[English] 日本語
Yorodumi
- PDB-5tf4: Crystal structure of enoyl-(acyl carrier protein) reductase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tf4
TitleCrystal structure of enoyl-(acyl carrier protein) reductase from Bartonella henselae in complext with NAD
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / SSGCID / Bartonella henselae / Enoyl-[acyl-carrier-protein] reductase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


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 speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of enoyl-(acyl carrier protein) reductase from Bartonella henselae in complext with NAD
Authors: Abendroth, J. / Phan, J.N. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,72217
Polymers177,2816
Non-polymers4,44111
Water14,718817
1
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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,20912
Polymers118,1874
Non-polymers3,0228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15770 Å2
ΔGint-101 kcal/mol
Surface area33340 Å2
MethodPISA
2
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,02510
Polymers118,1874
Non-polymers2,8386
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area16450 Å2
ΔGint-104 kcal/mol
Surface area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.440, 76.860, 171.600
Angle α, β, γ (deg.)90.000, 107.730, 90.000
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 29546.826 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Cell line: 49882 / Gene: fabI2 / Plasmid: BaheA.00010.b.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0H3M2Q2, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: RigakuReagents JCSG+ screen, B12: 20% PEG 3350, 200mM Potassium citrate tribasic; BaheA.00010.b.A1.PW25955 at 20.8mg/ml + 4mM NAD; cryo: 20% EG + 8mM NAD; tray 274390b12, puck yts5-10; GOL ...Details: RigakuReagents JCSG+ screen, B12: 20% PEG 3350, 200mM Potassium citrate tribasic; BaheA.00010.b.A1.PW25955 at 20.8mg/ml + 4mM NAD; cryo: 20% EG + 8mM NAD; tray 274390b12, puck yts5-10; GOL close to NAD tentatively modeled, purification buffer contains GOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 6, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→49 Å / Num. obs: 110388 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.81 % / Biso Wilson estimate: 25.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.46
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.95-23.820.5672.870.854199.6
2-2.060.4423.630.899199.8
2.06-2.120.3724.280.928199.7
2.12-2.180.2895.320.951199.7
2.18-2.250.226.790.972199.8
2.25-2.330.1927.60.975199.8
2.33-2.420.1519.360.983199.8
2.42-2.520.13310.50.985199.8
2.52-2.630.10812.40.99199.9
2.63-2.760.0914.490.993199.9
2.76-2.910.07317.390.995199.8
2.91-3.080.05721.830.996199.9
3.08-3.30.04625.690.998199.6
3.3-3.560.03632.010.998199.8
3.56-3.90.0336.960.999199.8
3.9-4.360.02543.230.999199.6
4.36-5.030.02345.870.999199.5
5.03-6.170.02443.880.999199.5
6.17-8.720.02246.610.999199.5
8.72-490.0249.870.999194.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.11rc1_2513refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4eit
Resolution: 1.95→40.863 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4
RfactorNum. reflection% reflection
Rfree0.1869 2005 1.82 %
Rwork0.1509 --
obs0.1516 110338 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.24 Å2 / Biso mean: 34.5054 Å2 / Biso min: 10.82 Å2
Refinement stepCycle: final / Resolution: 1.95→40.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11675 0 294 821 12790
Biso mean--34.93 38.7 -
Num. residues----1573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712383
X-RAY DIFFRACTIONf_angle_d0.83516885
X-RAY DIFFRACTIONf_chiral_restr0.0521961
X-RAY DIFFRACTIONf_plane_restr0.0052240
