[English] 日本語
Yorodumi
- PDB-3ibb: Propionyl-CoA Carboxylase Beta Subunit, D422A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ibb
TitlePropionyl-CoA Carboxylase Beta Subunit, D422A
ComponentsPropionyl-CoA carboxylase complex B subunit
KeywordsBIOSYNTHETIC PROTEIN / ACCase / PCCase / ACC / PCC / Propionyl-CoA / CT / Carboxyltransferase / Polyketide / Fatty Acid / PKS / FAS / Polyketide Synthase / Fatty Acid Synthase / Carboxylase / beta subunit / PccB / Acyl-CoA / Acyl-CoA C arboxylase / Streptomces / Streptomyces coelicolor / Biotin
Function / homology
Function and homology information


propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / fatty acid biosynthetic process
Similarity search - Function
Acetyl-CoA carboxylase carboxyl transferase, beta subunit / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Acetyl-CoA carboxylase carboxyl transferase, beta subunit / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Propionyl-CoA carboxylase complex B subunit
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsDiacovich, L. / Arabolaza, A. / Shillito, E.M. / Lin, T.-W. / Mitchell, D.L. / Pham, H. / Melgar, M.M.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal structures and mutational analyses of acyl-CoA carboxylase beta subunit of Streptomyces coelicolor.
Authors: Arabolaza, A. / Shillito, M.E. / Lin, T.W. / Diacovich, L. / Melgar, M. / Pham, H. / Amick, D. / Gramajo, H. / Tsai, S.C.
History
DepositionJul 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Propionyl-CoA carboxylase complex B subunit
B: Propionyl-CoA carboxylase complex B subunit
C: Propionyl-CoA carboxylase complex B subunit
D: Propionyl-CoA carboxylase complex B subunit
E: Propionyl-CoA carboxylase complex B subunit
F: Propionyl-CoA carboxylase complex B subunit


Theoretical massNumber of molelcules
Total (without water)343,0816
Polymers343,0816
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45510 Å2
ΔGint-225 kcal/mol
Surface area101560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.060, 183.328, 228.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Propionyl-CoA carboxylase complex B subunit


Mass: 57180.156 Da / Num. of mol.: 6 / Mutation: D422A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3 / Gene: pccB, SCK13.18c, SCO4926 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X4K7

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 7
Details: Bis-Tris,(NH4)SO4, PEG 3350, pH 7.0, sitting drop vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2005 / Details: Si
RadiationMonochromator: Double Crystal, Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 46071 / Redundancy: 5.7 % / Net I/σ(I): 11.2
Reflection shellHighest resolution: 3.5 Å

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.851 / Occupancy max: 1 / Occupancy min: 1 / SU B: 69.964 / SU ML: 0.502 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.711 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2294 5 %RANDOM
