[English] 日本語
Yorodumi
- PDB-4q9n: Crystal structure of Chlamydia trachomatis enoyl-ACP reductase (F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q9n
TitleCrystal structure of Chlamydia trachomatis enoyl-ACP reductase (FabI) in complex with NADH and AFN-1252
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
Keywordsoxidoreductase/oxidoreductase inhibitor / Enoyl-ACP reductase / NADH / AFN-1252 / fatty acid synthesis / Chlamydia / oxidoreductase-oxidoreductase inhibitor complex
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-0WE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / :
Function and homology information
Biological speciesChlamydia trachomatis F/11-96 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.795 Å
AuthorsYao, J. / Abdelrahman, Y. / Robertson, R.M. / Cox, J.V. / Belland, R.J. / White, S.W. / Rock, C.O.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Type II Fatty Acid Synthesis Is Essential for the Replication of Chlamydia trachomatis.
Authors: Yao, J. / Abdelrahman, Y.M. / Robertson, R.M. / Cox, J.V. / Belland, R.J. / White, S.W. / Rock, C.O.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)264,26724
Polymers255,9248
Non-polymers8,34316
Water17,222956
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)132,13412
Polymers127,9624
Non-polymers4,1728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22080 Å2
ΔGint-155 kcal/mol
Surface area37220 Å2
MethodPISA
2
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)132,13412
Polymers127,9624
Non-polymers4,1728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22150 Å2
ΔGint-152 kcal/mol
Surface area37070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.146, 96.146, 263.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

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


Mass: 31990.541 Da / Num. of mol.: 8 / Fragment: FabI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis F/11-96 (bacteria)
Strain: D/UW-3/CX / Gene: fabI(CT104), O173_00565 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Tuner
References: UniProt: T1TQB5, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-0WE / N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)propanamide


Mass: 377.436 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C22H23N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 956 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 28% PEG300, 0.2M potassium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 6, 2014 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 218541 / Num. obs: 218541 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 20.45 Å2 / Rmerge(I) obs: 0.122 / Χ2: 1.232 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.853.40.616175000.696195.1
1.85-1.914.70.588182420.777199.1
1.91-1.9860.529184010.809199.9
1.98-2.066.90.439184240.8651100
2.06-2.157.20.362184120.919199.9
2.15-2.277.10.282183761.041199.7
2.27-2.4170.224183491.188199.6
2.41-2.66.90.181182541.093199.1
2.6-2.866.70.134181431.578198.4
2.86-3.276.30.103180501.864197.8
3.27-4.125.70.075179831.966197.3
4.12-5070.062184071.687199

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å48.07 Å
Translation2.7 Å48.07 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.1phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EN0

1en0
PDB Unreleased entry


Resolution: 1.795→38.607 Å / FOM work R set: 0.8329 / SU ML: 0.26 / σ(F): 1.36 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 10931 5.01 %Random
