[English] 日本語
Yorodumi
- PDB-7k6c: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k6c
TitleCrystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium abscessus ATCC 19977 / DSM 44196 with NADP and inhibitor P218
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / SSGCID / SDDC / inhibitor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-MMV / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Santhakumar, V. / Walpole, C. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
CitationJournal: J.Med.Chem. / Year: 2024
Title: Rational Exploration of 2,4-Diaminopyrimidines as DHFR Inhibitors Active against Mycobacterium abscessus and Mycobacterium avium , Two Emerging Human Pathogens.
Authors: Andrade Meirelles, M. / Almeida, V.M. / Sullivan, J.R. / de Toledo, I. / Dos Reis, C.V. / Cunha, M.R. / Zigweid, R. / Shim, A. / Sankaran, B. / Woodward, E.L. / Seibold, S. / Liu, L. / Mian, ...Authors: Andrade Meirelles, M. / Almeida, V.M. / Sullivan, J.R. / de Toledo, I. / Dos Reis, C.V. / Cunha, M.R. / Zigweid, R. / Shim, A. / Sankaran, B. / Woodward, E.L. / Seibold, S. / Liu, L. / Mian, M.R. / Battaile, K.P. / Riley, J. / Duncan, C. / Simeons, F.R.C. / Ferguson, L. / Joji, H. / Read, K.D. / Lovell, S. / Staker, B.L. / Behr, M.A. / Pilli, R.A. / Counago, R.M.
History
DepositionSep 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
C: Dihydrofolate reductase
D: Dihydrofolate reductase
E: Dihydrofolate reductase
F: Dihydrofolate reductase
G: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,81031
Polymers130,5517
Non-polymers8,25924
Water15,331851
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7944
Polymers18,6501
Non-polymers1,1443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8966
Polymers18,6501
Non-polymers1,2465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8565
Polymers18,6501
Non-polymers1,2064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8164
Polymers18,6501
Non-polymers1,1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8164
Polymers18,6501
Non-polymers1,1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8164
Polymers18,6501
Non-polymers1,1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8164
Polymers18,6501
Non-polymers1,1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.630, 62.490, 124.550
Angle α, β, γ (deg.)90.000, 94.670, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 12 or resid 14...
21(chain B and (resid 4 through 12 or resid 14...
31(chain C and (resid 4 through 12 or resid 14...
41(chain D and (resid 4 through 12 or resid 14...
51(chain E and (resid 4 through 12 or resid 14...
61(chain F and (resid 4 through 12 or resid 14...
71(chain G and (resid 4 through 12 or resid 14...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 12 or resid 14...A4 - 12
121(chain A and (resid 4 through 12 or resid 14...A14 - 30
131(chain A and (resid 4 through 12 or resid 14...A32 - 35
141(chain A and (resid 4 through 12 or resid 14...A3 - 200
151(chain A and (resid 4 through 12 or resid 14...A3 - 200
161(chain A and (resid 4 through 12 or resid 14...A3 - 200
171(chain A and (resid 4 through 12 or resid 14...A3 - 200
181(chain A and (resid 4 through 12 or resid 14...A3 - 200
191(chain A and (resid 4 through 12 or resid 14...A3 - 200
211(chain B and (resid 4 through 12 or resid 14...B4 - 12
221(chain B and (resid 4 through 12 or resid 14...B14 - 19