Rwork0.19 ---
obs0.194 46011 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 20 Å2 / Biso mean: 2.033 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å20 Å20 Å2
2---1.6 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23700 0 0 0 23700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0590.02224180
X-RAY DIFFRACTIONr_angle_refined_deg3.951.95732856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.63653120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.09223.6761110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.089153792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.43215192
X-RAY DIFFRACTIONr_chiral_restr0.2150.23708
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0218738
X-RAY DIFFRACTIONr_nbd_refined0.340.313632
X-RAY DIFFRACTIONr_nbtor_refined0.380.516817
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.51648
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.356
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4180.54
X-RAY DIFFRACTIONr_mcbond_it0.121216262
X-RAY DIFFRACTIONr_mcangle_it0.183324876
X-RAY DIFFRACTIONr_scbond_it0.11229356
X-RAY DIFFRACTIONr_scangle_it0.17637980
LS refinement shellResolution: 3.5→3.547 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 138 -
Rwork0.216 2829 -
all-2967 -
obs--83.84 %
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)
118.026-3.75-8.905830.0502-4.98485.9971-0.0327-1.5569-0.31870.21640.4619-0.00010.06010.4171-0.42910.4079-0.06070.1052-0.13880.05-0.1192-111.1138-117.4892187.6058
28.0832-11.3336-1.865618.9915.17442.5423-0.932-1.37840.21831.19681.03360.00340.31430.0376-0.1017-0.1206-0.03130.15940.1051-0.03410.1331-120.0618-93.9735182.1799
32.23280.3604-0.12611.46370.0412.130.0142-0.1388-0.05870.1601-0.04580.07680.1484-0.00640.03160.0760.01860.0339-0.02250.04490.1038-106.2045-97.6481175.8538
41.00910.13150.3892.13560.44560.2236-0.0354-0.07640.03170.3438-0.01840.3963-0.144-0.15930.05380.1321-0.03050.05540.02550.0023-0.042-107.287-81.8398170.4775
57.0489-2.12038.97840.7481-2.973512.11120.08670.17860.3887-0.1051-0.2451-0.2402-0.0896-0.32040.15850.244-0.0104-0.02530.0616-0.0053-0.0306-111.805-91.5477138.264
60.42040.82710.5983.9177-0.58972.2125-0.0193-0.00230.1301-0.21490.03460.5485-0.2099-0.4944-0.01520.10170.041-0.02110.0747-0.02810.0542-114.9831-76.2736143.6061
71.0278-1.48360.00713.5583-0.12662.97570.14930.21450.51340.2474-0.03450.1968-0.4592-0.3931-0.11480.04710.03620.05160.0597-0.0360.0618-105.0604-75.6485149.4241
84.127-0.325-0.54441.97421.89161.8256-0.2916-0.75190.41790.30070.40240.1189-0.66060.0159-0.11070.1059-0.0233-0.0114-0.11780.056-0.0088-98.5225-64.6299152.8635
90.03180.167-0.05121.34590.16280.4795-0.06050.02840.43540.2691-0.0548-0.2042-0.2544-0.07410.11520.21410.0873-0.06070.01030.01750.0492-101.2617-68.8078137.6913
101.73820.85290.02632.9789-0.42721.54970.05580.04640.4549-0.0526-0.25610.105-0.546-0.11220.20020.3070.0536-0.03140.1279-0.00550.0449-103.364-58.0326129.7791