Rwork0.1863 ---
obs0.1884 218306 98.64 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.455 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 83.81 Å2 / Biso mean: 25.43 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1--5.2808 Å2-0 Å20 Å2
2---5.2808 Å2-0 Å2
3---10.5616 Å2
Refinement stepCycle: LAST / Resolution: 1.795→38.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17700 0 576 956 19232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618740
X-RAY DIFFRACTIONf_angle_d1.05725529
X-RAY DIFFRACTIONf_chiral_restr0.0692832
X-RAY DIFFRACTIONf_plane_restr0.0053181
X-RAY DIFFRACTIONf_dihedral_angle_d11.9036631
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 (%)
1.7949-1.81530.34183330.32616448678191
1.8153-1.83670.32933480.30876732708096
1.8367-1.8590.33343740.28646813718798
1.859-1.88260.31883600.26576932729299
1.8826-1.90740.32953700.251769287298100
1.9074-1.93350.29593590.226970097368100
1.9335-1.96110.26913710.213570417412100
1.9611-1.99040.27323490.214769487297100
1.9904-2.02150.23923820.193469467328100
2.0215-2.05460.27073740.19870337407100
2.0546-2.090.26253650.198370547419100
2.09-2.1280.24833970.193569127309100
2.128-2.1690.26683660.19869417307100
2.169-2.21320.23893440.183969937337100
2.2132-2.26140.24123790.179870127391100
2.2614-2.3140.24223500.174270027352100
2.314-2.37180.25343860.18546903728999
2.3718-2.43590.24213460.18476985733199
2.4359-2.50760.24853550.196971732699
2.5076-2.58850.25893800.19456936731699
2.5885-2.6810.23993580.19066902726099
2.681-2.78830.23163460.186922726898
2.7883-2.91520.2253730.19296875724898
2.9152-3.06880.22994000.19486787718798
3.0688-3.2610.22433600.18946858721898
3.261-3.51260.23243690.19266835720498
3.5126-3.86580.21443370.17566864720197
3.8658-4.42450.17683680.14696777714597
4.4245-5.57180.16113510.14127011736299
5.5718-38.61570.173810.16467005738699
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)
11.10940.2892-0.52011.0801-0.18370.9362-0.1599-0.0857-0.47630.02760.04490.06910.18570.00340.04360.1465-0.02150.03510.14740.07930.2223102.7552-16.538710.2064
21.9167-0.73870.26121.8499-0.09532.63750.0798-0.1733-0.3996-0.0195-0.07230.44930.1696-0.4897-0.17010.0889-0.03470.04580.15760.080.135589.4946-7.064211.8602
31.36890.19370.65360.7450.22933.4235-0.019-0.001-0.05910.00440.0310.10180.0046-0.0654-0.02010.10.00080.01160.08290.02380.0873102.12862.1820.7445
41.4258-0.3188-0.30241.4850.44581.86940.04390.1611-0.1915-0.1804-0.04650.08840.1293-0.1636-0.02910.0978-0.012-0.01490.09010.01090.1169115.3336-7.5352-3.7685
50.5813-0.01650.70790.8195-0.29841.31750.02310.20650.2365-0.10580.14560.1533-0.19040.0254-0.08570.18530.02740.02040.27220.13920.1812100.122628.8796-21.2829
61.0499-0.5161-0.01860.37050.0310.83680.13210.17650.4221-0.03240.07980.2631-0.3776-0.1175-0.08280.11020.14580.0630.16450.16330.426792.330131.9243-16.641
71.2426-0.6028-0.69141.14021.21731.70130.01380.0558-0.12790.086-0.15090.6076-0.111-0.46460.02940.14220.09410.09340.31980.10290.684877.056118.458-9.1432
81.5582-0.0702-0.47680.69350.21182.5520.02230.4546-0.0797-0.21730.0720.6138-0.0174-0.3245-0.05910.11630.0052-0.06350.32070.11570.344989.710719.4915-24.5992
90.80810.1947-0.14140.4958-0.23974.82640.04910.08750.072-0.01980.05750.0738-0.0766-0.0722-0.08730.10240.0197-0.00760.09820.02740.120599.776713.1585-8.6241
