[English] 日本語
Yorodumi
- PDB-5koi: Crystal Structure of a Possible Enoyl-(acyl-carrier-protein) Redu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5koi
TitleCrystal Structure of a Possible Enoyl-(acyl-carrier-protein) Reductase from Brucella melitensis
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / SSGCID / NAD / reductase / fatty acid biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBrucella abortus biovar 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Possible Enoyl-(acyl-carrier-protein) Reductase from Brucella melitensis
Authors: Dranow, D.M. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,28116
Polymers252,9748
Non-polymers5,3078
Water29,8331656
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5704
Polymers63,2432
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-30 kcal/mol
Surface area22930 Å2
MethodPISA
2
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5704
Polymers63,2432
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-28 kcal/mol
Surface area22850 Å2
MethodPISA
3
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5704
Polymers63,2432
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-28 kcal/mol
Surface area22740 Å2
MethodPISA
4
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5704
Polymers63,2432
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-26 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.910, 83.830, 106.290
Angle α, β, γ (deg.)90.250, 100.080, 90.820
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 31621.695 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus biovar 1 (strain 9-941) (bacteria)
Strain: 9-941 / Gene: fabI-2, BruAb1_2144 / Plasmid: BrabA.00010.c.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q57A95, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1656 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: BrabA.00010.c.A1.PS000047 at 18.1 mg/ml, incubated with 4 mM NAD, protein mixed 1:1 and incubated with an equal volume PACT(a6): 25% (w/v) PEG-1500, 10 % (v/v) 10x SPG, pH=9, and ...Details: BrabA.00010.c.A1.PS000047 at 18.1 mg/ml, incubated with 4 mM NAD, protein mixed 1:1 and incubated with an equal volume PACT(a6): 25% (w/v) PEG-1500, 10 % (v/v) 10x SPG, pH=9, and cryoprotected with 20% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 236079 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 19.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2% possible all
1.7-1.7440.4742.910.89895.6
1.74-1.790.3823.570.92495.8
1.79-1.840.3134.320.94796.1
1.84-1.90.2355.60.96796.3
1.9-1.960.187.030.98296.4
1.96-2.030.1448.660.98796.6
2.03-2.110.1210.360.98996.9
2.11-2.190.09812.560.99197.2
2.19-2.290.08314.480.99397.4
2.29-2.40.07416.010.99497.6
2.4-2.530.06517.680.99597.8
2.53-2.690.05819.970.99598.1
2.69-2.870.05321.860.99698.3
2.87-3.10.04624.360.99798.4
3.1-3.40.041270.99798.6
3.4-3.80.03928.990.99798.9
3.8-4.390.03431.110.99899
4.39-5.380.03331.390.99899.4
5.38-7.60.03430.940.99899.6
7.60.03332.920.99799.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GRK