231(chain B and (resid 4 through 12 or resid 14...B20
241(chain B and (resid 4 through 12 or resid 14...B3 - 200
251(chain B and (resid 4 through 12 or resid 14...B3 - 200
261(chain B and (resid 4 through 12 or resid 14...B3 - 200
271(chain B and (resid 4 through 12 or resid 14...B3 - 200
311(chain C and (resid 4 through 12 or resid 14...C4 - 12
321(chain C and (resid 4 through 12 or resid 14...C14 - 19
331(chain C and (resid 4 through 12 or resid 14...C20
341(chain C and (resid 4 through 12 or resid 14...C3 - 200
351(chain C and (resid 4 through 12 or resid 14...C3 - 200
361(chain C and (resid 4 through 12 or resid 14...C3 - 200
371(chain C and (resid 4 through 12 or resid 14...C3 - 200
411(chain D and (resid 4 through 12 or resid 14...D4 - 12
421(chain D and (resid 4 through 12 or resid 14...D14 - 19
431(chain D and (resid 4 through 12 or resid 14...D4 - 200
441(chain D and (resid 4 through 12 or resid 14...D4 - 200
451(chain D and (resid 4 through 12 or resid 14...D4 - 200
461(chain D and (resid 4 through 12 or resid 14...D4 - 200
471(chain D and (resid 4 through 12 or resid 14...D4 - 200
481(chain D and (resid 4 through 12 or resid 14...D4 - 200
511(chain E and (resid 4 through 12 or resid 14...E4 - 12
521(chain E and (resid 4 through 12 or resid 14...E14 - 19
531(chain E and (resid 4 through 12 or resid 14...E20
541(chain E and (resid 4 through 12 or resid 14...E3 - 200
551(chain E and (resid 4 through 12 or resid 14...E3 - 200
561(chain E and (resid 4 through 12 or resid 14...E3 - 200
571(chain E and (resid 4 through 12 or resid 14...E3 - 200
611(chain F and (resid 4 through 12 or resid 14...F4 - 12
621(chain F and (resid 4 through 12 or resid 14...F14 - 19
631(chain F and (resid 4 through 12 or resid 14...F20
641(chain F and (resid 4 through 12 or resid 14...F3 - 200
651(chain F and (resid 4 through 12 or resid 14...F3 - 200
661(chain F and (resid 4 through 12 or resid 14...F3 - 200
671(chain F and (resid 4 through 12 or resid 14...F3 - 200
711(chain G and (resid 4 through 12 or resid 14...G4 - 12
721(chain G and (resid 4 through 12 or resid 14...G14 - 19
731(chain G and (resid 4 through 12 or resid 14...G20
741(chain G and (resid 4 through 12 or resid 14...G3 - 200
751(chain G and (resid 4 through 12 or resid 14...G3 - 200
761(chain G and (resid 4 through 12 or resid 14...G3 - 200
771(chain G and (resid 4 through 12 or resid 14...G3 - 200

-
Components

-
Protein , 1 types, 7 molecules ABCDEFG

#1: Protein
Dihydrofolate reductase


Mass: 18650.094 Da / Num. of mol.: 7 / Mutation: C84S, E141T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: MAB_3090c / Plasmid: MyabA.01062.a.B15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B1MD46, dihydrofolate reductase

-
Non-polymers , 5 types, 875 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MMV / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid


Mass: 360.408 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H24N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Optimization screen based on Microlytics MCSG1 B6: 200mM CaOAc2, 20% (w/V) PEG 8000, 100mM MES / NaOH pH 6.5: MyabA.01062.a.B15.PS38597 at 12.39mg/ml + 3.5mM NADP + 3mM P218: tray 317391 F7: ...Details: Optimization screen based on Microlytics MCSG1 B6: 200mM CaOAc2, 20% (w/V) PEG 8000, 100mM MES / NaOH pH 6.5: MyabA.01062.a.B15.PS38597 at 12.39mg/ml + 3.5mM NADP + 3mM P218: tray 317391 F7: cryo 20% EG + compounds: puck kdu7-5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→37.69 Å / Num. obs: 78407 / % possible obs: 99.7 % / Redundancy: 3.737 % / Biso Wilson estimate: 31.922 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.084 / Χ2: 0.911 / Net I/σ(I): 13.87 / Num. measured all: 292968 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.053.2830.5452.2418775575757180.760.65399.3
