[English] 日本語
Yorodumi
- PDB-6jrg: Crystal structure of ZmMoc1 H253A mutant in complex with Holliday... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jrg
TitleCrystal structure of ZmMoc1 H253A mutant in complex with Holliday junction
Components
  • DNA (32-MER)
  • DNA (33-MER)
  • Monokaryotic chloroplast 1
KeywordsDNA BINDING PROTEIN/DNA / Holliday junction resolvase-DNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homologyHolliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / DNA / DNA (> 10) / Holliday junction resolvase MOC1, chloroplastic
Function and homology information
Biological speciesZea mays (maize)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsLin, Z. / Lin, H. / Zhang, D. / Yuan, C.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Structural basis of sequence-specific Holliday junction cleavage by MOC1.
Authors: Lin, H. / Zhang, D. / Zuo, K. / Yuan, C. / Li, J. / Huang, M. / Lin, Z.
History
DepositionApr 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monokaryotic chloroplast 1
B: Monokaryotic chloroplast 1
C: DNA (33-MER)
D: DNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6136
Polymers57,5654
Non-polymers492
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-84 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.572, 77.841, 63.854
Angle α, β, γ (deg.)90.00, 97.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Monokaryotic chloroplast 1


Mass: 18645.277 Da / Num. of mol.: 2 / Mutation: H253A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: Moc1, 100192759, ZEAMMB73_Zm00001d040409 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4FCI7
#2: DNA chain DNA (33-MER)


Mass: 10121.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (32-MER)


Mass: 10152.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 37.5% Polyethylene glycol 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34594 / % possible obs: 99.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Χ2: 0.888 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.60.49216630.8220.2420.550.78196.4
2.03-2.075.10.43316810.8880.2040.480.82798
2.07-2.115.40.39617070.9060.1810.4370.80598.3
2.11-2.155.60.34517190.9260.1560.380.8698
2.15-2.260.32717170.9420.1430.3580.87899.4
2.2-2.256.50.41917020.9220.1760.4551.74599
2.25-2.316.90.25217360.9720.1030.2730.85399
2.31-2.376.90.20717170.9810.0840.2230.86299.2
2.37-2.446.90.18517370.9840.0750.20.88299.4
2.44-2.526.90.16417090.9850.0670.1770.90599.5
2.52-2.616.80.1417340.9880.0580.1520.89899.5
2.61-2.716.50.12217390.9890.0510.1320.88499.6
2.71-2.846.30.10617320.9910.0450.1150.89599.6
2.84-2.996.80.0917580.9930.0370.0970.90499.7
2.99-3.177.10.07517400.9950.030.0810.87499.9
3.17-3.4270.06517290.9950.0260.070.84599.8
3.42-3.766.70.05817620.9960.0240.0630.80799.9
3.76-4.316.10.05317530.9950.0230.0580.76199.9
4.31-5.4370.05317580.9960.0220.0580.734100
5.43-506.30.05318010.9950.0230.0580.71499.5

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IS9
Resolution: 2.005→34.25 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.95
RfactorNum. reflection% reflection
Rfree0.2315 1651 4.87 %
Rwork0.1856 --
obs0.1878 33891 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.005→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 1324 2 309 4113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074091
X-RAY DIFFRACTIONf_angle_d0.8365844
X-RAY DIFFRACTIONf_dihedral_angle_d16.0122734