3grk


Resolution: 1.7→48.675 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 16.75
RfactorNum. reflection% reflection
Rfree0.1756 11802 5 %
Rwork0.1465 --
obs0.148 236058 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.3 Å2 / Biso mean: 25.2716 Å2 / Biso min: 9.44 Å2
Refinement stepCycle: final / Resolution: 1.7→48.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16065 0 572 1677 18314
Biso mean--29.66 34.39 -
Num. residues----2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617437
X-RAY DIFFRACTIONf_angle_d0.83523833
X-RAY DIFFRACTIONf_chiral_restr0.0532724
X-RAY DIFFRACTIONf_plane_restr0.0053334
X-RAY DIFFRACTIONf_dihedral_angle_d14.47710677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.25283880.21667375776395
1.7193-1.73950.24713830.21737286766996
1.7395-1.76070.23893900.20147400779096
1.7607-1.7830.25753880.20017371775996
1.783-1.80650.22393900.19017415780596
1.8065-1.83120.23243840.19497303768796
1.8312-1.85740.22273910.18077419781096
1.8574-1.88510.20323880.1737381776996
1.8851-1.91460.21693910.17087419781096
1.9146-1.9460.20633900.16247423781396
1.946-1.97950.2143890.16027391778097
1.9795-2.01550.19193930.14977454784797
2.0155-2.05430.18973910.1517440783197
2.0543-2.09620.19733940.15357471786597
2.0962-2.14180.16823900.14537417780797
2.1418-2.19160.18483950.1467510790597
2.1916-2.24640.18373940.14677472786697
2.2464-2.30710.18383940.13797486788097
2.3071-2.3750.17643940.13977493788798
2.375-2.45170.17693940.14177495788998
2.4517-2.53930.18833980.14627556795498
2.5393-2.6410.17153960.1397517791398
2.641-2.76120.18213960.14717527792398
2.7612-2.90670.20113980.15267562796098
2.9067-3.08880.18264010.15147629803099
3.0888-3.32720.16143970.14477536793399
3.3272-3.6620.16324010.14157623802499
3.662-4.19160.13644010.12187607800899
4.1916-5.280.13314020.11737643804599
5.28-48.69470.1524010.1447635803699
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)
13.45270.1940.42192.170.28214.8769-0.21050.16490.3321-0.04160.04710.0277-0.52630.20770.10230.2835-0.0165-0.04060.07010.03940.2401-7.499560.92030.0015
22.3272-0.28940.11071.9070.53684.8361-0.01740.17130.2362-0.0453-0.03-0.0033-0.2967-0.03020.06670.2512-0.0024-0.0370.10380.04140.2293-9.336561.4178-2.3819
34.4729-0.9143-0.68759.9075.19012.7327-0.28650.34510.2961-0.1152-0.13880.4678-0.842-0.13610.37830.3411-0.0132-0.09310.20670.0890.3166-13.315366.0725-11.5066
41.29280.25830.24135.73392.30613.4443-0.10660.31780.0928-0.36340.042-0.3913-0.39520.48710.05940.281-0.0703-0.00270.27160.11830.23380.905860.3054-12.9855
51.45180.81590.78672.12980.90761.2537-0.03780.23480.0871-0.11730.0289-0.0716-0.16560.12430.0240.1831-0.02460.00010.19560.03780.112-5.429645.1399-11.7132
62.49490.44740.77220.83510.14371.3558-0.0590.10580.1601-0.07030.01410.0383-0.09840.03350.06390.1395-0.01050.00470.11910.01080.1152-7.102343.4104-2.3762
72.33971.1415-0.45042.40320.40952.15770.00590.10390.2878-0.1622-0.0490.1472-0.1268-0.15110.11780.15560.0248-0.01490.1729-0.00550.2269-26.800943.29832.5014
