[English] 日本語
Yorodumi
- PDB-6cyx: Crystal structure analysis of the L80F mutant of Superoxide Dismu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cyx
TitleCrystal structure analysis of the L80F mutant of Superoxide Dismutase from Trichoderma reesei
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / enzymatic activity
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / mitochondrion / metal ion binding
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMendoza Rengifo, E. / Ferreira Jr., J.R.S. / Garratt, R.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/01855-2 Brazil
CitationJournal: To Be Published
Title: Crystal structure analysis of the L80F mutant of Superoxide Dismutase from Trichoderma reesei
Authors: Mendoza Rengifo, E. / Ferreira Jr., J.R.S. / Garratt, R.C.
History
DepositionApr 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
E: Superoxide dismutase
F: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,30812
Polymers138,9796
Non-polymers3306
Water1,928107
1
A: Superoxide dismutase
hetero molecules

A: Superoxide dismutase
hetero molecules

D: Superoxide dismutase
hetero molecules

D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8728
Polymers92,6524
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_455x-1,-y,-z1
Buried area8290 Å2
ΔGint-53 kcal/mol
Surface area32830 Å2
MethodPISA
2
B: Superoxide dismutase
C: Superoxide dismutase
E: Superoxide dismutase
F: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8728
Polymers92,6524
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-55 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.420, 75.340, 242.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 4 through 209)
21(chain B and resid 4 through 209)
31chain C
41(chain D and resid 4 through 209)
51(chain E and resid 4 through 209)
61(chain F and resid 4 through 209)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 4 - 209 / Label seq-ID: 3 - 208

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 4 through 209)AA
2(chain B and resid 4 through 209)BB
3chain CCC
4(chain D and resid 4 through 209)DD
5(chain E and resid 4 through 209)EE
6(chain F and resid 4 through 209)FF

-
Components

#1: Protein
Superoxide dismutase


Mass: 23163.109 Da / Num. of mol.: 6 / Mutation: L80F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (strain QM6a) (fungus)
Strain: QM6a / Gene: TRIREDRAFT_66345 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0RQS7, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 100mM Bis-Tris pH 6.8, 25% PEG3350 / PH range: 6.5-6.9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→75.34 Å / Num. all: 40915 / Num. obs: 40915 / % possible obs: 68.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 36.27 Å2 / CC1/2: 0.958 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.109 / Rrim(I) all: 0.203 / Rsym value: 0.168 / Net I/σ(I): 3.2 / Num. measured all: 99493
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.3-2.422.10.72161180.3130.0510.1060.09270.5
7.27-75.343.90.09214440.9480.0690.150.13269.5