1145.867316.280518.230232.549513.450324.82790.9017-0.401-0.8701-1.4731-0.56310.66111.08170.9094-0.33860.1817-0.09120.055-0.18140.0291-0.2128-99.8818-89.6675135.1943
1210.0724-4.59466.99835.4091-5.51916.49640.19761.1757-0.9010.4220.1861-0.0490.9750.5911-0.38380.36460.0848-0.05570.0212-0.0882-0.1079-85.2717-80.1936152.7505
135.5373-5.4811-7.13926.57729.927216.30860.3050.3915-0.1161-1.4572-0.24740.6257-0.8581-0.1157-0.05760.3910.151-0.03480.17730.08960.1243-106.6522-70.6061114.0121
141.714-1.15370.4843.15741.12581.02170.04350.35960.106-0.30910.06160.2689-0.38030.0875-0.10510.23710.0433-0.03590.0655-0.0101-0.0493-94.1329-80.7609118.1644
150.04020.21390.11612.9133-0.13840.6587-0.2163-0.30940.2936-0.20740.0101-0.1411-0.1509-0.2070.20620.06730.03380.07220.08130.00150.0398-82.1106-82.2141120.2608
163.4261.94251.65421.69871.41841.1852-0.17740.93460.1825-0.62450.0987-0.0613-0.1430.63740.07870.15420.03550.08160.0670.09590.0775-79.8674-87.9318108.9805
170.4041-0.0445-0.73340.6227-0.31021.5785-0.21020.51320.1966-0.66730.1004-0.02780.2814-0.11850.10980.20130.01420.04430.0301-0.0028-0.0051-83.3676-95.1473107.8977
182.32850.26790.374717.96567.81293.4264-0.14010.1148-0.0459-0.61-0.39961.302-0.5451-0.30660.53980.492-0.0484-0.0551-0.0050.142-0.0856-93.4891-118.2041125.1457
193.18730.0391-0.43224.4231.04750.3092-0.0921-0.01020.1201-0.71170.16930.033-0.0160.2299-0.07720.20870.0113-0.03550.00710.0431-0.0589-83.306-117.165112.5352
200.64910.0671-0.05110.91870.13160.44380.00980.3380.1392-0.23870.1073-0.23620.1540.2596-0.11710.1615-0.00060.00970.0311-0.03640.0005-70.0752-114.1884118.3815
2139.2061-11.74189.95079.102-14.265348.30271.66821.058-1.5647-1.3917-1.4509-0.49490.6391-0.9351-0.2173-0.10690.1160.2331-0.4926-0.1751-0.0541-46.2126-134.7178105.3322
223.9736-0.8534-0.84980.4818-0.75643.1348-0.00730.271-0.6551-0.526-0.07590.07660.3365-0.02080.08320.2515-0.05720.0998-0.0981-0.0417-0.0004-68.8692-131.5481119.5492
2312.932714.0647-5.516933.406-0.86973.80660.5769-1.4706-0.63461.4967-0.0641-0.4517-0.5482-1.385-0.51280.2120.08470.0515-0.07750.0866-0.0089-85.6417-118.422133.9839
2415.2742-2.8981.64238.2191-6.680123.66790.7178-0.1409-0.5523-0.3830.60881.70050.3784-1.2742-1.32650.0615-0.0060.1185-0.0984-0.25920.1573-68.4334-100.0688134.158
251.3931-2.0628-0.13083.9722-0.46411.4765-0.1307-0.66780.02180.54870.36020.09770.02790.292-0.22950.18250.0107-0.09220.0348-0.07330.0065-70.0754-92.2072196.7612
262.6280.2627-1.71892.52051.09911.9130.1554-0.04050.03050.373-0.13560.1099-0.0484-0.0825-0.01990.17570.0129-0.091-0.0230.0101-0.0993-77.9548-99.8272187.63
271.04371.0151.42372.77220.45542.4253-0.1289-0.38810.0896-0.0726-0.1510.12860.4514-0.03770.27980.22370.06480.0514-0.0320.0384-0.0582-75.5724-106.8379177.1795
281.78840.7607-0.36574.3861-0.05430.07730.2265-0.6523-0.08190.4105-0.2524-0.22370.150.21440.02590.1988-0.0404-0.07460.0199-0.012-0.1261-66.9216-116.7289185.0167
2913.1218-5.8306-7.40776.50474.32234.4533-0.64120.03620.90220.41470.5329-0.888-0.11950.44080.10830.13640.0295-0.01990.10050.0643-0.1951-47.8993-103.3655162.5965