82.29810.83160.32781.10220.23340.82470.0164-0.00660.10270.033-0.0510.0053-0.1176-0.00210.03660.1657-0.0032-0.00710.1333-0.00120.1455-12.223246.28927.6569
97.71894.843.96399.44465.35559.0876-0.0525-0.103-0.0925-0.0632-0.16350.1497-0.2031-0.41390.20090.09690.00960.02740.20530.0030.1753-36.543429.11483.6043
103.98130.5798-1.72541.5757-0.73784.4867-0.0255-0.006-0.2843-0.0580.00910.04370.4031-0.135-0.01380.2122-0.0483-0.02620.08020.00580.2507-15.02210.807612.934
115.3199-0.6713-3.75983.21462.02478.4046-0.149-0.2468-0.5302-0.2420.11830.43210.381-0.51720.02710.2954-0.0816-0.04140.24950.07740.3789-24.8274-3.344119.6118
121.1763-0.27690.06731.18770.08280.82640.0165-0.1145-0.21470.1594-0.01480.04560.1484-0.0639-0.00140.1613-0.03780.01210.15440.02010.1865-14.384813.348822.5894
131.3241-0.4169-0.06961.21780.21.046-0.0232-0.0057-0.13490.05110.01110.14120.0739-0.0928-0.03120.1451-0.03330.00890.12320.01520.1619-12.455718.279715.252
143.0734-1.59110.79311.5256-0.18770.6150.0830.0335-0.1126-0.0407-0.06750.08710.0761-0.0571-0.0160.1331-0.01510.00550.1396-0.01860.1501-18.738517.64492.7618
154.4453-2.5987-0.55722.70040.94757.6033-0.22180.1380.2135-0.3385-0.0620.5792-0.1501-0.62670.2690.1809-0.0021-0.06120.26120.00230.2638-34.279636.1838-3.8635
162.895-0.2262-0.20242.7737-0.04242.88710.16460.4009-0.3081-0.13830.01910.05750.42060.2473-0.07220.22450.0465-0.03770.1999-0.11430.2121-2.42118.3662-13.9722
172.4151-0.4639-1.07662.77840.08962.60510.17080.3949-0.281-0.3031-0.0405-0.31620.31250.5212-0.03880.19240.06120.0090.3508-0.12770.25233.50579.2042-17.0153
180.95190.01530.0414.49330.07552.08240.16630.4805-0.1545-0.6013-0.0674-0.04030.14040.0802-0.11520.32060.02420.00460.4266-0.14120.1907-3.772716.8191-26.8962
191.60720.83130.54422.3920.53970.8295-0.04620.4392-0.2405-0.25580.1665-0.1989-0.05480.2775-0.09890.1725-0.00060.01730.2979-0.05560.15581.200123.4956-14.4406
201.34550.67150.45391.57860.27311.260.02410.1684-0.0645-0.1117-0.0129-0.0237-0.01260.1013-0.02160.12670.01380.0250.2175-0.02740.1393-2.023628.8089-11.7116
212.19530.74160.45061.23770.269810.0280.1103-0.1085-0.0440.0111-0.09210.00070.1139-0.03210.14660.01460.010.1786-0.03390.1254-5.789824.9196-7.3112
221.5970.40440.6710.64150.27980.69660.04990.0811-0.172-0.00810.0195-0.12290.07120.1201-0.08620.12690.01090.00240.1555-0.01760.16423.005716.02821.3892
231.7316-0.351.56282.01330.27443.6902-0.12350.02250.290.1864-0.0404-0.054-0.16770.28490.13650.1584-0.01280.00670.17050.00410.15549.21525.691312.1775
242.91340.23221.2222.3142-1.10374.43520.0512-0.16090.1010.0548-0.05880.0695-0.2987-0.0583-0.00740.1942-0.0085-0.01120.1085-0.07430.1499-8.587252.621529.3285
254.07932.2905-1.95039.1883-6.46814.6033-0.0157-0.4064-0.21640.3117-0.1445-0.76510.0703-0.23430.1730.291-0.0367-0.08140.2154-0.05230.2053-3.907352.025340.1185
261.9861-0.54-0.68888.7066-0.64132.7921-0.0066-0.3484-0.01840.5868-0.04520.4539-0.0715-0.28280.05090.2267-0.01250.03140.3085-0.09190.1779-18.248345.710738.7214
271.9025-1.48360.30623.48820.00910.9753-0.036-0.20720.05090.1898-0.0108-0.0435-0.0148-0.06280.04690.1338-0.02430.01410.1663-0.00560.0921-11.172233.164229.9023