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→73.42 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.05
RfactorNum. reflection% reflection
Rfree0.2915 2140 5.23 %
Rwork0.2414 --
obs0.244 40879 67.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.39 Å2 / Biso mean: 51.6524 Å2 / Biso min: 15.06 Å2
Refinement stepCycle: final / Resolution: 2.3→73.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9768 0 6 107 9881
Biso mean--62.44 33.25 -
Num. residues----1258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210044
X-RAY DIFFRACTIONf_angle_d0.48613666
X-RAY DIFFRACTIONf_chiral_restr0.0391464
X-RAY DIFFRACTIONf_plane_restr0.0041750
X-RAY DIFFRACTIONf_dihedral_angle_d10.6045834
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5860X-RAY DIFFRACTION8.102TORSIONAL
12B5860X-RAY DIFFRACTION8.102TORSIONAL
13C5860X-RAY DIFFRACTION8.102TORSIONAL
14D5860X-RAY DIFFRACTION8.102TORSIONAL
15E5860X-RAY DIFFRACTION8.102TORSIONAL
16F5860X-RAY DIFFRACTION8.102TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35350.35951340.33562662279670
2.3535-2.41240.38471410.33742588272969
2.4124-2.47760.35311550.32362585274069
2.4776-2.55050.37511410.31452571271268
2.5505-2.63280.39421500.31712513266366
2.6328-2.7270.3321100.31582500261065
2.727-2.83610.3581400.30842455259564
2.8361-2.96520.39191500.31012363251363
2.9652-3.12160.36221320.28852444257664
3.1216-3.31710.34971630.28762420258364
3.3171-3.57320.34911250.2652548267366
3.5732-3.93280.29891670.22482585275268
3.9328-4.50180.19511290.18422824295372
4.5018-5.67150.19991400.17632853299372
5.6715-73.45740.20931630.16912828299169
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)
10.87220.40620.5080.67560.81741.24290.2148-0.15990.05960.447-0.0589-0.36750.6137-0.0975-0.10620.7273-0.0971-0.21520.38110.06640.3898-12.7275-14.887621.5017
23.6092-0.14880.64111.8352-0.40632.35870.3965-0.0621-0.131-0.22930.1133-0.27510.57150.0782-0.42180.3281-0.07410.03090.2208-0.03840.4877-14.6773-14.7189.3516
32.3188-0.30890.70130.6637-0.35970.43630.03580.3284-0.4430.10430.2529-0.90090.16130.64380.00520.16250.0517-0.3560.8031-0.45261.07568.61580.139317.184
42.16891.7040.18561.66160.19472.3463-0.24390.1083-0.43220.1080.4308-0.48730.1490.733-0.26020.27070.0377-0.11470.2911-0.03640.485-5.1037-1.097911.4221
51.86531.36012.5836.15850.55124.08910.00980.18590.04270.51280.6757-0.90930.15680.3663-0.54810.46290.0937-0.13690.3256-0.04020.4999-2.1462-5.07138.2667
60.54010.3302-0.23110.3611-0.4670.99050.2267-0.0604-0.2151-0.04750.0844-0.3968-0.1039-0.0697-0.30820.37440.1025-0.06320.4340.02350.3588-11.99853.14824.4115
72.1337-1.2654-0.33950.78320.06030.79830.0016-0.07570.1260.19770.2207-0.3090.0410.6192-0.2930.0516-0.0247-0.07440.49-0.19541.1769-0.93764.000224.0317
80.00860.0039-0.02430.0145-0.03480.1011-0.0955-0.0048-0.0527-0.13140.079-0.08060.26310.3247-0.332-0.0140.352-0.68380.715-0.17411.37268.5687-10.339116.1306
92.74680.8489-2.52080.3737-0.97142.68910.46240.2854-0.82180.01880.1876-0.05120.2125-0.128-0.50080.52420.1837-0.19710.618-0.17510.5383-1.1828-20.253912.7515