2.05-2.113.730.4922.9120977563156240.850.57599.9
2.11-2.173.7870.3743.7520693547254640.9140.43699.9
2.17-2.243.7860.314.5320205534753370.9310.36199.8
2.24-2.313.7850.2685.2919478515651460.9490.31299.8
2.31-2.393.7950.2246.218928499449880.9630.26199.9
2.39-2.483.7920.1957.0118246482348120.970.22799.8
2.48-2.583.7990.1538.717580463346280.9820.17899.9
2.58-2.73.7910.13110.0816895446744570.9860.15299.8
2.7-2.833.7960.10912.0216126425942480.990.12799.7
2.83-2.983.7910.08414.9515485409540850.9940.09899.8
2.98-3.163.7920.06418.7214507383238260.9960.07599.8
3.16-3.383.780.0522.9813590360235950.9970.05899.8
3.38-3.653.7760.04127.7512732338733720.9980.04899.6
3.65-43.760.03432.2511659311231010.9980.03999.6
4-4.473.7570.02837.2410596282628200.9990.03399.8
4.47-5.163.7520.02737.99332249524870.9990.03299.7
5.16-6.323.7210.0334.667929213621310.9990.03699.8
6.32-8.943.6770.02638.416071165716510.9990.0399.6
8.94-37.693.450.02343.731649449170.9990.02797.1

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2w3v as per MORDA

2w3v


Resolution: 2→37.69 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 2082 2.66 %0
Rwork0.1655 76298 --
obs0.1666 78380 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.19 Å2 / Biso mean: 30.7549 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: final / Resolution: 2→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8374 0 546 853 9773
Biso mean--27.1 35.24 -
Num. residues----1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079294
X-RAY DIFFRACTIONf_angle_d0.93112771
X-RAY DIFFRACTIONf_dihedral_angle_d15.6943467
X-RAY DIFFRACTIONf_chiral_restr0.0571389
X-RAY DIFFRACTIONf_plane_restr0.0081759
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4335X-RAY DIFFRACTION4.878TORSIONAL
12B4335X-RAY DIFFRACTION4.878TORSIONAL
13C4335X-RAY DIFFRACTION4.878TORSIONAL
14D4335X-RAY DIFFRACTION4.878TORSIONAL
15E4335X-RAY DIFFRACTION4.878TORSIONAL
16F4335X-RAY DIFFRACTION4.878TORSIONAL
17G4335X-RAY DIFFRACTION4.878TORSIONAL
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 (%)
2-2.050.24571460.21855017516399
2.05-2.10.29391330.215150495182100
2.1-2.150.26661410.206650685209100
2.15-2.220.22621280.193450475175100
2.22-2.290.25891480.190150815229100
2.29-2.370.2541350.185650305165100
2.37-2.470.22241270.187650835210100
2.47-2.580.25791190.180151075226100
2.58-2.710.22031640.185850825246100
2.71-2.880.21651340.173950635197100
2.88-3.110.21651420.170250735215100
3.11-3.420.21641470.163651125259100
3.42-3.910.1541410.143551225263100
3.91-4.930.15781510.123151115262100
4.93-37.690.20681260.15835253537999
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)
13.3229-1.035-0.13323.034-0.48780.10920.044-0.74010.0275-0.02990.32220.10940.0160.1938-0.1520.13780.04190.01160.65460.01340.24858.4322-2.874850.914
21.658-0.6003-0.01910.3975-0.35231.6354-0.0682-1.83060.4222-0.03830.29960.20730.0617-0.405-0.24470.2241-0.00230.1031.1448-0.01910.25843.6925-0.495358.6136