281.5689-0.6550.37891.4592-0.10641.1914-0.0348-0.07710.16140.0901-0.02-0.1632-0.03930.01590.05460.1404-0.01570.01090.1267-0.01570.1367-9.029137.331320.56
295.5111-1.4936-1.32265.8448-2.86412.29380.1438-0.41820.06940.3504-0.0049-0.3163-0.08680.0876-0.10840.2113-0.0371-0.05220.2112-0.02150.203112.243935.35319.3347
302.9895-0.9091-0.38270.59620.15430.67660.00220.00330.07220.0212-0.0329-0.044-0.08260.08540.02990.1562-0.0223-0.00920.11520.00310.1511-2.0544.563114.0383
318.7-4.88370.40029.9654-0.47175.3526-0.04310.0914-0.10290.01280.0018-0.208-0.09240.12390.04910.1284-0.02340.01210.26260.00060.183220.100127.85128.2165
323.4914-1.19280.32023.41-0.76853.6331-0.1284-0.10990.3871-0.12320.01890.0291-0.4594-0.16170.10220.29710.0144-0.08520.0702-0.05070.300613.6043101.948163.8472
332.1093-0.0302-0.09192.8434-2.08944.723-0.0396-0.27430.297-0.03830.01610.0264-0.4346-0.08290.01170.28250.0013-0.08740.1122-0.06680.312515.9355102.135666.388
344.52412.3799-2.33927.4057-5.21663.81160.0913-0.48420.47460.1558-0.130.0532-0.9320.56350.07020.35620.0173-0.1030.2413-0.12050.34819.7417107.008975.5926
351.4458-0.1648-0.05394.153-0.96512.0606-0.1034-0.35610.3670.2488-0.04410.4167-0.4399-0.25750.12230.33280.0864-0.05060.2842-0.14770.33335.6827100.976277.0205
361.1835-0.47340.64872.227-0.62341.3775-0.0765-0.2830.15650.15990.049-0.0051-0.1165-0.12770.03310.17960.0326-0.00480.2188-0.06250.139512.285485.965775.9521
372.2909-0.22680.57891.7189-0.13671.9371-0.0208-0.03340.06580.0316-0.0110.0156-0.05810.01250.0420.1329-0.0047-00.143-0.02350.128215.947183.652565.711
383.2348-0.26411.71331.1997-0.33272.5577-0.1188-0.21490.24260.08720.01130.0527-0.1678-0.13940.0630.15240.0140.01470.1582-0.02840.15117.531381.733966.9466
391.7155-0.85020.64681.5758-0.00461.5661-0.1994-0.19950.21790.23820.1464-0.2526-0.14950.05710.10540.18360.0215-0.03240.1293-0.04180.201920.839987.936467.1217
401.9586-0.76070.47061.0742-0.06790.637-0.0519-0.01720.22890.0279-0.0162-0.1606-0.09650.07260.08130.1626-0.0174-0.01320.1330.00830.195924.341285.874858.2404
419.3882-4.00852.39898.7443-2.20516.88640.0725-0.39860.01970.07620.033-0.1931-0.17640.2296-0.07360.1251-0.01570.02190.2772-0.00370.226943.652669.743961.2979
424.2796-0.7748-0.44563.1594-0.23823.49210.15890.1677-0.18030.01730.0670.02740.46820.1884-0.18660.26570.0692-0.04110.1047-0.03240.250922.499541.394951.8665
432.7796-2.31760.9557.7417-2.59533.25730.24640.3663-0.3519-0.0689-0.1791-0.42510.49250.4383-0.0350.38420.1267-0.0230.2638-0.09550.378228.080439.581942.5828
441.55241.9429-2.46174.24-4.77775.50060.20370.4361-0.2842-0.5880.0520.55350.6738-0.1013-0.14460.42110.0702-0.07950.226-0.10060.342215.43640.488436.8126
451.8530.7906-0.09741.9458-0.2611.09050.05130.1785-0.0758-0.08380.0017-0.06990.12830.1306-0.03590.14830.02790.01610.1683-0.02180.155223.42958.133140.2774
461.10291.79720.59343.93770.59521.28630.0484-0.1138-0.03810.0549-0.05380.13090.1156-0.0329-0.00110.13560.01480.00650.15010.00260.161220.904259.295551.4529
