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- PDB-9l7s: Crystal structure of P450 BM3 F87A/V78S mutant -

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Basic information

Entry
Database: PDB / ID: 9l7s
TitleCrystal structure of P450 BM3 F87A/V78S mutant
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / cytochrome p450
Function / homology
Function and homology information


aromatase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / cytosol
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDong, S. / Feng, Y.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071266 China
National Natural Science Foundation of China (NSFC)32171203 China
CitationJournal: To Be Published
Title: Crystal structure of P450cam-F87R mutant
Authors: Dong, S. / Feng, Y.G.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 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: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
C: Bifunctional cytochrome P450/NADPH--P450 reductase
D: Bifunctional cytochrome P450/NADPH--P450 reductase
E: Bifunctional cytochrome P450/NADPH--P450 reductase
F: Bifunctional cytochrome P450/NADPH--P450 reductase
G: Bifunctional cytochrome P450/NADPH--P450 reductase
H: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)423,62532
Polymers417,7008
Non-polymers5,92524
Water32,3191794
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9534
Polymers52,2131
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-20 kcal/mol
Surface area19600 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9534
Polymers52,2131
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-21 kcal/mol
Surface area19700 Å2
MethodPISA
3
C: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9534
Polymers52,2131
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-21 kcal/mol
Surface area19600 Å2
MethodPISA
4
D: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9534
Polymers52,2131
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-20 kcal/mol
Surface area19520 Å2
MethodPISA
5
E: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9534
Polymers52,2131
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-20 kcal/mol
Surface area19730 Å2
MethodPISA
6
F: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9534
Polymers52,2131
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-20 kcal/mol
Surface area19820 Å2
MethodPISA
7
G: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9534
Polymers52,2131
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21 kcal/mol
Surface area19670 Å2
MethodPISA
8
H: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9534
Polymers52,2131
Non-polymers7413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-22 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.074, 167.999, 228.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Bifunctional cytochrome P450/NADPH--P450 reductase