X-RAY DIFFRACTIONf_chiral_restr0.053653
X-RAY DIFFRACTIONf_plane_restr0.006522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0054-2.06440.29441230.21442211X-RAY DIFFRACTION80
2.0644-2.1310.25391470.20092503X-RAY DIFFRACTION92
2.131-2.20720.25261290.20262663X-RAY DIFFRACTION97
2.2072-2.29550.2741310.20162730X-RAY DIFFRACTION99
2.2955-2.40.23171480.18912730X-RAY DIFFRACTION100
2.4-2.52650.27821470.192725X-RAY DIFFRACTION99
2.5265-2.68470.23371420.192783X-RAY DIFFRACTION100
2.6847-2.89190.25771270.19972750X-RAY DIFFRACTION100
2.8919-3.18270.25071470.18892753X-RAY DIFFRACTION100
3.1827-3.64280.22421390.17392763X-RAY DIFFRACTION100
3.6428-4.58780.19321370.16122798X-RAY DIFFRACTION100
4.5878-34.25530.20461340.19132831X-RAY DIFFRACTION100
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)
16.458-2.3655-4.82123.66442.25196.83680.2913-0.14280.29460.1504-0.28770.0285-0.3848-0.4737-0.00390.12660.00650.02080.1565-0.05790.19474.8391-29.181828.4173
23.6532-1.3630.34663.55330.5752.87030.0434-0.1420.1161-0.1030.1259-0.3860.04370.5088-0.06530.13380.00660.01840.1275-0.01250.198416.2383-36.625925.3394
34.1209-1.9997-1.20671.79381.77372.444-0.0105-0.28690.24750.3115-0.02460.3611-0.25590.19280.13740.1866-0.00790.06470.2082-0.01550.2425.8878-26.274235.3561
40.5567-0.85140.00794.94031.47421.24-0.1147-0.2618-0.09950.52860.1533-0.26580.27490.25030.01660.20180.00420.01370.1807-0.0180.11915.8724-40.742431.1524
53.99980.1405-1.14092.99122.32247.6576-0.02640.014-0.04910.24560.3157-0.24340.60790.2399-0.09860.27930.1080.04180.19690.01490.200524.931-55.673722.3343
65.5742-3.2997-2.0842.98051.83081.09580.55580.35070.046-0.3824-0.4012-0.06590.25150.2622-0.01890.30090.10780.00470.15820.0180.142121.8104-49.245123.3925
74.486-3.70561.48296.50211.7324.4545-0.263-0.2388-0.80190.49340.09230.29620.3542-0.170.11780.263-0.08770.08850.2525-0.00250.23828.1984-46.665429.1409
82.3883-0.33431.16612.4161-1.81931.755-0.3325-0.1969-0.18691.0556-0.12080.44870.0899-0.85250.00080.2852-0.11420.18770.3209-0.06120.19182.8781-39.269532.7428
90.9694-0.0394-0.56742.39950.39462.8584-0.17870.2276-0.0677-0.1368-0.00950.20890.0632-0.51530.03290.10550.00730.00970.1842-0.04450.24953.9221-31.225423.9111
103.789-1.7718-1.91273.02431.23992.8928-0.26620.8771-0.21220.8343-0.18070.3398-0.1872-0.15740.07240.3388-0.06370.01720.25230.00520.186821.2081-34.851410.4066
113.26680.4332-0.79051.6326-0.14112.3899-0.1249-0.3427-0.0836-0.08610.0934-0.37240.15790.6245-0.09130.0967-0.00740.03270.16260.00550.139620.9271-44.137313.1752
124.2044-0.4972-0.7851.46790.78921.94420.15360.10570.15610.1142-0.18930.280.0412-0.17780.00680.1207-0.04420.01150.1323-0.04930.17375.702-39.54221.3054
130.41-0.148-0.13651.9980.68871.206-0.02310.02630.0655-0.2203-0.0559-0.0857-0.34260.09090.08880.2401-0.03670.0110.18820.01130.201614.4196-24.216118.1249
144.44230.869-4.34752.2334-2.45548.95610.1350.40930.343-0.0760.1487-0.08350.32760.1237-0.02710.2488-0.1662-0.00060.30280.00320.343126.1677-19.685116.5711
154.3842-1.7176-2.0091.79280.72285.41720.35910.22260.632-0.40710.0038-0.7988-0.32240.7512-0.07390.2212-0.035-0.03010.41-0.02660.417728.1333-24.603124.4435
163.8573-2.3988-2.28332.03420.5912.78030.32520.16470.23011.0191-0.0455-0.8515-0.26330.1447-0.03640.1659-0.1021-0.08420.1336-0.05950.29521.4572-21.571231.0962
171.27310.3392-1.57874.73710.46732.23860.0783-0.1437-0.19450.7541-0.0846-0.050.17940.40210.02710.2174-0.021-0.05610.2289-0.04220.218817.7953-25.075938.0345
