structure of CYP119 with T213A and C317H mutations -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bv5
TitleStructure of CYP119 with T213A and C317H mutations
ComponentsCytochrome P450 119
KeywordsOXIDOREDUCTASE / P450 / heme / P420 / cytochrome
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / peroxidase / lactoperoxidase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytoplasm
Similarity search - Function
: / Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 4-PHENYL-1H-IMIDAZOLE / PHOSPHATE ION / Cytochrome P450 119
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsBuller, A.R. / Heel, T. / McIntosh, J.A. / Arnold, F.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32GM110851 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32GM101792 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Structural Adaptability Facilitates Histidine Heme Ligation in a Cytochrome P450.
Authors: McIntosh, J.A. / Heel, T. / Buller, A.R. / Chio, L. / Arnold, F.H.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 119
B: Cytochrome P450 119
D: Cytochrome P450 119
C: Cytochrome P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,80413
Polymers171,7164
Non-polymers3,0889
Water19811
1
A: Cytochrome P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6403
Polymers42,9291
Non-polymers7112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7854
Polymers42,9291
Non-polymers8563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Cytochrome P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6903
Polymers42,9291
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Cytochrome P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6903
Polymers42,9291
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Cytochrome P450 119
D: Cytochrome P450 119
hetero molecules

A: Cytochrome P450 119
C: Cytochrome P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,80413
Polymers171,7164
Non-polymers3,0889
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area13250 Å2
ΔGint-108 kcal/mol
Surface area53720 Å2
MethodPISA
6
B: Cytochrome P450 119
hetero molecules

C: Cytochrome P450 119
hetero molecules

A: Cytochrome P450 119
hetero molecules

D: Cytochrome P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,80413
Polymers171,7164
Non-polymers3,0889
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation2_444-x-1,y-1/2,-z-11
crystal symmetry operation2_343-x-2,y-1/2,-z-21
Buried area9860 Å2
ΔGint-103 kcal/mol
Surface area57110 Å2
MethodPISA
7
A: Cytochrome P450 119
hetero molecules

D: Cytochrome P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3306
Polymers85,8582
Non-polymers1,4724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area4600 Å2
ΔGint-56 kcal/mol
Surface area29420 Å2
MethodPISA
8
B: Cytochrome P450 119
hetero molecules

C: Cytochrome P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4747
Polymers85,8582
Non-polymers1,6165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area4190 Å2
ΔGint-43 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.486, 137.871, 91.779
Angle α, β, γ (deg.)90.00, 101.18, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Cytochrome P450 119


Mass: 42929.008 Da / Num. of mol.: 4 / Mutation: T213A, C317H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q55080*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#4: Chemical ChemComp-PIM / 4-PHENYL-1H-IMIDAZOLE


Mass: 144.173 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C9H8N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.25 / Details: 0.1 M Tris-HCl, 5 % PEG 4000 / PH range: 7.25