301.88211.0213-1.53042.7442-0.23591.4172-0.1405-0.30120.040.35770.2123-0.4322-0.02370.4488-0.07180.16240.0828-0.10370.069-0.04390.0392-47.5006-119.4046168.5137
311.8762-2.81680.16745.6305-1.02294.4609-0.135-0.3555-0.6363-0.0255-0.1368-0.79970.39010.060.27180.07560.0636-0.0890.132-0.1295-0.0119-56.3436-122.7844167.7736
320.00370.05130.0652.33441.12711.17980.25380.0531-0.3044-0.0332-0.32040.3967-0.11020.15390.06660.13740.05110.0018-0.0647-0.10850.1526-60.3143-119.7367163.8219
333.64710.3189-0.96830.0291-0.07130.4008-0.2159-0.1025-0.5917-0.06460.1733-0.0680.27620.09030.04260.12810.0061-0.0026-0.0583-0.0610.0176-62.6814-125.506161.0411
342.47582.38181.12093.15282.18491.9287-0.3122-0.4494-0.29170.2860.1817-0.38090.06730.12360.13040.06730.0012-0.01270.07450.0496-0.04-53.2729-128.483153.3069
351.96020.65990.21784.28592.8224.08920.0642-0.0467-0.7510.33980.0318-0.73690.74850.142-0.0960.02560.0839-0.01040.0297-0.03320.2438-47.1794-136.6772149.7369
3613.41334.9396-3.50482.1704-1.03381.10370.5280.94740.19940.3181-0.0585-0.2435-0.3526-0.1746-0.46950.11620.0253-0.03560.07760.00870.1061-65.4906-110.2981154.1764
371.79222.2423-1.92227.7148-14.538332.04950.1492-0.3218-0.3198-1.0102-0.4602-0.06432.6350.64950.3110.23690.01790.1196-0.0916-0.13040.0257-74.758-144.0532126.1784
385.7732-1.52920.10951.6583-0.1692.83870.02850.3893-0.24140.1441-0.11-0.21610.3299-0.06250.08150.1445-0.04910.0323-0.0738-0.038-0.0033-75.3587-137.0359138.9214
390.80940.48350.21910.34370.29870.5726-0.0218-0.12040.0079-0.1458-0.006-0.20720.01890.20170.02780.10340.01020.0385-0.05660.01550.0125-73.0784-129.6073148.9468
403.7564-0.90131.92923.5103-0.92623.8069-0.038-0.1439-0.75140.29990.38610.07330.4321-0.0795-0.34810.0986-0.0243-0.0115-0.0983-0.0812-0.0766-78.9688-138.3541159.3546
417.6072.2821-5.40133.8007-3.56265.0456-0.03850.6968-0.6253-0.59250.06570.159-0.4662-0.9698-0.02720.1578-0.1122-0.02760.0363-0.08390.1395-107.6337-120.8941160.8455
426.86840.6876-1.84281.68631.52316.5349-0.4698-0.1213-0.11470.197-0.01050.13631.0045-0.32710.48030.1023-0.05360.0579-0.27390.0215-0.0682-99.1892-129.6896172.0636
434.41740.8442.07812.92360.04164.64840.225-0.0549-0.40280.0144-0.029-0.01840.2778-0.0023-0.1960.145-0.03090.0232-0.0476-0.0422-0.0764-89.7252-124.8672168.4135
441.2995-2.02891.42883.6119-2.07484.3983-0.2360.16560.35970.1214-0.3442-0.68290.3240.46940.58030.0112-0.0220.0207-0.0930.008-0.082-83.1465-123.2882175.9441
451.3931-0.29260.24940.82611.30532.45520.0549-0.129-0.32930.4297-0.1615-0.0670.1617-0.14620.10660.2429-0.02140.0198-0.0770.0176-0.0477-91.5827-115.7961178.8182
460.60430.62740.61662.38930.56813.35870.2391-0.8001-0.23650.9178-0.0052-0.2177-0.2192-0.0259-0.23390.00650.02260.00760.24860.03430.0092-96.4509-115.2448197.2511
474.0387-0.72033.70347.0071-2.51073.8936-0.4866-0.0123-0.20810.630.82980.3767-1.0427-1.6371-0.34320.3-0.0274-0.0487-0.12-0.0144-0.0706-106.8881-115.4016167.5522
