[English] 日本語
Yorodumi
- PDB-8a8k: PAP phosphatase from Methanothermococcus thermolithotrophicus ref... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a8k
TitlePAP phosphatase from Methanothermococcus thermolithotrophicus refined to 3.1 A
ComponentsPAP phosphatase from Methanothermococcus thermolithotrophicus
KeywordsHYDROLASE / sulfate assimilation / methanogens / archaea / PAP / thermophile / inorganic phosphate / AMP / methane / detoxification / marine / manganese dependent / DHH-motif / RecJ
Function / homologyADENOSINE MONOPHOSPHATE / :
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsJespersen, M. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)WA 4053/1-1 Germany
CitationJournal: Nat Microbiol / Year: 2023
Title: Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus.
Authors: Jespersen, M. / Wagner, T.
History
DepositionJun 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PAP phosphatase from Methanothermococcus thermolithotrophicus
B: PAP phosphatase from Methanothermococcus thermolithotrophicus
C: PAP phosphatase from Methanothermococcus thermolithotrophicus
D: PAP phosphatase from Methanothermococcus thermolithotrophicus
E: PAP phosphatase from Methanothermococcus thermolithotrophicus
F: PAP phosphatase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,90322
Polymers228,0106
Non-polymers2,89316
Water00
1
A: PAP phosphatase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4413
Polymers38,0021
Non-polymers4392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PAP phosphatase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6255
Polymers38,0021
Non-polymers6244
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PAP phosphatase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4413
Polymers38,0021
Non-polymers4392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PAP phosphatase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4043
Polymers38,0021
Non-polymers4022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: PAP phosphatase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4964
Polymers38,0021
Non-polymers4943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: PAP phosphatase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4964
Polymers38,0021
Non-polymers4943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.054, 174.054, 183.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 0 through 315)
21(chain B and resid 0 through 315)
31(chain C and resid 0 through 315)
41(chain D and resid 0 through 315)
51(chain E and resid 0 through 315)
61(chain F and resid 0 through 315)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 0 - 315 / Label seq-ID: 20 - 335

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 0 through 315)AA
2(chain B and resid 0 through 315)BB
3(chain C and resid 0 through 315)CC
4(chain D and resid 0 through 315)DD
5(chain E and resid 0 through 315)EE
6(chain F and resid 0 through 315)FF

-
Components

#1: Protein
PAP phosphatase from Methanothermococcus thermolithotrophicus


Mass: 38001.621 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The gene construct was expressed in the pET-28a(+) vector. The protein product contains a His-Tag in its N-terminal part, with a thrombin cleavage site in-between.
Source: (gene. exp.) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Strain: DSM 2095 / Tissue: / / Cell: / / Cell line: / / Organ: / / Variant: / / Plasmid: pET-28a(+)
Details (production host): The synthetic gene was cloned in pET-28a(+) by using the restriction sites NdeI and BamHI. A stop codon (TGA) was incorporated before BamHI site.
Cell (production host): / / Cell line (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Tissue (production host): / / Variant (production host): / / References: 3'(2'),5'-bisphosphate nucleotidase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.79 % / Description: Crystals were transparent bipyramids.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: The PAP phosphatase from Methanothermococcus thermolithotrophicus was concentrated to 20 mg.ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol, and 150 mM NaCl. The protein ...Details: The PAP phosphatase from Methanothermococcus thermolithotrophicus was concentrated to 20 mg.ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol, and 150 mM NaCl. The protein was co-crystallized with Tb-Xo4 (10 mM final concentration), MnCl2 (2 mM final) and 2 mM PAP. The Tb-Xo4 is a nucleating/phasing agent, which should increase the crystallization performance, however, in this case the same crystalline form has been obtained in absence of the compound and diffracted to similar resolution. Crystals were obtained by mixing 0.7 ul of the sample with 1.6 M tri-sodium citrate in a 96-Well MRC 2-drop crystallization plates in polystyrene (SWISSCI) containing 90 ul of crystallization solution in the reservoir. No cryoprotectant was used.
PH range: / / Temp details: 291 +/- 1 K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.64566 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.64566 Å / Relative weight: 1
ReflectionResolution: 3.1→126.38 Å / Num. obs: 45681 / % possible obs: 92.1 % / Redundancy: 13.3 % / Biso Wilson estimate: 91.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.056 / Rrim(I) all: 0.204 / Net I/σ(I): 12.3
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 14.3 % / Rmerge(I) obs: 2.483 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7240 / CC1/2: 0.477 / Rpim(I) all: 0.68 / Rrim(I) all: 2.575 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold model