101.7884-0.25840.0023.04520.03622.79490.33230.1098-0.4338-1.0366-0.51850.779-0.3262-0.6647-0.00290.4932-0.0271-0.09660.4696-0.08560.459-5.4565-42.437133.3864
111.03440.71620.2462.63142.06683.8806-0.02810.02530.1319-0.64290.04340.3589-0.311-0.09080.02830.52740.0720.02770.3470.0290.18762.606-34.407936.3571
120.61430.0656-0.33951.1206-0.21050.2157-0.03421.1989-0.2663-1.00440.11330.35110.7194-0.5417-0.09621.1314-0.0473-0.32690.6571-0.05060.4699-0.2898-49.466211.3304
131.27161.5687-1.44463.6019-0.10423.3255-0.29950.1976-0.0348-0.9425-0.1358-0.15930.32970.06320.33750.8808-0.01020.04670.45310.04940.7114.5642-42.38738.0064
142.36120.0997-0.19611.3158-0.45091.3178-0.13150.4106-0.3928-0.7494-0.0951-0.15630.41640.0105-0.09680.87660.0638-0.03290.203-0.33870.721416.7315-50.590617.7007
153.105-0.30940.20770.602-1.52993.9352-0.15270.13180.6117-0.6834-0.46-0.2333-0.1312-0.00090.42410.58280.0894-0.01960.24370.0510.387613.7875-40.835524.1686
161.3758-0.58830.57010.2472-0.17613.37980.12970.1580.10340.0598-0.21260.2884-0.11310.25810.05330.39950.02780.0620.239-0.02220.42337.415-47.844528.8069
171.45260.23680.40821.14981.10212.2683-0.1660.41-0.142-0.5160.00290.1203-0.1204-0.10990.25140.89790.155-0.1950.4263-0.35070.65138.102-55.883520.9205
183.96130.61941.32530.72360.79211.28860.31561.0361-0.0128-0.9102-0.27450.14530.0612-0.1584-0.10020.97710.2032-0.11140.6631-0.06160.37613.0553-41.012112.3116
192.7958-0.0799-3.72153.061-2.31048.4873-0.05590.45540.4712-0.4517-0.29060.3629-0.7207-0.67610.18960.80830.2453-0.31280.5744-0.15030.4268-0.9931-31.282121.3347
200.91050.0082-0.51381.0213-0.32070.76150.2582-0.37310.0403-0.5082-0.0912-0.3193-0.15910.92150.0810.3914-0.25030.16660.72730.0260.289539.8932-30.024832.3086
212.83690.7833-0.96582.5007-0.06962.7255-0.1462-0.2280.0603-0.4924-0.1129-0.2457-0.06680.0745-0.18840.4088-0.22390.36890.2067-0.01080.581825.9716-25.648324.5267
221.8627-0.2966-0.60842.56990.73791.52960.2615-0.17960.7166-0.36240.0083-0.5597-0.25010.0967-0.20660.442-0.21250.0640.4487-0.0130.435535.134-25.325226.9495
232.50951.2903-0.79974.0955-0.9062.1515-0.14020.01180.2946-0.020.3351-0.1475-0.0466-0.0528-0.23120.36650.04240.11620.4138-0.02920.483345.894617.538423.9246
240.4712-0.1954-0.70811.0527-0.37064.130.2326-0.03980.0771-0.07540.0349-0.2565-0.8860.1837-0.01590.2871-0.08380.04040.2823-0.00840.469256.217718.857614.7929
250.2636-0.35910.1951.06110.59372.1263-0.008-0.002-0.282-0.0286-0.21550.3505-0.2386-0.59360.1050.2471-0.09430.08390.3463-0.05210.412640.65638.107612.6429
265.1168-2.6322-1.09544.5591-0.76341.44320.18970.9985-0.0998-0.24520.13440.25260.1539-0.2905-0.32910.2938-0.06890.07550.2897-0.04010.182941.94212.9928.0785
270.6596-0.07670.29132.20950.01790.79150.2245-0.11090.01610.0289-0.1650.03670.2079-0.23910.08650.2674-0.07710.040.3973-0.02550.421345.5033.428418.8767
280.24560.2265-0.3720.41330.17811.99480.12440.03150.1351-0.116-0.34440.5437-0.4228-0.59050.25270.2820.02250.01670.4565-0.36850.85730.767112.150915.1229
294.87310.01070.95182.2129-0.53163.67910.1445-0.11460.5612-0.3206-0.38780.4994-0.5645-0.23590.23320.35230.1710.0590.47870.04460.375738.365420.46627.6471