X-RAY DIFFRACTIONf_dihedral_angle_d15.787422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.99880.28641210.229377097830100
1.9988-2.05280.23741500.203276667816100
2.0528-2.11320.24031400.193177207860100
2.1132-2.18140.24281540.179476947848100
2.1814-2.25940.2061330.165677737906100
2.2594-2.34990.21421530.156876387791100
2.3499-2.45680.20241690.151976857854100
2.4568-2.58630.20361380.155377957933100
2.5863-2.74830.2031230.155177127835100
2.7483-2.96040.22381330.155877827915100
2.9604-3.25830.16991430.156577497892100
3.2583-3.72950.20851480.139277677915100
3.7295-4.69760.13881510.118877867937100
4.6976-40.87220.14211490.14187857800699
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)
13.14810.3613-0.16843.4746-1.22913.43130.0185-0.0420.0178-0.0244-0.06830.32440.0872-0.39670.02230.1317-0.0638-0.0030.3428-0.06140.2572-23.614510.245643.88
23.5123-1.5140.02138.0629-1.18882.25540.18-0.438-0.41430.3306-0.27641.05480.2655-1.06180.08540.3071-0.14840.0890.6138-0.13840.5348-32.48024.578349.8725
32.2802-0.31871.05140.9847-0.67691.29990.1267-0.0793-0.3103-0.1114-0.01480.24040.3804-0.3625-0.06910.2573-0.12120.02470.2715-0.03430.2547-14.9345-2.208949.4096
41.6916-0.14461.1361.7962-0.48010.93310.0046-0.1564-0.03090.098-0.00470.05930.1107-0.29880.02290.1772-0.08560.0220.1895-0.02970.1983-8.03153.636950.305
55.12210.26842.09253.6183-0.65785.2294-0.0008-0.87390.23210.2878-0.02810.2396-0.3576-0.8870.00970.22450.065-0.00060.3884-0.09570.2221-10.520718.572465.2037
62.6983-0.14680.741.3541-0.32970.5097-0.2008-0.12830.27970.07510.01920.0601-0.088-0.21270.17330.188-0.0277-0.01590.1617-0.0310.2201-7.39216.514452.2346
72.19610.5760.30453.7220.25533.2124-0.13630.1141-0.0319-0.0397-0.0205-0.2878-0.01580.39850.13590.1173-0.0426-0.00680.22960.03450.170933.92339.651870.064
86.0507-3.5131.6682.088-0.91395.5025-0.28690.07440.6854-0.38920.1239-0.19-0.38110.30310.18820.232-0.082-0.06410.28760.03760.231837.777920.185775.6117
90.20770.3529-0.65742.4784-0.36953.4418-0.25660.60530.51010.0238-0.099-0.51720.09791.33450.30580.1483-0.2821-0.01940.7130.22490.407541.239719.211561.3083
103.3805-2.0240.88452.9948-0.4181.2005-0.24960.00030.4994-0.01420.0045-0.04-0.45870.23660.20770.3304-0.1234-0.07790.2130.02520.286520.648326.10660.9532
115.4936-2.3340.75151.76480.40742.81810.07470.6534-0.0398-0.3955-0.0546-0.0848-0.16891.3160.06670.2449-0.11880.02360.58530.07880.211633.258316.373552.5321
123.403-0.67521.34043.3557-0.13191.7773-0.13130.1020.39110.04930.0111-0.1103-0.22440.1360.04080.1961-0.0625-0.00490.1130.01180.121617.601314.517361.1192
132.4897-2.1823-0.3855.072.81373.4093-0.24860.36620.1821-0.05820.0808-0.0904-0.06560.2380.1690.2064-0.1044-0.00630.21540.0450.178920.580915.311253.1373
143.3234-0.0003-0.39381.2985-0.16072.378-0.1245-0.2470.37570.13030.03110.0761-0.2061-0.02340.07120.1723-0.005-0.00890.1177-0.01790.181313.950713.773971.5571
151.65350.36831.18222.24651.28535.0837-0.09930.1642-0.10040.11450.0451-0.13620.25220.33090.0630.1279-0.01540.03080.14190.01640.179924.80012.365563.8132
164.5022-1.23541.4324.01710.55733.5074-0.1321-0.3097-0.20320.1860.0230.3578-0.1168-0.29170.13250.1715-0.02530.02810.1167-0.00130.15086.75658.315567.6896
173.85331.53591.11783.70371.07573.09120.26210.0736-0.7901-0.1686-0.0773-0.26120.59270.1953-0.15540.33520.06290.02870.14310.01460.410619.3212-17.685565.4733
184.0987-0.1130.57020.74160.07630.95060.47050.139-1.1307-0.4658-0.16010.09160.81870.0816-0.22980.65210.0376-0.03880.2297-0.01510.733512.3929-26.829563.3391
191.63710.11720.21071.7508-0.5581.01850.0219-0.1227-0.53690.00840.02420.10430.4469-0.0203-0.08320.3894-0.07640.04590.20680.05050.42476.9862-19.188369.371
201.9091-0.11251.74711.8997-0.74151.93720.05660.2864-0.4997-0.45750.11750.18730.70080.0699-0.1420.4452-0.10670.01490.2427-0.07670.3522-3.4465-12.8746.9084