101.38180.2670.81891.17870.53971.74930.0399-0.07020.24580.0268-0.05120.0987-0.1546-0.23650.01260.08820.02770.03120.12580.03560.1541109.17626.4243-8.5412
113.5554-1.2749-0.40334.0637-2.44691.9056-0.0835-0.41950.08510.33840.0014-0.1396-0.4407-0.04280.12770.16140.02730.02820.10360.01860.0981118.540823.4719-1.5508
123.20380.8674-0.61450.2356-0.11731.77640.10920.21380.6111-0.0759-0.018-0.080.0812-0.1409-0.08190.17140.02620.04620.18130.10950.1971126.96929.3744-27.3607
131.19370.2522-0.98391.7404-0.3971.27570.15630.4120.3208-0.2828-0.0663-0.23170.0073-0.1197-0.03940.19850.03450.07640.20540.08190.239134.81626.515-32.4459
144.7702-2.4264-1.59322.23451.28665.07820.1344-0.0305-0.1438-0.04660.079-0.50270.28660.5202-0.10250.15440.04860.09150.1505-0.01710.5478153.919821.9793-23.7074
153.72851.62060.2345.0776-1.52182.8524-0.05640.19340.45770.02830.1284-0.2753-0.35990.1616-0.07290.1465-0.00110.04970.1350.02060.2086138.536134.6988-20.3101
161.2361-1.0586-0.28734.32580.47980.67420.07910.09820.0958-0.1554-0.0821-0.1644-0.0253-0.03110.01290.09960.00090.01170.11370.02460.0914133.858516.6316-13.121
170.92520.2883-0.03522.59190.90341.05840.08660.220.0537-0.1783-0.0735-0.08590.0232-0.1618-0.00230.12680.02090.02640.17730.04360.0966122.113614.7692-24.0012
182.5556-1.5087-0.23532.3867-2.58484.98650.20840.057-0.3453-0.2899-0.18480.20560.53460.1442-0.07670.16650.045-0.01970.17540.00750.0872115.1375.6827-19.5353
192.7065-0.3654-0.0210.75320.43081.6765-0.041-0.2291-0.42430.2399-0.0391-0.1532-0.00910.04670.08540.1223-0.0103-0.01660.15080.07170.2293135.8672-6.906812.4968
201.6914-0.36020.53121.23410.02531.3480.0558-0.3182-0.12970.3324-0.0699-0.3054-0.070.17640.02490.175-0.0225-0.07760.18770.04750.2025143.7757-2.240915.7149
216.09351.43551.02385.25473.58546.90610.27420.161-0.02280.04590.2132-0.6938-0.09111.1283-0.29370.1318-0.0154-0.0230.2665-0.00780.3143158.72436.19582.6269
221.4102-0.5214-0.09693.0217-1.11992.54560.0113-0.012-0.53290.0448-0.0579-0.20040.20760.26940.0190.12030.0027-0.05860.13730.02020.2569146.372-9.64332.6424
230.97820.6512-0.08264.00830.79860.56350.0218-0.06090.00890.144-0.0456-0.250.020.0030.02510.1016-0.0001-0.02450.10280.02580.1037136.21276.6692-2.6418
241.1583-0.8085-0.24222.17540.94171.32060.0036-0.1640.10820.15420.0373-0.3513-0.0738-0.0112-0.03050.13170.0042-0.04040.1430.01950.1412127.05136.169710.6897
253.8816-1.3051.07274.1486-2.31921.769-0.2202-0.07660.3140.4680.0546-0.0706-0.37320.09630.16270.1822-0.0293-0.02390.14710.01680.0896117.424613.23938.0928
260.9948-0.5013-0.45471.76770.24730.8289-0.0538-0.3443-0.25270.24530.04940.23680.2017-0.0433-0.06810.1811-0.03550.01260.26310.12320.210752.061719.190540.3116
270.96190.4146-0.00550.55250.08730.56210.0856-0.197-0.37130.08660.04990.31060.2769-0.1805-0.04880.1127-0.1658-0.04230.16850.18870.440444.215816.159735.5954
280.46920.44790.8811.5991.93392.67290.1772-0.2340.1413-0.1133-0.27140.75040.1872-0.64380.04690.1537-0.0611-0.09030.33070.09640.695729.096529.724128.3786
292.5849-0.17460.20111.20240.50922.6372-0.0745-0.6234-0.14680.3150.04680.59630.1891-0.40360.05550.1334-0.00510.05650.30510.07950.297241.635828.658343.5667
300.7954-0.046-0.00420.6262-0.00784.20740.0334-0.0762-0.06160.03670.03880.06850.076-0.1497-0.07040.0871-0.01830.00960.10050.02680.104251.706534.951127.58
311.4584-0.2943-0.92571.18790.78041.9103-0.01380.0802-0.2483-0.0342-0.05780.13870.1306-0.23580.0540.0967-0.0212-0.02840.11460.03470.161561.09421.714327.4906