183.9098-0.99731.20321.97160.172.9765-0.0278-0.48320.10670.31740.1143-0.3360.11840.60720.01970.19710.0328-0.02680.2839-0.02040.317225.1105-31.302433.1158
192.9397-1.47231.96972.7846-1.64824.34290.02370.32820.215-0.1138-0.2163-0.3192-0.33080.24350.15850.1037-0.0349-0.02360.1289-0.02160.180915.6759-28.366827.4199
201.8266-0.8056-0.32621.07970.34443.2947-0.0563-0.13290.46120.0269-0.11720.3274-0.3512-0.1005-0.05360.30820.0203-0.06020.13210.00610.265510.9869-18.311426.192
215.53230.7562-1.86661.6479-0.66131.9466-0.2901-0.4595-0.60050.09680.09950.26770.7801-0.2668-0.04330.1933-0.17390.04620.0935-0.05050.2181-2.0611-61.314317.4578
221.8490.92260.19143.7222-1.58633.2964-0.11480.1631-0.0383-0.4216-0.1617-0.20820.09840.26650.08970.246-0.05780.02570.1551-0.00160.18934.191-53.36487.9613
231.42410.9085-0.49963.3719-2.69232.19370.2177-0.61370.00160.6163-0.06141.21160.5424-0.5195-0.08280.3045-0.35460.17060.2808-0.07180.3662-8.0806-65.30615.6915
241.02251.94810.43016.2488-0.08890.2289-0.08580.28450.1316-0.08620.19620.48060.0168-0.26690.01150.1438-0.0403-0.03340.2195-0.02290.2018-3.4597-52.77567.8802
256.56091.1851-0.26592.75660.10874.1723-0.0893-0.16640.2266-0.169-0.00750.0072-0.17150.1562-0.00130.2293-0.0239-0.0010.18770.08130.2598.8059-34.29491.5034
262.15132.3845-2.74282.7606-2.70873.8695-0.32890.0031-0.131-0.0064-0.4851-0.5934-0.2950.36290.10550.20450.0169-0.01540.19930.06510.27897.3831-40.56483.6922
273.02623.3212-0.64474.2744-2.66797.07510.3420.02420.81460.2695-0.31380.9752-0.959-0.5216-0.04920.1828-0.01170.04140.305-0.09820.3746-2.3042-43.731214.5723
280.8036-0.1442-0.77022.4629-1.52452.96090.1824-0.64330.23540.9261-0.4891.1533-0.2297-0.4571-0.6381-0.0403-0.32270.24410.18540.0090.2285-5.9026-54.262320.8482
295.8971.0485-1.49855.591-0.6593.4314-0.00610.2776-0.2472-0.33350.4783-0.17910.34760.0406-0.12560.1794-0.05310.0320.13820.01090.17436.2345-59.830816.5637
301.39121.4458-0.65741.5127-0.66330.3070.1379-0.435-0.20740.36170.33281.14580.04230.1079-0.04980.19470.03650.03370.25050.0070.318418.2354-55.4989.5282
312.8344-0.3341-0.73741.71770.37093.23160.14440.4213-0.0076-0.77620.0397-0.0069-0.12620.5255-0.03720.1669-0.01360.01780.22380.00230.139720.4395-46.59775.6444
323.06881.9742-2.04722.8498-1.96165.82510.18390.2126-0.3202-0.3053-0.2535-0.0388-0.15670.048-0.0710.1092-0.00250.00020.1245-0.02610.116411.2961-47.167212.3975
331.56921.0307-0.14331.4053-0.89992.51910.0293-0.3240.46030.3337-0.21950.4740.1293-0.23980.02870.1807-0.05970.07360.1538-0.04180.11112.7641-51.595421.0507
340.8689-0.0688-0.10042.17321.27621.5160.370.1412-0.1534-0.2912-0.2784-0.214-0.11440.0336-0.05020.28330.04080.02050.2025-0.04050.236511.2316-64.796212.3225
355.5827-2.223-2.68343.76841.42256.51290.19930.35020.078-0.3360.2599-0.43640.35420.5393-0.06050.34790.0638-0.01810.2496-0.11010.27812.8009-70.18953.4182
365.631.3461-1.1463.9233-2.33223.1389-0.38120.492-0.6941-0.4817-0.3353-0.80490.71020.30120.06120.4862-0.07140.01750.3281-0.14580.20517.5635-65.8395-2.7473
372.28621.88020.5011.88640.52743.66090.2769-0.2090.1933-0.4427-0.00080.1320.5183-0.1778-0.07150.2691-0.0327-0.04330.1129-0.04780.1806-4.1042-68.52623.739
380.9904-0.28210.64020.49380.92723.5086-0.18990.22490.3303-0.66920.21390.2850.3233-0.2783-0.03540.4205-0.0724-0.0810.2358-0.03480.2106-2.4882-60.0898-2.1777
395.3622-2.84042.20544.3394-2.42174.36860.68390.43550.1528-0.0728-0.7148-0.12510.390.1395-0.00220.2323-0.02880.00740.1606-0.0380.14962.2575-61.67147.2493