36.5442-3.0984-1.75394.45671.62733.1667-0.2213-1.7567-0.70070.9338-0.17330.91540.2860.3670.23590.2928-0.02650.05490.67040.13970.5-8.5721-5.788356.6692
40.9441-0.21330.07250.82090.06931.31920.012-0.7725-0.6180.12070.0408-0.09840.1582-0.1966-0.05930.2099-0.0369-0.03870.50230.19050.33740.2045-8.922547.8019
51.3398-0.7471-0.33081.8098-0.0653.33980.1726-1.0684-0.0383-0.04610.1654-0.23940.0555-0.214-0.11150.17090.0192-0.03020.6327-0.02050.212714.6829-3.773153.3677
62.2823-1.4281-3.77953.61791.10576.8106-0.2308-1.33730.82820.34780.1894-0.1877-0.556-0.0812-0.38990.33890.1004-0.02140.9488-0.43590.667717.579.726560.4736
72.3287-0.7009-1.04184.26740.61065.23730.2694-0.69990.8962-0.14850.1444-0.3421-0.54720.0951-0.84320.1890.04640.01170.4236-0.16770.337815.1383.021949.2643
84.23970.20450.15121.9242-1.33944.8941-0.04440.2147-0.0603-0.05470.0010.0606-0.12980.00520.04770.14930.0175-0.00820.0601-0.01730.1721-16.326-8.03710.691
97.2606-0.68154.65084.3121-2.08564.0466-0.162-0.11080.6934-0.0031-0.02370.2178-0.2889-0.12980.18130.1513-0.0172-0.00010.0872-0.00450.2366-11.16792.68523.4897
103.8914-0.01560.54883.7192-0.39193.6611-0.07930.18280.1114-0.12250.0035-0.11460.03250.15730.07150.1166-0.0041-0.00960.08560.00210.1263-1.972-8.20194.0767
112.2064-0.23260.64754.0190.40192.4116-0.0638-0.0154-0.2203-0.42840.2079-0.33960.38190.07470.02780.26220.01910.05090.19160.00580.27493.855-18.74884.8006
124.3303-0.6247-0.05992.4471-0.04872.8511-0.1412-0.4213-0.15670.06010.06830.14640.1288-0.15220.07390.17450.00720.0010.11560.00820.1384-7.6973-13.122213.0291
132.9609-0.377-0.86112.26580.37193.50630.00150.0704-0.36620.02530.0630.20.1009-0.2457-0.06770.13570.0054-0.00350.15730.03190.2333-21.5086-8.67086.3017
143.7275-0.1711-2.82362.1135-0.75477.31770.41240.19970.2302-0.05680.0270.2463-0.6932-0.0822-0.2960.27510.06490.0170.23370.04340.3139-24.32624.2693-1.7306
154.05730.2649-1.0313.4152-1.00875.78990.1894-0.46990.11860.29650.14940.1322-0.1746-0.3632-0.21010.19110.0337-0.01260.18990.0120.2525-22.5788-1.149310.1165
163.41360.83350.73734.10551.07653.28760.0316-0.12740.2550.20610.1101-0.4036-0.01820.2525-0.13010.1486-0.00470.00260.2091-0.08480.2403-32.34220.084756.4319
172.67030.38412.23652.85550.64894.7232-0.0012-0.44580.46990.1637-0.09930.20790.0326-0.350.04480.16010.00230.05810.2802-0.08160.2781-46.1469-0.0355.3502
183.9863-0.39680.60978.4261-1.83974.190.2423-0.13650.0314-0.1193-0.3760.03710.319-0.06630.0670.1955-0.0335-0.00030.2398-0.03690.1929-48.2008-9.123449.7194
193.8674-0.9209-0.21162.9147-0.08763.4575-0.0567-0.28380.00840.25-0.0438-0.05870.11720.04980.08560.1516-0.0291-0.0250.12270.00450.155220.0563-23.971634.2891
203.1119-0.21360.43914.11581.1455.10880.0278-0.05260.0421-0.0821-0.01860.04660.0473-0.17560.00330.1083-0.0183-0.00070.095-0.00250.11725.9069-24.951527.0443
213.8908-1.0261.35695.04910.16471.8844-0.16580.14540.3461-0.06140.10590.0082-0.2454-0.14160.06120.14830.0009-0.01860.15410.02810.15699.5991-16.08122.0697
223.972-0.15991.16673.8361-0.24975.493-0.06270.073-0.04540.0175-0.0784-0.13710.02870.11980.15410.0682-0.0190.03170.13220.00860.170722.8606-23.389726.5748
232.8560.77930.02091.38050.07793.92980.018-0.15410.06640.08190.0311-0.1390.0155-0.0412-0.03540.19220.0179-0.01150.1718-0.00440.239129.8255-19.674736.0714