300.4069-0.0285-0.47770.1490.19570.7386-0.0918-0.2529-0.2135-0.2982-0.25550.02320.33560.45170.35410.57270.19070.21660.41710.12150.562416.5499-67.332346.6805
313.38681.0953-1.20051.9619-0.94841.7979-0.29890.1606-0.6735-0.1560.0814-0.40480.21950.35270.18730.43440.09910.05070.3723-0.02560.308525.1206-56.358439.3035
320.55370.1118-0.10590.2801-0.95683.4473-0.0891-0.3889-0.22780.44110.00060.06880.0219-0.1983-0.14520.80010.32340.14560.46280.27420.41469.6037-65.047561.699
331.6337-0.7764-1.4791.8357-1.50976.2668-0.4208-0.7054-0.13040.51250.14550.13120.56380.50430.08570.29610.11360.07870.43080.06650.472410.9735-47.884258.9157
343.44930.32891.17781.1245-1.48634.18210.0835-0.0095-0.06710.00910.3913-0.3553-0.00590.5972-0.2850.50020.09820.18540.4994-0.05550.459319.0351-50.45651.5002
352.1304-0.0057-0.89371.9205-0.2911.8485-0.4191-0.6382-0.379-0.13150.05320.01740.6410.06050.04930.44950.09270.17280.39610.10820.3158.3124-57.360952.1998
361.0016-1.48670.09042.3538-0.21590.0588-0.1529-1.20910.46450.23210.4737-0.49940.20010.6378-0.35250.3346-0.0305-0.07850.80790.23480.645129.0101-59.209854.1642
373.0401-0.6097-0.81931.16340.08641.67560.5921-0.45190.4151-0.2698-0.2914-0.0375-0.85020.3933-0.29680.9931-0.14820.19340.335-0.05520.281916.7038-11.616946.7982
381.42560.23460.09371.65411.32213.4330.0211-0.24520.2726-0.1939-0.14750.0407-0.86320.34690.05470.6515-0.11260.20970.3527-0.05250.190311.6276-21.891943.6474
392.78180.1823-0.13591.13740.80361.73960.2661-1.095-0.16970.14350.091-0.1924-0.21720.516-0.19570.3072-0.2621-0.0231.2983-0.0610.593823.7049-23.037970.3313
401.2120.10230.1640.95910.65324.3505-0.1525-0.69110.10010.2976-0.3476-0.59250.06291.1740.33430.4356-0.16080.00490.8219-0.01470.330731.1471-30.266462.1903
412.14470.8641-0.4471.6035-0.13981.41690.001-0.4649-0.256-0.22820.3664-0.2961-0.14410.2685-0.16520.2671-0.15160.20350.46970.03040.603922.4023-28.806453.8828
421.83750.8382-0.30422.0652-0.69341.312-0.114-0.533-0.07570.00930.4115-0.16150.17180.1143-0.3531-0.0059-0.0946-0.16110.77910.11820.490719.4935-32.911657.8603
433.4743-0.19211.28731.1541.54163.26250.0601-0.39730.006-0.0409-0.024-0.4426-0.0470.73230.05410.3374-0.18150.01080.39740.00320.321317.4615-26.086754.0617
442.2220.81060.61230.29850.21580.1937-0.0134-0.52630.4305-0.36830.1749-0.2352-0.31780.1551-0.07730.5048-0.27610.10890.7571-0.08720.796433.8274-18.373548.2059
450.5937-0.8362-0.54331.19770.76370.5055-0.2777-0.38980.18850.03020.0853-0.1344-0.38841.07390.14490.8913-0.46860.05871.227-0.15570.417833.4569-20.299959.2295
460.5352-0.08330.93751.20540.58744.50780.0179-0.42570.0541-0.02920.2463-0.2116-0.45560.51260.0260.66610.04740.05070.9664-0.16030.120316.6872-21.150567.2803
470.76450.14020.26860.3180.11760.11060.1112-0.60150.12730.0382-0.11960.052-0.3004-0.0333-0.09520.68080.04450.09370.4481-0.00250.11567.2291-18.080857.3776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 54 )A2 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 83 )A55 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 124 )A84 - 124
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 136 )A125 - 136