Mass: 52212.508 Da / Num. of mol.: 8 / Mutation: V79S,F88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F2Q7T0, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1794 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Magnesium chloride, 0.1M Bis-Tris pH5.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→49.52 Å / Num. obs: 235986 / % possible obs: 99.6 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.031 / Rrim(I) all: 0.106 / Χ2: 1.02 / Net I/σ(I): 18.6 / Num. measured all: 2955814
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 99.9 % / Redundancy: 12.9 % / Rmerge(I) obs: 1.061 / Num. measured all: 149335 / Num. unique obs: 11594 / CC1/2: 0.835 / Rpim(I) all: 0.305 / Rrim(I) all: 1.105 / Χ2: 0.86 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.52 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 11775 5.01 %
Rwork0.2083 --
obs0.2103 234931 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29300 0 407 1794 31501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00830424
X-RAY DIFFRACTIONf_angle_d1.00341224
X-RAY DIFFRACTIONf_dihedral_angle_d8.6653976
X-RAY DIFFRACTIONf_chiral_restr0.0514392
X-RAY DIFFRACTIONf_plane_restr0.0085368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.35764100.31497404X-RAY DIFFRACTION100
2.12-2.150.34644210.2927375X-RAY DIFFRACTION100
2.15-2.180.33583690.27377394X-RAY DIFFRACTION99
2.18-2.20.28463900.25777425X-RAY DIFFRACTION100
2.2-2.230.31764150.26157394X-RAY DIFFRACTION100
2.23-2.260.583730.53926941X-RAY DIFFRACTION93
2.26-2.290.46753770.37917047X-RAY DIFFRACTION95
2.29-2.330.31513780.28337440X-RAY DIFFRACTION100
2.33-2.370.31293590.24217454X-RAY DIFFRACTION100
2.37-2.40.26553700.23027448X-RAY DIFFRACTION100
2.4-2.450.27033940.22127437X-RAY DIFFRACTION100
2.45-2.490.28783980.22477449X-RAY DIFFRACTION100
2.49-2.540.31353900.25627431X-RAY DIFFRACTION100
2.54-2.590.27774030.22677475X-RAY DIFFRACTION100
2.59-2.650.28264310.22537394X-RAY DIFFRACTION100
2.65-2.710.33414170.27787385X-RAY DIFFRACTION99
2.71-2.770.28873380.23297474X-RAY DIFFRACTION100
2.78-2.850.26433830.22817374X-RAY DIFFRACTION98
2.85-2.930.29164240.23757407X-RAY DIFFRACTION100
2.93-3.030.27663920.22017490X-RAY DIFFRACTION100
3.03-3.140.27253710.2277488X-RAY DIFFRACTION100
3.14-3.260.27683490.22367534X-RAY DIFFRACTION100
3.26-3.410.2533800.21187540X-RAY DIFFRACTION100
3.41-3.590.24573710.19817511X-RAY DIFFRACTION100
3.59-3.820.22434170.18147500X-RAY DIFFRACTION100
3.82-4.110.21284120.17397373X-RAY DIFFRACTION98
4.11-4.520.17354130.1457528X-RAY DIFFRACTION100
4.52-5.180.17534350.13817541X-RAY DIFFRACTION100
5.18-6.520.18063740.16437711X-RAY DIFFRACTION100
6.52-49.520.15024210.14097792X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0091-0.01660.10260.6367-0.05232.22720.02350.1263-0.0076-0.01450.10630.09140.0317-0.197-0.14640.2329-0.01150.02490.25640.02110.263-44.51642.0038-38.6137
21.4890.36260.37371.0508-0.160.4595-0.01810.0646-0.2624-0.01020.0747-0.03570.05020.0682-0.04440.29150.0038-0.00970.2175-0.03170.2876-19.8177-1.1166-31.4747
30.88740.7443-0.87011.1951-1.35252.66680.1163-0.1820.01740.109-0.02620.0512-0.01740.1844-0.0260.26490.03030.00020.2466-0.02170.225-27.98213.4751-22.6208
42.18820.3563-0.22770.823-0.13180.64410.02980.07910.34820.03870.06070.0452-0.1818-0.0114-0.0830.31350.0260.02410.18380.01580.2436-29.571816.6137-38.2522
51.2768-0.27730.17751.1018-0.42481.90330.00530.1893-0.131-0.01040.0642-0.35160.0430.2121-0.06690.3639-0.03620.07030.3851-0.09440.3457-7.6683.0338-67.1086
61.2371-0.01370.24831.27260.0470.73060.00740.159-0.1966-0.120.12220.023-0.07120.0251-0.10620.2905-0.00280.04010.4173-0.02870.2294-30.7793-1.8819-83.2793
71.1543-0.7225-0.3422.03111.05592.14390.05550.2668-0.0235-0.50510.0153-0.0038-0.18830.1375-0.08310.4223-0.04860.07990.4468-0.01530.2641-27.02332.3255-90.3643
81.9769-0.17080.50021.0191-0.07071.1108-0.03350.1360.2387-0.10910.1359-0.0632-0.24160.0387-0.08710.366-0.01240.08030.3055-0.01470.2342-25.474316.0181-75.3516
91.9295-1.1213-0.12661.22150.13510.4340.07420.0984-0.1937-0.0262-0.12110.0062-0.01510.03260.04320.2787-0.0663-0.04510.26870.02770.368419.4552-10.3456-34.1607
102.4990.2344-0.33882.34450.11681.1690.08080.44350.1402-0.2937-0.10590.0261-0.1301-0.11220.00330.3737-0.0065-0.05740.4250.10990.450214.40870.6276-47.6137
112.0501-0.8681-0.51871.10580.08140.8544-0.0531-0.32260.09790.19930.053-0.2048-0.07670.191-0.00360.277-0.0697-0.10110.26460.03370.296622.2641-4.9705-22.562
123.1296-0.6469-1.62740.84260.48473.14930.043-0.116-0.19490.0127-0.0360.3619-0.2848-0.22450.0720.34190.00960.02520.28550.07130.39365.5407-9.7945-19.7751
131.3961-0.4144-0.11321.20670.51630.7148-0.0054-0.2392-0.1710.1483-0.04510.03190.1121-0.08580.0560.2283-0.0424-0.01310.28290.09990.2223-46.6451-24.4235-8.025
141.98480.4559-0.54912.4492-0.18311.8626-0.12540.1535-0.4304-0.03220.102-0.02190.2493-0.25240.01270.2309-0.0534-0.0270.31190.05330.4022-52.0797-35.8728-21.0401