244.8612-0.9266-0.0171.51920.86086.52710.10920.31270.4461-0.097-0.0202-0.1058-0.45050.292-0.07520.1594-0.0337-0.03740.1302-0.0030.232427.7976-13.886231.9518
255.7076-2.08660.72765.896-0.2144.01360.01740.24750.30160.13040.0253-0.3394-0.01180.44120.11560.1628-0.00510.00040.19080.07350.238933.0422-3.11926.8551
263.7058-1.67271.0133.2224-0.79722.72210.05450.2207-0.3186-0.16980.02520.24080.20910.1052-0.10580.2015-0.0055-0.00410.14410.03470.241625.5167-10.13293.3045
272.0190.5076-1.13462.52730.48921.5673-0.15790.6770.7512-0.39030.18470.83160.1693-0.29910.06010.3589-0.0948-0.09890.33880.17530.502313.22040.2349-4.6744
285.0257-2.83951.6715.92991.63832.885-0.2380.16690.3640.02210.149-0.0955-0.02380.26490.08920.1787-0.0247-0.01720.20650.10570.268324.85243.26944.7028
295.01110.29790.75725.0039-0.68315.7685-0.10020.7622-0.0667-0.2916-0.1004-0.32580.32290.48580.14630.16460.00920.04790.32090.03870.209637.0842-7.42322.3717
303.4290.60651.56944.0457-1.57016.9283-0.35350.73720.637-0.1950.3223-0.1514-0.33340.7419-0.06080.256-0.02570.02720.28870.06630.340542.11292.66247.5347
315.42262.92111.49846.51421.64412.75650.20460.0054-0.8431-0.1587-0.2283-0.09380.1325-0.11380.05970.28340.07290.03610.30040.03290.405542.1985-17.60799.8127
324.6612-1.64790.34757.8494-1.42984.3447-0.0203-0.11630.21920.1821-0.199-0.1177-0.34990.45890.12770.18470.02020.01570.27490.02450.22839.9379-6.031411.7487
334.2464-0.25961.49551.654-1.14674.46320.013-0.07390.0899-0.01040.05550.2504-0.0722-0.0966-0.06750.1611-0.01550.02130.0763-0.03820.144-0.737918.504522.4072
347.7021-1.144.99253.7316-2.72284.31810.30640.141-0.50410.0104-0.03330.4120.4523-0.0857-0.18020.2299-0.04660.03250.163-0.01020.203-4.27836.891922.9922
352.87980.44080.40422.0841-0.73512.44880.087-0.3639-0.0230.2438-0.04160.0923-0.1185-0.0379-0.04020.199-0.00370.01190.13510.00020.13171.775714.4534.5979
360.5249-0.52740.84753.23770.65523.5920.02810.21730.0565-0.22910.0008-0.1570.0970.59320.07410.18110.00180.03350.261-0.00710.1733.448914.902515.5632
373.83341.40750.90961.5267-0.25823.26340.084-0.1896-0.4888-0.183-0.0419-0.15360.55970.2003-0.0580.23340.11760.01940.2364-0.00370.2509-28.7447-26.057331.6852
382.73720.80381.9370.84550.1352.511-0.11210.0357-0.42030.01290.2588-0.15030.07750.7131-0.02670.20310.13970.02650.4023-0.00530.2548-19.5043-21.109129.4216
392.23091.11930.19050.9136-0.0552.01170.15590.1364-0.552-0.1996-0.106-0.25880.50740.869-0.02410.29330.2224-0.00030.7093-0.03310.3137-12.8436-22.946631.5777
402.9204-1.02982.39643.2134-0.84511.96790.0219-0.4824-0.57780.12870.1137-0.42450.4970.6595-0.26040.38020.1937-0.0510.81190.13860.3954-9.3735-25.583844.3986
414.42870.15252.42780.92280.23431.7658-0.2036-0.47660.21110.1133-0.07-0.1081-0.07550.67990.27330.19010.03340.01190.54080.0140.2457-16.8007-14.159339.7587
426.35011.30221.45584.6820.35924.12840.128-1.05330.00990.4147-0.19750.05370.29450.23-0.00590.23470.05940.010.4585-0.03330.2291-26.0787-19.085242.7892
435.4262-0.4114-0.13225.86780.82445.53260.13740.28420.4163-0.534-0.1605-0.0691-0.05120.2970.09140.17470.06910.01780.3028-0.00630.206-31.6407-17.93730.4828
443.6687-2.02680.0834.3203-1.09414.5746-0.0094-0.4371-0.53380.1395-0.0680.24340.517-0.17930.05980.2299-0.02830.01880.26480.00830.3295-34.7908-26.251937.2694
453.8083-0.7788-1.03361.77910.66494.18950.00920.4599-0.1634-0.33250.0676-0.03960.1740.09160.11740.21580.0013-0.00190.2447-0.01540.2288-36.2969-20.589122.6297