211.98870.21020.88542.087-1.33222.5905-0.0117-0.0434-0.2941-0.01740.04960.04260.2913-0.13830.00310.2053-0.04050.04840.1206-0.01620.25535.9503-8.361161.4773
222.2790.51692.51791.38882.14467.32990.1219-0.0585-0.17380.07290.1176-0.02630.41010.1252-0.20490.1713-0.04770.0480.11610.0050.20452.5535-3.744461.1716
232.9531-0.00590.47952.4024-0.94620.43940.08850.477-0.4933-0.33530.0224-0.01311.0353-0.0485-0.00540.3675-0.04980.0180.1808-0.08050.291812.4263-9.403155.1635
242.2644-0.67181.5193.933-0.29884.52260.08720.702-0.3562-0.4733-0.05530.02410.34880.5068-0.05320.27270.03760.0380.4462-0.13180.273820.9352-5.125542.3413
252.1974-0.43370.73792.90890.15592.36510.0959-0.0684-0.24510.0604-0.0171-0.13670.12270.1548-0.01350.1657-0.01690.03230.10340.01330.20519.285-4.550265.2589
262.8797-0.50440.99174.7111-0.80441.9838-0.06360.5764-0.0001-0.5118-0.0859-0.23040.17120.53180.15490.2025-0.05890.03540.3111-0.02580.169117.60642.780946.3033
272.9103-0.1599-1.82281.91630.82634.0408-0.1690.79010.5427-0.4814-0.23570.4239-0.8786-0.42650.37740.4738-0.0229-0.2420.34510.08010.5053-4.665232.865136.8479
281.84370.164-0.51422.04380.35150.4627-0.27030.56080.6241-0.5060.04640.3278-0.62350.09110.08080.5337-0.111-0.21220.31390.19430.4759-1.763833.673234.6793
295.78310.2512-1.00752.20920.13541.48520.07560.01320.3987-0.6035-0.029-0.0931-0.9310.6615-0.01640.8546-0.3961-0.20630.70740.38090.56045.255439.961428.8161
301.2095-1.4140.27311.8794-0.99622.1159-0.20.03610.61680.00410.2220.1453-0.80750.54320.10980.7503-0.1666-0.25450.20470.18230.77175.324643.756143.0635
311.662-0.37190.61631.4759-0.38631.6727-0.19780.260.3933-0.166-0.06040.0045-0.540.30950.26270.4027-0.1532-0.12050.26590.09370.351113.068330.167846.1449
322.1003-0.08090.24271.2806-0.17052.0361-0.22150.16160.2984-0.1040.02420.0814-0.35490.14820.15410.2478-0.0925-0.07410.1710.030.24427.621322.031148.9381
332.4951-1.08040.88113.49210.8951.947-0.16620.22060.5478-0.31250.2019-0.3223-0.23150.5445-0.10390.276-0.127-0.07160.25730.04140.29476.37722.342440.051
342.4054-0.8517-0.27782.32530.7732.4607-0.06250.48260.1136-0.22980.009-0.1643-0.03440.24960.02020.1898-0.0946-0.02920.28120.02490.18293.895112.262736.2214
352.5904-0.08890.92863.6965-1.27645.23070.1187-0.1950.01160.1776-0.10490.1725-0.2505-0.536-0.05680.16820.07420.03520.444-0.05330.2399-23.344414.541314.9938
363.88480.41870.13752.86191.23051.5950.0228-0.120.5417-0.2469-0.24790.494-0.6068-0.72690.17330.33480.1739-0.03710.5288-0.06550.3302-24.507422.364111.2078
372.1632-0.2326-1.21551.52060.12243.22110.0939-0.14080.2841-0.0019-0.12140.0756-0.4819-0.13380.02090.21090.0288-0.02840.2397-0.02710.2281-9.550120.30885.7584
380.8431-0.22071.27091.5013-3.29089.87160.011-0.018-0.01740.0052-0.0176-0.0245-0.1725-0.05160.00730.11220.00170.00180.1865-0.01480.1732-3.057613.16657.4455
393.40850.8343.8521.5771.41015.5015-0.1288-0.11080.0946-0.17140.06970.2617-0.9115-1.08560.00280.2340.08490.00960.4007-0.0050.2089-15.254510.57563.989
402.2892-0.47950.0291.7491-0.09732.25710.11360.16560.0334-0.2103-0.06920.13750.0955-0.5714-0.04470.146-0.0202-0.00340.30810.01250.1978-17.21552.1539-2.4151
413.67481.01350.65784.2959-0.02593.74470.31380.2291-0.2269-0.046-0.0876-0.2570.31040.769-0.23860.32230.23190.03850.5341-0.10410.236320.5653-15.286-17.7643
421.3151-0.8485-1.08791.3252-0.2562.25850.17110.5462-0.4663-0.4492-0.1145-0.19010.61920.4037-0.02440.47470.2435-0.01490.5619-0.16060.333318.3151-19.879-22.1332
433.6507-0.1001-0.85191.24540.2062.09880.06440.1379-0.6463-0.0062-0.0523-0.10270.61250.21870.01930.39760.0885-0.06730.2654-0.03840.29610.178-23.9786-8.2085
444.8492-0.3438-1.05811.94660.29492.18730.28610.018-0.3137-0.1131-0.14090.01510.22440.1576-0.14890.25190.0126-0.01610.2609-0.01880.15615.8839-10.8963-8.3766