402.44981.37681.04632.69440.64362.2727-0.02950.1052-0.4592-0.1511-0.22850.50050.09490.03780.03640.2932-0.0382-0.08340.1937-0.02440.23992.0933-71.846711.9524
410.8657-0.7065-0.19861.80461.93393.35020.0197-0.0978-0.23470.21690.2106-0.3392-0.01110.672-0.10220.15570.0332-0.01880.40480.06030.228430.0407-47.892318.8115
420.029-0.0008-0.070.00150.03122.54040.37790.5493-1.3225-0.7730.31160.4015-0.13821.7398-0.17011.33650.22330.33040.85950.13011.083528.9035-75.727216.3084
431.93881.947-1.05182.92590.01732.10050.18410.4339-0.6042-0.4562-0.05280.35530.11320.4387-0.03840.33390.0733-0.11790.3751-0.03980.226418.2502-55.7782-0.645
443.38991.8550.37742.11270.49012.14690.02380.64430.336-0.72380.1880.0473-0.319-0.3024-0.04980.30280.0489-0.01780.42010.12490.128714.3132-39.7649-2.4426
450.56150.1270.33620.62440.54030.558-0.13370.72890.0405-0.69980.6259-0.0696-0.98020.2236-0.08340.80340.5051-0.13981.2505-0.13621.266214.7246-18.4732-4.5121
462.0562-0.7208-0.72772.57621.49541.8830.01980.04350.09440.40960.219-0.4842-0.43950.86030.12720.3038-0.0373-0.06960.41140.01370.27730.322-35.724118.0109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 109:114)
2X-RAY DIFFRACTION2(chain A and resid 115:123)
3X-RAY DIFFRACTION3(chain A and resid 124:132)
4X-RAY DIFFRACTION4(chain A and resid 133:139)
5X-RAY DIFFRACTION5(chain A and resid 140:146)
6X-RAY DIFFRACTION6(chain A and resid 147:151)
7X-RAY DIFFRACTION7(chain A and resid 152:158)
8X-RAY DIFFRACTION8(chain A and resid 159:164)
9X-RAY DIFFRACTION9(chain A and resid 165:174)
10X-RAY DIFFRACTION10(chain A and resid 175:181)
11X-RAY DIFFRACTION11(chain A and resid 182:192)
12X-RAY DIFFRACTION12(chain A and resid 193:207)
13X-RAY DIFFRACTION13(chain A and resid 208:221)
14X-RAY DIFFRACTION14(chain A and resid 222:225)
15X-RAY DIFFRACTION15(chain A and resid 226:231)
16X-RAY DIFFRACTION16(chain A and resid 232:239)
17X-RAY DIFFRACTION17(chain A and resid 240:246)
18X-RAY DIFFRACTION18(chain A and resid 247:254)
19X-RAY DIFFRACTION19(chain A and resid 255:262)
20X-RAY DIFFRACTION20(chain A and resid 263:271)
21X-RAY DIFFRACTION21(chain B and resid 109:114)
22X-RAY DIFFRACTION22(chain B and resid 115:123)
23X-RAY DIFFRACTION23(chain B and resid 124:129)
24X-RAY DIFFRACTION24(chain B and resid 130:139)
25X-RAY DIFFRACTION25(chain B and resid 140:146)
26X-RAY DIFFRACTION26(chain B and resid 147:151)
27X-RAY DIFFRACTION27(chain B and resid 152:158)
28X-RAY DIFFRACTION28(chain B and resid 159:169)
29X-RAY DIFFRACTION29(chain B and resid 170:174)
30X-RAY DIFFRACTION30(chain B and resid 175:179)
31X-RAY DIFFRACTION31(chain B and resid 180:188)
32X-RAY DIFFRACTION32(chain B and resid 189:196)
33X-RAY DIFFRACTION33(chain B and resid 197:207)
34X-RAY DIFFRACTION34(chain B and resid 208:219)
35X-RAY DIFFRACTION35(chain B and resid 220:224)
36X-RAY DIFFRACTION36(chain B and resid 225:235)
37X-RAY DIFFRACTION37(chain B and resid 236:242)
38X-RAY DIFFRACTION38(chain B and resid 243:254)
39X-RAY DIFFRACTION39(chain B and resid 255:262)
40X-RAY DIFFRACTION40(chain B and resid 263:271)
41X-RAY DIFFRACTION41(chain C and resid 1:14)
42X-RAY DIFFRACTION42(chain C and resid 15:18)
43X-RAY DIFFRACTION43(chain C and resid 19:33)
44X-RAY DIFFRACTION44(chain D and resid 1:15)
45X-RAY DIFFRACTION45(chain D and resid 17:20)
46X-RAY DIFFRACTION46(chain D and resid 21:33)

+
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