471.16930.47060.17210.931-0.1791.12670.00340.0705-0.1825-0.0733-0.019-0.20110.08250.1245-0.04110.14420.01450.01120.1084-0.00670.174519.997658.443749.2453
481.44990.34690.4540.57170.1550.67730.0649-0.0241-0.03480.0239-0.0189-0.0810.08070.0684-0.02370.14320.0045-0.00250.150.02170.16125.954758.366961.7711
495.34214.9184-0.58187.768-2.38236.7664-0.2116-0.06520.40410.1141-0.083-0.4963-0.37250.75560.28380.2136-0.0119-0.10130.3168-0.00220.373641.466877.452967.8018
501.8851.0716-0.23792.606-0.33733.03390.2681-0.669-0.28390.2959-0.07920.05070.3184-0.55620.010.2502-0.0839-0.01630.40920.13270.22246.322649.512980.7944
511.151-0.20820.43721.3283-0.19691.1530.0062-0.3866-0.10270.23790.05570.05280.0552-0.1923-0.03970.1663-0.00640.01770.32050.03350.12538.798265.675380.4568
520.6146-0.5402-0.00181.2417-0.21460.9501-0.0525-0.2087-0.08710.07060.08330.1497-0.0259-0.2017-0.02560.1186-0.01230.00530.19170.03910.108810.231465.296571.7333
532.6502-0.74640.9380.7301-0.20891.05530.0556-0.1607-0.14090.00790.01310.08340.087-0.1131-0.07250.1081-0.02210.0070.11460.01730.12274.835458.379861.5374
542.3608-1.78161.25116.9155-2.52881.9611-0.07660.03550.3691-0.35530.12810.90150.0243-0.77730.04840.2201-0.0373-0.06330.33060.00920.2989-11.175370.380746.0391
552.1843-0.26490.55242.58180.96983.19790.08220.25470.2907-0.0972-0.0177-0.1195-0.3318-0.0001-0.07520.2379-0.00310.00530.14170.11650.248915.241592.742334.7713
561.5351-0.3256-0.54522.8877-0.38071.57450.15470.48510.1988-0.5215-0.1761-0.0502-0.03080.07570.01030.30690.02820.03380.3290.12850.244519.416787.721524.7702
571.72431.2290.0843.7645-0.00220.61960.01760.19240.0863-0.1822-0.0443-0.0794-0.06840.03180.02550.1508-0.00150.01520.16190.03630.096118.348673.452934.4317
581.23940.18870.22911.2747-0.0681.2193-0.07260.16670.2061-0.13490.0260.0116-0.0910.03620.03850.1308-0.00690.01070.10820.03020.137816.122877.750543.3846
593.25951.3897-0.16121.3436-0.28340.4257-0.029-0.02190.1179-0.01250.00360.0734-0.0677-0.07380.02890.14860.01420.00160.1194-0.00110.15131.917679.843250.1511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 20 )A2 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 42 )A21 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 56 )A43 - 56
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 82 )A57 - 82
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 135 )A83 - 135
6X-RAY DIFFRACTION6chain 'A' and (resid 136 through 203 )A136 - 203
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 222 )A204 - 222
8X-RAY DIFFRACTION8chain 'A' and (resid 223 through 259 )A223 - 259
9X-RAY DIFFRACTION9chain 'A' and (resid 260 through 272 )A260 - 272
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 42 )B2 - 42
11X-RAY DIFFRACTION11chain 'B' and (resid 43 through 56 )B43 - 56
12X-RAY DIFFRACTION12chain 'B' and (resid 57 through 157 )B57 - 157
13X-RAY DIFFRACTION13chain 'B' and (resid 158 through 203 )B158 - 203
14X-RAY DIFFRACTION14chain 'B' and (resid 204 through 259 )B204 - 259
15X-RAY DIFFRACTION15chain 'B' and (resid 260 through 272 )B260 - 272