456.44122.12291.92931.90141.20654.27810.15060.0764-0.0356-0.0365-0.0824-0.09320.30260.2332-0.07520.23080.05770.01380.1875-0.01090.16137.9428-13.2128-0.7431
464.3778-2.55672.22763.1486-1.62843.78140.14670.2986-0.4032-0.2538-0.04640.32470.2823-0.0729-0.09570.1754-0.00890.02560.2853-0.04460.17291.3346-7.1353-18.6376
471.9730.44350.05041.10940.38263.21460.02040.27250.0113-0.1592-0.0295-0.01050.00790.1004-0.01470.18940.02760.01920.24170.00870.12457.8655-0.825-13.429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 44 )A4 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 59 )A45 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 159 )A60 - 159
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 205 )A160 - 205
5X-RAY DIFFRACTION5chain 'A' and (resid 206 through 224 )A206 - 224
6X-RAY DIFFRACTION6chain 'A' and (resid 225 through 267 )A225 - 267
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 44 )B4 - 44
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 59 )B45 - 59
9X-RAY DIFFRACTION9chain 'B' and (resid 60 through 86 )B60 - 86
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 124 )B87 - 124
11X-RAY DIFFRACTION11chain 'B' and (resid 125 through 138 )B125 - 138
12X-RAY DIFFRACTION12chain 'B' and (resid 139 through 159 )B139 - 159
13X-RAY DIFFRACTION13chain 'B' and (resid 160 through 183 )B160 - 183
14X-RAY DIFFRACTION14chain 'B' and (resid 184 through 224 )B184 - 224
15X-RAY DIFFRACTION15chain 'B' and (resid 225 through 246 )B225 - 246
16X-RAY DIFFRACTION16chain 'B' and (resid 247 through 262 )B247 - 262
17X-RAY DIFFRACTION17chain 'C' and (resid 4 through 44 )C4 - 44
18X-RAY DIFFRACTION18chain 'C' and (resid 45 through 71 )C45 - 71
19X-RAY DIFFRACTION19chain 'C' and (resid 72 through 100 )C72 - 100
20X-RAY DIFFRACTION20chain 'C' and (resid 101 through 124 )C101 - 124
21X-RAY DIFFRACTION21chain 'C' and (resid 125 through 159 )C125 - 159
22X-RAY DIFFRACTION22chain 'C' and (resid 160 through 183 )C160 - 183
23X-RAY DIFFRACTION23chain 'C' and (resid 184 through 205 )C184 - 205
24X-RAY DIFFRACTION24chain 'C' and (resid 206 through 224 )C206 - 224
25X-RAY DIFFRACTION25chain 'C' and (resid 225 through 246 )C225 - 246
26X-RAY DIFFRACTION26chain 'C' and (resid 247 through 263 )C247 - 263
27X-RAY DIFFRACTION27chain 'D' and (resid 4 through 23 )D4 - 23
28X-RAY DIFFRACTION28chain 'D' and (resid 24 through 44 )D24 - 44
29X-RAY DIFFRACTION29chain 'D' and (resid 45 through 59 )D45 - 59
30X-RAY DIFFRACTION30chain 'D' and (resid 60 through 85 )D60 - 85
31X-RAY DIFFRACTION31chain 'D' and (resid 86 through 138 )D86 - 138
32X-RAY DIFFRACTION32chain 'D' and (resid 139 through 183 )D139 - 183
33X-RAY DIFFRACTION33chain 'D' and (resid 184 through 205 )D184 - 205
34X-RAY DIFFRACTION34chain 'D' and (resid 206 through 271 )D206 - 271
35X-RAY DIFFRACTION35chain 'E' and (resid 4 through 23 )E4 - 23
36X-RAY DIFFRACTION36chain 'E' and (resid 24 through 71 )E24 - 71
37X-RAY DIFFRACTION37chain 'E' and (resid 72 through 159 )E72 - 159
38X-RAY DIFFRACTION38chain 'E' and (resid 160 through 183 )E160 - 183
39X-RAY DIFFRACTION39chain 'E' and (resid 184 through 206 )E184 - 206
40X-RAY DIFFRACTION40chain 'E' and (resid 207 through 271 )E207 - 271
41X-RAY DIFFRACTION41chain 'F' and (resid 6 through 23 )F6 - 23
42X-RAY DIFFRACTION42chain 'F' and (resid 24 through 59 )F24 - 59
43X-RAY DIFFRACTION43chain 'F' and (resid 60 through 137 )F60 - 137
44X-RAY DIFFRACTION44chain 'F' and (resid 138 through 159 )F138 - 159
45X-RAY DIFFRACTION45chain 'F' and (resid 160 through 183 )F160 - 183
46X-RAY DIFFRACTION46chain 'F' and (resid 184 through 224 )F184 - 224
47X-RAY DIFFRACTION47chain 'F' and (resid 225 through 265 )F225 - 265

+
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