464.7549-2.2909-2.10546.13553.35938.35030.1372-0.16520.2969-0.08860.04570.0764-0.424-0.0162-0.13340.21580.0210.01520.1951-0.01150.2084-35.054-15.13928.4432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 12 )A3 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 52 )A13 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 79 )A53 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 111 )A80 - 111
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 140 )A112 - 140
6X-RAY DIFFRACTION6chain 'A' and (resid 141 through 152 )A141 - 152
7X-RAY DIFFRACTION7chain 'A' and (resid 153 through 161 )A153 - 161
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 27 )B3 - 27
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 38 )B28 - 38
10X-RAY DIFFRACTION10chain 'B' and (resid 39 through 68 )B39 - 68
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 79 )B69 - 79
12X-RAY DIFFRACTION12chain 'B' and (resid 80 through 111 )B80 - 111
13X-RAY DIFFRACTION13chain 'B' and (resid 112 through 139 )B112 - 139
14X-RAY DIFFRACTION14chain 'B' and (resid 140 through 152 )B140 - 152
15X-RAY DIFFRACTION15chain 'B' and (resid 153 through 162 )B153 - 162
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 111 )C3 - 111
17X-RAY DIFFRACTION17chain 'C' and (resid 112 through 139 )C112 - 139
18X-RAY DIFFRACTION18chain 'C' and (resid 140 through 161 )C140 - 161
19X-RAY DIFFRACTION19chain 'D' and (resid 4 through 38 )D4 - 38
20X-RAY DIFFRACTION20chain 'D' and (resid 39 through 79 )D39 - 79
21X-RAY DIFFRACTION21chain 'D' and (resid 80 through 101 )D80 - 101
22X-RAY DIFFRACTION22chain 'D' and (resid 102 through 130 )D102 - 130
23X-RAY DIFFRACTION23chain 'D' and (resid 131 through 152 )D131 - 152
24X-RAY DIFFRACTION24chain 'D' and (resid 153 through 162 )D153 - 162
25X-RAY DIFFRACTION25chain 'E' and (resid 3 through 12 )E3 - 12
26X-RAY DIFFRACTION26chain 'E' and (resid 13 through 68 )E13 - 68
27X-RAY DIFFRACTION27chain 'E' and (resid 69 through 79 )E69 - 79
28X-RAY DIFFRACTION28chain 'E' and (resid 80 through 111 )E80 - 111
29X-RAY DIFFRACTION29chain 'E' and (resid 112 through 130 )E112 - 130
30X-RAY DIFFRACTION30chain 'E' and (resid 131 through 139 )E131 - 139
31X-RAY DIFFRACTION31chain 'E' and (resid 140 through 152 )E140 - 152
32X-RAY DIFFRACTION32chain 'E' and (resid 153 through 161 )E153 - 161
33X-RAY DIFFRACTION33chain 'F' and (resid 3 through 27 )F3 - 27
34X-RAY DIFFRACTION34chain 'F' and (resid 28 through 38 )F28 - 38
35X-RAY DIFFRACTION35chain 'F' and (resid 39 through 121 )F39 - 121
36X-RAY DIFFRACTION36chain 'F' and (resid 122 through 161 )F122 - 161
37X-RAY DIFFRACTION37chain 'G' and (resid 3 through 27 )G3 - 27
38X-RAY DIFFRACTION38chain 'G' and (resid 28 through 52 )G28 - 52
39X-RAY DIFFRACTION39chain 'G' and (resid 53 through 68 )G53 - 68
40X-RAY DIFFRACTION40chain 'G' and (resid 69 through 79 )G69 - 79
41X-RAY DIFFRACTION41chain 'G' and (resid 80 through 101 )G80 - 101
42X-RAY DIFFRACTION42chain 'G' and (resid 102 through 111 )G102 - 111
43X-RAY DIFFRACTION43chain 'G' and (resid 112 through 121 )G112 - 121
44X-RAY DIFFRACTION44chain 'G' and (resid 122 through 136 )G122 - 136
45X-RAY DIFFRACTION45chain 'G' and (resid 137 through 151 )G137 - 151
46X-RAY DIFFRACTION46chain 'G' and (resid 152 through 162 )G152 - 162

+
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://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