322.58681.19470.53052.5714-2.20053.0689-0.16970.279-0.0394-0.32390.0901-0.14080.50080.04260.13190.1875-0.0232-0.00090.11350.02250.108570.536224.672220.5361
333.0922-1.09430.80281.39640.24480.6316-0.03910.2920.431-0.01120.1471-0.178-0.0540.0262-0.11990.1284-0.02020.00240.13960.06840.159160.904360.86186.2894
340.4208-0.43330.4741.3781-0.35480.9729-0.17190.10190.5684-0.02390.06480.0928-0.1434-0.02970.04250.1430.0073-0.03770.14950.08760.290152.954165.76749.3992
356.8001-2.7838-2.16286.60411.86815.83630.1758-0.04560.56070.2112-0.11090.54-0.323-0.77970.04450.1450.03190.0420.27260.03830.375334.018456.25313.1276
362.60480.7275-0.98652.3842-0.28584.2102-0.11940.63070.3904-0.4030.00280.3328-0.1366-0.20610.11470.16820.019-0.040.20580.04560.167249.548153.96620.5261
371.2144-0.1675-0.64160.66530.27433.1557-0.02710.03660.0656-0.02760.01760.09660.0364-0.05580.00350.1025-0.0021-0.00840.08120.02220.081654.068245.919818.2012
381.47680.52290.21181.50460.37772.15180.072-0.09510.27170.124-0.03160.0424-0.2044-0.1987-0.05530.08890.02250.00420.09980.01480.142565.736756.746920.7065
393.6171-0.67-0.12233.008-1.16394.7003-0.0177-0.2912-0.05720.4790.01950.0894-0.21280.25910.01050.14540.00380.01410.10810.01480.111572.694251.813729.5582
403.64871.071-0.50251.370.78382.4076-0.04920.16050.2351-0.1978-0.0742-0.3303-0.0748-0.02670.09540.11140.00540.02620.14550.06490.15387.158153.93425.0762
413.3586-2.69271.93855.40990.54082.59980.2230.39060.0599-0.3824-0.0534-0.20810.03270.4133-0.15410.1217-0.00940.07760.15990.03480.2697101.134147.51074.015
421.59370.83250.29341.3055-0.5954.8660.01570.34250.1279-0.24280.0114-0.0945-0.20340.3394-0.03470.17150.05350.10110.19450.04890.227196.281351.27142.7318
435.654-1.8307-1.38025.91562.63457.32060.2904-0.23780.0112-0.09460.0688-0.79390.15661.0251-0.30920.12950.02590.00230.2388-0.02590.3555110.635841.931216.2081
442.47341.04740.19921.6143-0.87251.971-0.00340.03380.515-0.0674-0.0456-0.3024-0.20850.1680.0380.1201-0.00730.04850.13140.03640.283798.368457.63916.2716
450.6367-0.57040.08074.48210.68520.52320.01330.0508-0.0538-0.1441-0.032-0.1613-0.0070.00660.01750.083-0.00510.02010.10560.02020.116888.1441.404221.5904
461.2531.05150.35432.91961.68421.3761-0.00730.1751-0.1643-0.15750.0563-0.36260.0434-0.0384-0.03460.1402-0.00370.03690.14960.02250.150579.469139.41766.6872
471.37711.31810.65154.08431.21611.24140.02190.0229-0.00550.06060.065-0.02040.10540.0131-0.08840.11230.0240.01180.14960.02080.101871.826842.637613.0158
481.1401-0.5765-0.36290.5526-0.25460.91340.0132-0.1573-0.39160.05860.01620.08690.0121-0.1126-0.01870.1368-0.03-0.05360.16790.11320.275278.868118.723246.3034
491.0523-0.13240.34151.5544-0.03340.81520.1488-0.329-0.17260.2366-0.0015-0.29870.029-0.0445-0.00150.1839-0.036-0.09020.18370.09730.178286.731321.569951.3843
503.55142.53571.25612.63710.93485.62090.0260.10680.08930.06510.087-0.4617-0.39010.4882-0.08650.1484-0.0097-0.08140.14020.00530.5321105.822826.092342.6122
513.318-1.6569-0.85214.2981-0.94552.6846-0.0411-0.1561-0.4719-0.02690.1528-0.07790.22740.2063-0.10620.12950.0033-0.05260.14290.03690.252590.435413.456239.3015
521.16461.12770.12234.10440.39840.66030.0648-0.1006-0.11890.1278-0.0808-0.10520.0219-0.03890.01220.09480.0029-0.01980.10090.02570.100785.784231.475232.045
530.92810.0020.04413.08480.96340.36910.1117-0.1735-0.03610.199-0.1047-0.05510.0057-0.11520.00330.138-0.0225-0.02570.1610.0460.098773.97133.093942.8887