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 40139 / % possible obs: 98.5 % / Redundancy: 3.3 % / Net I/σ(I): 10.7
Reflection shellHighest resolution: 2.7 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.6 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.889 / SU B: 36.336 / SU ML: 0.354 / Cross valid method: THROUGHOUT / ESU R: 2.27 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27673 2146 5.1 %RANDOM
Rwork0.23849 ---
obs0.24038 40139 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.526 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0.15 Å2
2---0.12 Å2-0 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9806 0 10 11 9827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01910047
X-RAY DIFFRACTIONr_bond_other_d0.0020.029307
X-RAY DIFFRACTIONr_angle_refined_deg0.8521.99313702
X-RAY DIFFRACTIONr_angle_other_deg0.643321205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.55751220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03223.326430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.134151549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2651573
X-RAY DIFFRACTIONr_chiral_restr0.0460.21550
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022343
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5543.3744943
X-RAY DIFFRACTIONr_mcbond_other0.5543.3744942
X-RAY DIFFRACTIONr_mcangle_it1.0365.0526142
X-RAY DIFFRACTIONr_mcangle_other1.0365.0526143
X-RAY DIFFRACTIONr_scbond_it0.473.3815104
X-RAY DIFFRACTIONr_scbond_other0.473.3815105
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8015.0867561
X-RAY DIFFRACTIONr_long_range_B_refined2.28327.18311342
X-RAY DIFFRACTIONr_long_range_B_other2.28327.18511343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 153 -
Rwork0.35 2926 -
obs--97.93 %
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)
13.0421-0.0182-1.42935.50751.72235.3608-0.0025-0.15860.0287-0.14560.0870.24820.2544-0.4817-0.08460.2473-0.006-0.07110.39350.12250.2779-36.486-33.444-5.295
23.614-2.5996-0.17765.66510.57711.1434-0.0123-0.23770.20220.02890.072-0.068-0.06550.0469-0.05970.4506-0.0345-0.13380.2119-0.08570.319-9-15.618-8.745
32.1384-0.36690.23734.310.75766.38830.2803-0.05510.04250.4092-0.175-0.06260.04120.1128-0.10520.5403-0.0129-0.08980.2094-0.01760.2667-13.447-6.3145.913
41.77570.20750.37590.3288-0.4060.8003-0.096-0.16170.0827-0.10480.1010.04690.0127-0.115-0.0050.52430.0204-0.11570.2420.02040.3004-23.631-28.678-12.627
57.13920.7968-5.727610.2627.219310.7144-0.2448-0.6498-0.8334-1.2867-0.2388-0.0043-0.85960.6980.48360.51010.1758-0.07370.6823-0.12680.2637-1.591-26.322-19.185
66.7193-2.24292.02861.9196-0.98290.6993-0.4157-0.4666-0.29650.23160.3832-0.4618-0.0874-0.20540.03250.56180.0608-0.1350.2149-0.00260.3676-7.91-35.599-5.96
74.0036-0.7009-0.8863.95611.17813.1907-0.1636-0.4731-0.49540.15280.28710.1753-0.0258-0.5359-0.12350.3128-0.1001-0.09870.38450.18530.3021-47.824-37.464-31.846
82.0090.3881-0.70957.5706-0.45210.7289-0.16380.4937-0.2934-0.1260.359-0.1612-0.02660.1377-0.19520.4162-0.0424-0.02240.4534-0.19890.305-23.347-33.68-56.597
92.51982.30233.94649.53613.96256.20030.17890.1774-0.0129-0.6279-0.25670.39520.11420.26670.07780.4783-0.0175-0.15940.2556-0.12630.4144-34.665-50.097-63.796
102.13720.8343-0.10080.4903-0.481.61670.06820.0384-0.068-0.07950.13450.03210.1220.0005-0.20270.4651-0.0318-0.11070.28830.03690.3017-36.627-33.579-39.621
114.321-0.03332.17430.0159-0.1854.18230.1865-0.4282-0.46560.0290.04920.02140.1622-0.1012-0.23570.48960.0229-0.04890.2960.11120.3155-34.772-33.304-32.985
122.0699-0.3399-0.71694.1146-1.2193.06840.10310.34970.0544-0.20510.0805-0.1694-0.1316-0.0271-0.18360.4277-0.0356-0.05320.2701-0.03030.2146-29.881-24.99-50.711
137.2189-1.12420.00881.8716-1.25042.3450.26740.20550.0072-0.44-0.10530.00430.23620.0664-0.16220.6630.0266-0.04610.1190.00060.2116-8.412-53.759-15.603
144.4851-1.313-0.31890.9304-1.20683.7851-0.243-0.7425-0.5642-0.1030.43420.15150.6192-0.1676-0.19120.4567-0.1272-0.13210.3650.04080.2314-17.424-62.35713.949
153.7234-3.27742.79043.3219-2.13952.3509-0.1924-0.5563-0.23490.18280.45510.2461-0.0073-0.3012-0.26270.5258-0.0027-0.11680.51190.09250.2486-15.021-55.65418.232
168.3726-1.395-0.12982.2581-0.02260.6035-0.1236-0.4990.41590.01110.2519-0.57880.0892-0.1687-0.12820.5268-0.0543-0.17180.2226-0.00640.35130.119-61.59819.036
172.7994-0.0318-2.05760.6926-0.41662.53060.1644-0.107-0.0761-0.25980.0319-0.0570.2573-0.2051-0.19630.554-0.0559-0.15310.16470.06270.3327-19.381-56.282-6.889
183.3588-1.9564-1.42694.53611.05684.9657-0.0809-0.30710.0491-0.0850.3955-0.05540.1366-0.1846-0.31460.4325-0.0571-0.17770.17890.10210.1982-22.815-52.856.75
193.6992-1.6691.41642.4320.47223.59390.04050.14130.2588-0.00550.4843-0.339-0.55350.5223-0.52480.2883-0.0642-0.00390.255-0.17060.4972-43.736-1.148-46.069
201.2766-0.6642-0.21625.2952-1.03511.3834-0.0259-0.1417-0.071-0.19950.25520.3180.107-0.3693-0.22930.4022-0.011-0.05310.40640.09060.2846-70.376-15.057-49.132
211.47031.91690.8886.007-1.11992.79790.0288-0.00470.0744-0.8230.45790.43540.2851-0.1577-0.48670.6-0.0157-0.05340.35290.05410.2571-68.795-6.484-66.57
220.1118-0.29090.07391.1389-0.35610.1412-0.1721-0.03450.08750.02970.1137-0.27350.0462-0.1310.05840.491-0.0019-0.12170.37470.00010.2856-58.708-10.552-45.271
237.14742.06363.95853.5638-3.48949.8534-1.06860.32270.7336-1.1346-0.454-0.930.81290.68981.52260.38770.03010.34940.34680.05261.2399-32.7814.995-47.885
243.09560.7380.1413.42440.2090.9745-0.1648-0.11940.13820.00370.3216-0.2168-0.0082-0.0751-0.15680.38170.0424-0.08370.2968-0.03610.2092-55.297-12.535-40.047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A73 - 133
3X-RAY DIFFRACTION3A134 - 207
4X-RAY DIFFRACTION4A208 - 330
5X-RAY DIFFRACTION5A331 - 339
6X-RAY DIFFRACTION6A340 - 365
7X-RAY DIFFRACTION7B1 - 87
8X-RAY DIFFRACTION8B88 - 133
9X-RAY DIFFRACTION9B134 - 204
10X-RAY DIFFRACTION10B205 - 279
11X-RAY DIFFRACTION11B280 - 320
12X-RAY DIFFRACTION12B321 - 365
13X-RAY DIFFRACTION13C1 - 42
14X-RAY DIFFRACTION14C43 - 115
15X-RAY DIFFRACTION15C116 - 161
16X-RAY DIFFRACTION16C162 - 213
17X-RAY DIFFRACTION17C214 - 312
18X-RAY DIFFRACTION18C313 - 364
19X-RAY DIFFRACTION19D1 - 92
20X-RAY DIFFRACTION20D93 - 134
21X-RAY DIFFRACTION21D135 - 190
22X-RAY DIFFRACTION22D192 - 256
23X-RAY DIFFRACTION23D257 - 276
24X-RAY DIFFRACTION24D277 - 366

+
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