484.8072-2.5723-1.52681.37650.8170.4849-0.04650.3870.13360.2214-0.0199-0.0614-0.28090.01390.06630.131-0.09050.04990.2336-0.00470.0711-83.2478-107.741162.8133
490.4763-0.25920.02251.36361.78242.63550.1330.2169-0.1092-0.0864-0.1245-0.5830.19770.0916-0.00850.05370.06050.09330.1135-0.00920.169-39.4903-120.1925136.8315
501.2182-0.5990.37162.95211.49681.17480.04330.14840.0303-0.12820.1333-0.21490.08810.1585-0.17660.0315-0.04370.03450.0279-0.01040.0545-50.8125-113.5194133.8115
515.02711.85582.02814.66983.18062.99670.14330.3166-0.1602-0.0816-0.08010.00110.1926-0.046-0.06320.15520.03460.0387-0.09040.059-0.1018-58.0165-107.7907129.0596
521.94540.24420.60390.081-0.38284.3610.1040.76970.1489-0.43510.1562-0.44540.10780.4875-0.26020.1380.0090.05610.0484-0.00270.0494-49.2733-101.612119.5493
530.66172.04470.46486.31821.43640.32660.5348-0.16250.14181.297-0.72920.0187-0.21640.57990.19430.2118-0.00120.13110.1422-0.08470.1954-51.716-76.6187139.6404
541.29832.4013-0.00315.69-0.6410.35030.20040.05270.0183-0.5011-0.0202-0.2743-0.1110.1482-0.18020.1051-0.02960.12390.1197-0.00490.0919-51.7537-77.6241123.0239
555.9708-1.07793.65761.91040.40954.11520.13050.5493-0.0345-0.2826-0.0652-0.4275-0.32340.2642-0.06530.1716-0.04680.14060.01440.02220.0818-58.9741-84.7028122.6155
560.41940.15440.06910.9374-0.17430.0567-0.05860.3781-0.0253-0.40360.1804-0.1047-0.1692-0.0938-0.12180.2754-0.09970.05490.0529-0.01420.0093-67.2458-79.3115120.4668
572.9648-0.51220.64232.3702-0.91736.8059-0.32260.85860.082-0.51770.18570.2826-0.9460.25970.13690.249-0.14010.03630.0597-0.0375-0.0258-70.5679-62.4306113.1151
5817.592622.7414-5.679329.3971-7.34141.83340.7111-1.05720.00891.24830.11680.5255-0.6505-0.0989-0.8280.09540.1998-0.01880.1122-0.10070.1408-62.0825-75.4738141.1488
599.08860.7664-4.08748.53026.36477.15560.4844-0.30750.69131.1534-0.3933-1.1654-1.1653-0.906-0.09110.43630.1107-0.11050.04140.0780.0273-76.3487-93.3727132.4252
602.71470.0941-2.4261.906-1.19993.51840.26110.03410.6609-0.31640.0193-0.0536-0.79690.0271-0.28040.2186-0.07890.0791-0.0761-0.02740.1202-67.8355-53.2865136.2449
612.90390.3112-0.39870.7772-0.50540.58410.08720.15580.0457-0.28170.05260.1919-0.0395-0.1742-0.13980.230.04650.0168-0.1075-0.007-0.0331-78.0005-60.4964137.1437
620.8826-0.00770.14982.336-2.01662.0519-0.01860.46840.13020.2050.12750.2422-0.2787-0.1618-0.10890.14960.03580.045-0.0413-0.0072-0.0504-83.3205-66.0661144.3541
632.6975-1.93390.53633.8955-1.08471.6884-0.1062-0.17110.37760.10110.27080.1999-0.3509-0.1315-0.16460.1343-0.05010.0907-0.06740.0129-0.0268-85.4813-57.3996156.3365
640.7001-1.4120.39343.21660.59625.4555-0.1943-0.1068-0.20170.08740.0486-0.4402-0.87310.75050.14570.0472-0.26-0.09240.09430.00640.052-64.8857-74.4645176.7038
654.9311-0.59910.62152.5389-0.29170.47550.2132-0.23910.09490.61510.24020.1011-0.36250.1138-0.45340.072-0.01630.0105-0.1248-0.05990.0779-77.7724-65.2187179.7988
667.0910.5175-1.31662.04880.17422.0110.0299-0.03540.47930.075-0.0685-0.079-0.05490.02730.03860.114-0.02010.0267-0.03340.0207-0.0105-82.0974-71.2028171.2404