543.51081.19120.79562.4846-2.96825.22520.087-0.13520.4150.2863-0.1360.098-0.31060.16610.00930.1439-0.03820.00890.13420.0120.081867.084242.39338.4662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:84)A2 - 84
2X-RAY DIFFRACTION2chain 'A' and (resseq 85:125)A85 - 125
3X-RAY DIFFRACTION3chain 'A' and (resseq 126:214)A126 - 214
4X-RAY DIFFRACTION4chain 'A' and (resseq 215:295)A215 - 295
5X-RAY DIFFRACTION5chain 'B' and (resseq 2:21)B2 - 21
6X-RAY DIFFRACTION6chain 'B' and (resseq 22:84)B22 - 84
7X-RAY DIFFRACTION7chain 'B' and (resseq 85:105)B85 - 105
8X-RAY DIFFRACTION8chain 'B' and (resseq 106:125)B106 - 125
9X-RAY DIFFRACTION9chain 'B' and (resseq 126:214)B126 - 214
10X-RAY DIFFRACTION10chain 'B' and (resseq 215:277)B215 - 277
11X-RAY DIFFRACTION11chain 'B' and (resseq 278:295)B278 - 295
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:21)C2 - 21
13X-RAY DIFFRACTION13chain 'C' and (resseq 22:84)C22 - 84
14X-RAY DIFFRACTION14chain 'C' and (resseq 85:105)C85 - 105
15X-RAY DIFFRACTION15chain 'C' and (resseq 106:125)C106 - 125
16X-RAY DIFFRACTION16chain 'C' and (resseq 126:214)C126 - 214
17X-RAY DIFFRACTION17chain 'C' and (resseq 215:277)C215 - 277
18X-RAY DIFFRACTION18chain 'C' and (resseq 278:295)C278 - 295
19X-RAY DIFFRACTION19chain 'D' and (resseq 2:21)D2 - 21
20X-RAY DIFFRACTION20chain 'D' and (resseq 22:84)D22 - 84
21X-RAY DIFFRACTION21chain 'D' and (resseq 85:105)D85 - 105
22X-RAY DIFFRACTION22chain 'D' and (resseq 106:125)D106 - 125
23X-RAY DIFFRACTION23chain 'D' and (resseq 126:214)D126 - 214
24X-RAY DIFFRACTION24chain 'D' and (resseq 215:277)D215 - 277
25X-RAY DIFFRACTION25chain 'D' and (resseq 278:295)D278 - 295
26X-RAY DIFFRACTION26chain 'E' and (resseq 2:21)E2 - 21
27X-RAY DIFFRACTION27chain 'E' and (resseq 22:84)E22 - 84
28X-RAY DIFFRACTION28chain 'E' and (resseq 85:105)E85 - 105
29X-RAY DIFFRACTION29chain 'E' and (resseq 106:125)E106 - 125
30X-RAY DIFFRACTION30chain 'E' and (resseq 126:214)E126 - 214
31X-RAY DIFFRACTION31chain 'E' and (resseq 215:277)E215 - 277
32X-RAY DIFFRACTION32chain 'E' and (resseq 278:295)E278 - 295
33X-RAY DIFFRACTION33chain 'F' and (resseq 2:21)F2 - 21
34X-RAY DIFFRACTION34chain 'F' and (resseq 22:84)F22 - 84
35X-RAY DIFFRACTION35chain 'F' and (resseq 85:105)F85 - 105
36X-RAY DIFFRACTION36chain 'F' and (resseq 106:125)F106 - 125
37X-RAY DIFFRACTION37chain 'F' and (resseq 126:214)F126 - 214
38X-RAY DIFFRACTION38chain 'F' and (resseq 215:277)F215 - 277
39X-RAY DIFFRACTION39chain 'F' and (resseq 278:295)F278 - 295
40X-RAY DIFFRACTION40chain 'G' and (resseq 2:35)G2 - 35
41X-RAY DIFFRACTION41chain 'G' and (resseq 36:54)G36 - 54
42X-RAY DIFFRACTION42chain 'G' and (resseq 55:84)G55 - 84
43X-RAY DIFFRACTION43chain 'G' and (resseq 85:105)G85 - 105
44X-RAY DIFFRACTION44chain 'G' and (resseq 106:125)G106 - 125
45X-RAY DIFFRACTION45chain 'G' and (resseq 126:214)G126 - 214
46X-RAY DIFFRACTION46chain 'G' and (resseq 215:266)G215 - 266
47X-RAY DIFFRACTION47chain 'G' and (resseq 267:295)G267 - 295
48X-RAY DIFFRACTION48chain 'H' and (resseq 2:21)H2 - 21
49X-RAY DIFFRACTION49chain 'H' and (resseq 22:84)H22 - 84
50X-RAY DIFFRACTION50chain 'H' and (resseq 85:105)H85 - 105
51X-RAY DIFFRACTION51chain 'H' and (resseq 106:125)H106 - 125
52X-RAY DIFFRACTION52chain 'H' and (resseq 126:214)H126 - 214
53X-RAY DIFFRACTION53chain 'H' and (resseq 215:277)H215 - 277
54X-RAY DIFFRACTION54chain 'H' and (resseq 278:295)H278 - 295

+
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