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 163 )A137 - 163
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 176 )A164 - 176
7X-RAY DIFFRACTION7chain 'A' and (resid 177 through 187 )A177 - 187
8X-RAY DIFFRACTION8chain 'A' and (resid 188 through 200 )A188 - 200
9X-RAY DIFFRACTION9chain 'A' and (resid 201 through 212 )A201 - 212
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 55 )B2 - 55
11X-RAY DIFFRACTION11chain 'B' and (resid 56 through 83 )B56 - 83
12X-RAY DIFFRACTION12chain 'B' and (resid 84 through 98 )B84 - 98
13X-RAY DIFFRACTION13chain 'B' and (resid 99 through 111 )B99 - 111
14X-RAY DIFFRACTION14chain 'B' and (resid 112 through 124 )B112 - 124
15X-RAY DIFFRACTION15chain 'B' and (resid 125 through 147 )B125 - 147
16X-RAY DIFFRACTION16chain 'B' and (resid 148 through 176 )B148 - 176
17X-RAY DIFFRACTION17chain 'B' and (resid 177 through 187 )B177 - 187
18X-RAY DIFFRACTION18chain 'B' and (resid 188 through 198 )B188 - 198
19X-RAY DIFFRACTION19chain 'B' and (resid 199 through 211 )B199 - 211
20X-RAY DIFFRACTION20chain 'C' and (resid 4 through 111 )C4 - 111
21X-RAY DIFFRACTION21chain 'C' and (resid 112 through 147 )C112 - 147
22X-RAY DIFFRACTION22chain 'C' and (resid 148 through 209 )C148 - 209
23X-RAY DIFFRACTION23chain 'D' and (resid 2 through 23 )D2 - 23
24X-RAY DIFFRACTION24chain 'D' and (resid 24 through 55 )D24 - 55
25X-RAY DIFFRACTION25chain 'D' and (resid 56 through 124 )D56 - 124
26X-RAY DIFFRACTION26chain 'D' and (resid 125 through 147 )D125 - 147
27X-RAY DIFFRACTION27chain 'D' and (resid 148 through 187 )D148 - 187
28X-RAY DIFFRACTION28chain 'D' and (resid 188 through 198 )D188 - 198
29X-RAY DIFFRACTION29chain 'D' and (resid 199 through 210 )D199 - 210
30X-RAY DIFFRACTION30chain 'E' and (resid 2 through 23 )E2 - 23
31X-RAY DIFFRACTION31chain 'E' and (resid 24 through 83 )E24 - 83
32X-RAY DIFFRACTION32chain 'E' and (resid 84 through 98 )E84 - 98
33X-RAY DIFFRACTION33chain 'E' and (resid 99 through 147 )E99 - 147
34X-RAY DIFFRACTION34chain 'E' and (resid 148 through 163 )E148 - 163
35X-RAY DIFFRACTION35chain 'E' and (resid 164 through 200 )E164 - 200
36X-RAY DIFFRACTION36chain 'E' and (resid 201 through 212 )E201 - 212
37X-RAY DIFFRACTION37chain 'F' and (resid 2 through 55 )F2 - 55
38X-RAY DIFFRACTION38chain 'F' and (resid 56 through 83 )F56 - 83
39X-RAY DIFFRACTION39chain 'F' and (resid 84 through 111 )F84 - 111
40X-RAY DIFFRACTION40chain 'F' and (resid 112 through 124 )F112 - 124
41X-RAY DIFFRACTION41chain 'F' and (resid 125 through 137 )F125 - 137
42X-RAY DIFFRACTION42chain 'F' and (resid 138 through 147 )F138 - 147
43X-RAY DIFFRACTION43chain 'F' and (resid 148 through 163 )F148 - 163
44X-RAY DIFFRACTION44chain 'F' and (resid 164 through 176 )F164 - 176
45X-RAY DIFFRACTION45chain 'F' and (resid 177 through 187 )F177 - 187
46X-RAY DIFFRACTION46chain 'F' and (resid 188 through 200 )F188 - 200
47X-RAY DIFFRACTION47chain 'F' and (resid 201 through 212 )F201 - 212

+
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://pdbjlvh1.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