670.778-0.4781.1680.4822-0.97592.1076-0.07230.0704-0.09710.1347-0.03640.20140.0278-0.33420.10860.1818-0.0723-0.00280.0098-0.03550.0071-89.9105-76.7672175.9603
686.08392.5345-2.19831.9436-1.01344.14820.3824-1.07120.8450.324-0.08860.3678-0.157-0.2938-0.29380.17810.01370.0066-0.0277-0.0073-0.0484-92.9219-79.158194.7236
6941.120110.29417.53464.028810.073529.7299-0.1087-0.2674-0.3179-0.50540.1884-0.40911.09531.3707-0.07980.25370.11140.0667-0.17550.0868-0.1016-70.0157-86.1971172.4219
7011.1343-10.55282.348817.75177.873215.99260.0813-0.47020.29021.03130.23450.28740.43161.6431-0.31590.1502-0.24520.13210.11310.0541-0.0644-90.843-86.3835158.6772
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 25
2X-RAY DIFFRACTION2A26 - 48
3X-RAY DIFFRACTION3A49 - 135
4X-RAY DIFFRACTION4A136 - 261
5X-RAY DIFFRACTION5A262 - 281
6X-RAY DIFFRACTION6A282 - 332
7X-RAY DIFFRACTION7A333 - 374
8X-RAY DIFFRACTION8A375 - 402
9X-RAY DIFFRACTION9A403 - 452
10X-RAY DIFFRACTION10A453 - 507
11X-RAY DIFFRACTION11A508 - 517
12X-RAY DIFFRACTION12A518 - 530
13X-RAY DIFFRACTION13B10 - 41
14X-RAY DIFFRACTION14B42 - 140
15X-RAY DIFFRACTION15B141 - 177
16X-RAY DIFFRACTION16B178 - 211
17X-RAY DIFFRACTION17B212 - 261
18X-RAY DIFFRACTION18B262 - 282
19X-RAY DIFFRACTION19B283 - 332
20X-RAY DIFFRACTION20B333 - 455
21X-RAY DIFFRACTION21B456 - 468
22X-RAY DIFFRACTION22B469 - 506
23X-RAY DIFFRACTION23B507 - 517
24X-RAY DIFFRACTION24B518 - 530
25X-RAY DIFFRACTION25C10 - 62
26X-RAY DIFFRACTION26C63 - 154
27X-RAY DIFFRACTION27C155 - 179
28X-RAY DIFFRACTION28C180 - 259
29X-RAY DIFFRACTION29C260 - 282
30X-RAY DIFFRACTION30C283 - 330
31X-RAY DIFFRACTION31C331 - 356
32X-RAY DIFFRACTION32C357 - 383
33X-RAY DIFFRACTION33C384 - 420
34X-RAY DIFFRACTION34C421 - 452
35X-RAY DIFFRACTION35C453 - 507
36X-RAY DIFFRACTION36C508 - 530
37X-RAY DIFFRACTION37D10 - 41
38X-RAY DIFFRACTION38D42 - 116
39X-RAY DIFFRACTION39D117 - 198
40X-RAY DIFFRACTION40D199 - 263
41X-RAY DIFFRACTION41D264 - 284
42X-RAY DIFFRACTION42D285 - 319
43X-RAY DIFFRACTION43D320 - 365
44X-RAY DIFFRACTION44D366 - 393
45X-RAY DIFFRACTION45D394 - 453
46X-RAY DIFFRACTION46D454 - 498
47X-RAY DIFFRACTION47D499 - 511
48X-RAY DIFFRACTION48D512 - 530
49X-RAY DIFFRACTION49E10 - 82
50X-RAY DIFFRACTION50E83 - 155
51X-RAY DIFFRACTION51E156 - 186
52X-RAY DIFFRACTION52E187 - 260
53X-RAY DIFFRACTION53E261 - 283
54X-RAY DIFFRACTION54E284 - 329
55X-RAY DIFFRACTION55E330 - 362
56X-RAY DIFFRACTION56E363 - 453
57X-RAY DIFFRACTION57E454 - 505
58X-RAY DIFFRACTION58E506 - 516
59X-RAY DIFFRACTION59E517 - 530
60X-RAY DIFFRACTION60F10 - 67
61X-RAY DIFFRACTION61F68 - 128
62X-RAY DIFFRACTION62F129 - 178
63X-RAY DIFFRACTION63F179 - 262
64X-RAY DIFFRACTION64F263 - 285
65X-RAY DIFFRACTION65F286 - 318
66X-RAY DIFFRACTION66F319 - 375
67X-RAY DIFFRACTION67F376 - 439
68X-RAY DIFFRACTION68F440 - 506
69X-RAY DIFFRACTION69F507 - 517
70X-RAY DIFFRACTION70F518 - 530

+
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