151.00350.1916-0.34590.98460.17980.80870.0196-0.4213-0.30970.2748-0.0505-0.21830.2090.01040.01440.3375-0.0338-0.06540.3470.17320.3206-37.055-32.7753-1.0359
161.4617-0.163-0.23931.28470.28150.86540.0497-0.5939-0.25070.4256-0.074-0.06550.08010.06940.0450.3495-0.0586-0.06810.39840.1410.2434-39.7379-25.73732.6151
171.040.20990.06640.70290.01561.4037-0.09120.3033-0.4239-0.20060.0616-0.24620.10470.05320.02720.2958-0.06040.04120.2995-0.13240.6226-2.6363-37.8449-54.2379
180.97560.3669-0.49790.7388-0.28240.89360.025-0.0069-0.21290.0798-0.006-0.1511-0.0128-0.0086-0.01620.2436-0.0009-0.02070.20130.02910.4753-15.9382-34.1093-32.3401
192.41881.14380.56831.50980.07080.9554-0.0848-0.1437-0.62040.087-0.0226-0.29060.01880.06980.08880.2617-0.0094-0.00480.23220.03480.5859-3.3637-38.2399-30.9633
200.79180.2863-0.08280.6957-0.12830.8493-0.11490.1637-0.7739-0.10670.0594-0.28270.2072-0.04650.01080.3432-0.04080.04610.2357-0.10420.875-13.5209-52.1084-43.459
211.82580.02810.01541.2596-0.01791.7217-0.1060.0102-0.14120.2229-0.0370.3552-0.0458-0.16130.14660.3325-0.01080.0170.3299-0.18090.5936-49.5213-38.7927-49.8944
220.2882-0.2934-0.41031.0921-0.04360.7360.1190.4054-0.2386-0.1434-0.28280.2895-0.1399-0.30350.10580.2980.0441-0.10720.5169-0.29220.6131-43.3235-35.1885-77.6164
232.0991-0.64250.40.9039-0.73731.07130.10020.4022-0.3062-0.3493-0.12870.38460.0932-0.42840.03350.39760.0453-0.13720.6341-0.35070.7164-51.4459-39.1519-80.5427
240.3212-0.2355-0.4540.5156-0.20540.8418-0.1960.2271-0.64250.0198-0.15230.240.2783-0.24190.21530.3394-0.06710.04170.4271-0.32330.8442-41.8303-52.5695-67.3943
250.5573-0.0856-0.24050.8299-0.55160.51930.2780.3854-0.0081-0.2784-0.4135-0.2928-0.14350.2273-0.71581.11450.42070.34720.51550.03450.27980.3809-14.294-113.1631
262.66690.147-0.86791.443-0.16082.02060.2552-0.0037-0.178-0.2864-0.4085-0.0033-0.1788-0.04770.14490.36230.1144-0.01770.3081-0.06060.2732-10.7732-33.6347-95.1837
273.8251-0.58260.96082.242-0.23282.62570.04570.1123-0.5541-0.1682-0.2194-0.11980.1375-0.12510.06970.4270.0960.07390.3615-0.03780.3211-5.6027-40.6178-98.9011
280.8628-0.147-0.09891.31030.031.2150.19860.7148-0.441-0.8836-0.317-0.0239-0.2141-0.48670.060.79730.3976-0.11080.7554-0.23590.2738-16.0619-31.1303-114.5392
292.18081.33460.09130.8583-0.11610.82350.1524-0.0369-0.0564-0.0431-0.22050.22480.105-0.04020.05330.31820.07510.00030.3607-0.07680.578929.0471-11.4186-79.7328
300.79140.7049-0.4141.3456-0.81040.80960.2094-0.4835-0.33340.1001-0.34560.06790.14430.19420.13830.3780.00260.01670.61010.03770.757142.783-9.903-68.7924
312.7751-2.07321.75352.30560.11133.77470.1979-0.32240.94910.29170.0722-0.0185-0.5943-0.0538-0.26120.6509-0.01990.09160.6454-0.32041.100528.546111.6947-68.117
323.26251.0621-0.28890.77250.03970.7874-0.07550.46970.1889-0.15460.01250.36210.0079-0.05680.06510.35050.065-0.0890.4097-0.03110.551528.962-6.7244-90.1073
332.5560.6758-1.24591.9115-1.01232.2283-0.10960.3343-0.2561-0.03340.03010.0998-0.0081-0.05670.08460.40230.1285-0.03520.3839-0.12470.516445.7464-11.4187-92.6855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 225 )
3X-RAY DIFFRACTION3chain 'A' and (resid 226 through 282 )
4X-RAY DIFFRACTION4chain 'A' and (resid 283 through 455 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 72 )
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 225 )
7X-RAY DIFFRACTION7chain 'B' and (resid 226 through 282 )
8X-RAY DIFFRACTION8chain 'B' and (resid 283 through 455 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 195 )
10X-RAY DIFFRACTION10chain 'C' and (resid 196 through 250 )
11X-RAY DIFFRACTION11chain 'C' and (resid 251 through 424 )
12X-RAY DIFFRACTION12chain 'C' and (resid 425 through 455 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 195 )
14X-RAY DIFFRACTION14chain 'D' and (resid 196 through 250 )
15X-RAY DIFFRACTION15chain 'D' and (resid 251 through 335 )
16X-RAY DIFFRACTION16chain 'D' and (resid 336 through 455 )
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 108 )
18X-RAY DIFFRACTION18chain 'E' and (resid 109 through 225 )
19X-RAY DIFFRACTION19chain 'E' and (resid 226 through 281 )
20X-RAY DIFFRACTION20chain 'E' and (resid 282 through 455 )
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 72 )
22X-RAY DIFFRACTION22chain 'F' and (resid 73 through 225 )
23X-RAY DIFFRACTION23chain 'F' and (resid 226 through 281 )
24X-RAY DIFFRACTION24chain 'F' and (resid 282 through 455 )
25X-RAY DIFFRACTION25chain 'G' and (resid 1 through 72 )
26X-RAY DIFFRACTION26chain 'G' and (resid 73 through 225 )
27X-RAY DIFFRACTION27chain 'G' and (resid 226 through 281 )
28X-RAY DIFFRACTION28chain 'G' and (resid 282 through 455 )
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 158 )
30X-RAY DIFFRACTION30chain 'H' and (resid 159 through 225 )
31X-RAY DIFFRACTION31chain 'H' and (resid 226 through 250 )
32X-RAY DIFFRACTION32chain 'H' and (resid 251 through 424 )
33X-RAY DIFFRACTION33chain 'H' and (resid 425 through 455 )

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