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 20 )C2 - 20
17X-RAY DIFFRACTION17chain 'C' and (resid 21 through 56 )C21 - 56
18X-RAY DIFFRACTION18chain 'C' and (resid 57 through 82 )C57 - 82
19X-RAY DIFFRACTION19chain 'C' and (resid 83 through 104 )C83 - 104
20X-RAY DIFFRACTION20chain 'C' and (resid 105 through 157 )C105 - 157
21X-RAY DIFFRACTION21chain 'C' and (resid 158 through 203 )C158 - 203
22X-RAY DIFFRACTION22chain 'C' and (resid 204 through 244 )C204 - 244
23X-RAY DIFFRACTION23chain 'C' and (resid 245 through 270 )C245 - 270
24X-RAY DIFFRACTION24chain 'D' and (resid 2 through 42 )D2 - 42
25X-RAY DIFFRACTION25chain 'D' and (resid 43 through 56 )D43 - 56
26X-RAY DIFFRACTION26chain 'D' and (resid 57 through 82 )D57 - 82
27X-RAY DIFFRACTION27chain 'D' and (resid 83 through 135 )D83 - 135
28X-RAY DIFFRACTION28chain 'D' and (resid 136 through 201 )D136 - 201
29X-RAY DIFFRACTION29chain 'D' and (resid 202 through 214 )D202 - 214
30X-RAY DIFFRACTION30chain 'D' and (resid 215 through 259 )D215 - 259
31X-RAY DIFFRACTION31chain 'D' and (resid 260 through 272 )D260 - 272
32X-RAY DIFFRACTION32chain 'E' and (resid 2 through 20 )E2 - 20
33X-RAY DIFFRACTION33chain 'E' and (resid 21 through 42 )E21 - 42
34X-RAY DIFFRACTION34chain 'E' and (resid 43 through 56 )E43 - 56
35X-RAY DIFFRACTION35chain 'E' and (resid 57 through 82 )E57 - 82
36X-RAY DIFFRACTION36chain 'E' and (resid 83 through 135 )E83 - 135
37X-RAY DIFFRACTION37chain 'E' and (resid 136 through 157 )E136 - 157
38X-RAY DIFFRACTION38chain 'E' and (resid 158 through 181 )E158 - 181
39X-RAY DIFFRACTION39chain 'E' and (resid 182 through 203 )E182 - 203
40X-RAY DIFFRACTION40chain 'E' and (resid 204 through 259 )E204 - 259
41X-RAY DIFFRACTION41chain 'E' and (resid 260 through 272 )E260 - 272
42X-RAY DIFFRACTION42chain 'F' and (resid 2 through 42 )F2 - 42
43X-RAY DIFFRACTION43chain 'F' and (resid 43 through 68 )F43 - 68
44X-RAY DIFFRACTION44chain 'F' and (resid 69 through 83 )F69 - 83
45X-RAY DIFFRACTION45chain 'F' and (resid 84 through 135 )F84 - 135
46X-RAY DIFFRACTION46chain 'F' and (resid 136 through 157 )F136 - 157
47X-RAY DIFFRACTION47chain 'F' and (resid 158 through 203 )F158 - 203
48X-RAY DIFFRACTION48chain 'F' and (resid 204 through 259 )F204 - 259
49X-RAY DIFFRACTION49chain 'F' and (resid 260 through 272 )F260 - 272
50X-RAY DIFFRACTION50chain 'G' and (resid 2 through 56 )G2 - 56
51X-RAY DIFFRACTION51chain 'G' and (resid 57 through 157 )G57 - 157
52X-RAY DIFFRACTION52chain 'G' and (resid 158 through 203 )G158 - 203
53X-RAY DIFFRACTION53chain 'G' and (resid 204 through 259 )G204 - 259
54X-RAY DIFFRACTION54chain 'G' and (resid 260 through 272 )G260 - 272
55X-RAY DIFFRACTION55chain 'H' and (resid 2 through 42 )H2 - 42
56X-RAY DIFFRACTION56chain 'H' and (resid 43 through 82 )H43 - 82
57X-RAY DIFFRACTION57chain 'H' and (resid 83 through 135 )H83 - 135
58X-RAY DIFFRACTION58chain 'H' and (resid 136 through 201 )H136 - 201
59X-RAY DIFFRACTION59chain 'H' and (resid 202 through 272 )H202 - 272

+
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