Resolution: 3.1→57.79 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.53 / Stereochemistry target values: ML
Details: The final refinement cycle was performed without hydrogens, with applying non-crystallography symmetry and translation-liberation screw.
RfactorNum. reflection% reflection
Rfree0.2196 2266 4.96 %
Rwork0.1857 43377 -
obs0.1874 45643 92.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.66 Å2 / Biso min: 53.33 Å2
Refinement stepCycle: final / Resolution: 3.1→57.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15234 0 183 0 15417
Biso mean--89.08 --
Num. residues----1898
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5748X-RAY DIFFRACTION1.685TORSIONAL
12B5748X-RAY DIFFRACTION1.685TORSIONAL
13C5748X-RAY DIFFRACTION1.685TORSIONAL
14D5748X-RAY DIFFRACTION1.685TORSIONAL
15E5748X-RAY DIFFRACTION1.685TORSIONAL
16F5748X-RAY DIFFRACTION1.685TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.170.34751730.335729313104100
3.17-3.240.331490.300629273076100
3.24-3.320.35261630.281629413104100
3.32-3.410.31981610.279129513112100
3.41-3.510.3228510.29741082113337
3.51-3.630.28371780.226229163094100
3.63-3.760.24431100.22451980209068
3.76-3.860.2351020.207521792281100
3.91-4.080.24711030.20682785288899
4.08-4.30.19511230.171629613084100
4.3-4.570.18791290.155929843113100
4.57-4.920.21841830.16129243107100
4.92-5.420.20981800.179729013081100
5.42-6.20.20851390.181929783117100
6.2-7.80.21471570.173129663123100
7.81-57.790.15471650.13332971313699
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)
10.06610.01930.46994.51012.76434.7460.19060.40290.0362-0.6692-0.46840.1721-0.0995-0.3620.30040.85710.09180.01881.00890.10190.76236.000630.069741.0444
24.77750.18172.00896.67961.49845.3790.01990.9158-0.7696-0.8541-0.11450.25990.1672-0.6250.08070.8608-0.0797-0.07641.1655-0.05850.76511.362323.070436.1096
33.66042.26524.02525.5841.65526.10490.3537-1.5241-0.498-0.11390.1809-2.03251.2069-0.0769-0.29471.225-0.24580.11590.8586-0.11451.2519-0.386715.995546.7941
46.3233-1.82520.1836.85452.54245.943-0.4032-1.007-0.84781.33250.0622-0.2531.74010.10430.3680.942-0.02830.05620.92090.03430.66156.161124.578655.336
55.1773-0.1119-0.56134.36850.77814.15590.10370.62350.4784-0.2634-0.2113-0.1733-0.32630.1490.01290.75650.0691-0.05830.76130.10920.78774.821841.414348.6685
63.4495-1.3104-2.21973.2587-1.02292.92670.3777-0.0220.9303-0.4079-0.38040.4379-0.96390.42460.10991.1861-0.2136-0.30941.2995-0.02340.9565-11.790548.517845.7229
76.22641.3217-0.88536.57061.75112.1441-0.25810.2477-0.1443-0.1574-0.07070.45190.03-0.0960.31980.66940.0391-0.09080.94710.03610.8541-18.566331.565751.1179
84.8642-1.119-0.88974.6248-1.35534.836-0.0074-0.1125-0.1035-0.28010.1627-0.2879-0.53330.1354-0.18710.78430.0766-0.05750.6746-0.12140.61584.021566.337-46.4612
96.5506-0.90870.58415.9247-1.20766.1914-0.08190.82440.6982-0.23490.020.318-0.5519-0.10440.05510.7590.09560.00850.6366-0.00490.7574-1.03871.3917-53.4125
103.0129-1.77132.48285.6255-2.2167.76570.26830.7179-0.3056-1.00430.15460.45580.7661-0.0117-0.39050.8107-0.0456-0.04990.787-0.05840.67222.174854.7406-51.3392
115.88860.482-0.45926.8161-0.14666.29630.075-0.94690.52060.26080.1036-0.2712-0.64950.3565-0.11650.59740.00220.00820.7612-0.02490.59154.615361.2342-34.2561
128.7655.0802-1.39965.5074-0.51032.19451.1397-1.6808-0.06121.4262-0.6510.0184-0.2944-0.4974-0.49190.85860.1006-0.24141.0151-0.04640.9285-12.231761.0604-27.3382
133.48041.35080.37052.0541-0.93085.8568-0.1254-0.0455-0.3097-0.20160.04340.26210.1229-0.20170.15850.54320.0809-0.05730.7739-0.04820.8451-17.922654.6568-41.6152
149.6161.05760.08573.9964-0.45877.4122-0.6240.3318-0.3604-0.3890.10190.80340.0102-0.39010.33770.644-0.01680.00570.8841-0.01050.7886-23.165457.1272-48.7157
153.9962-0.41531.73884.50210.04394.1520.33910.1237-0.2386-0.3361-0.36240.24250.8378-0.51660.18950.73320.0316-0.07840.7305-0.08850.764722.72153.734722.8286
165.6086-1.33411.11416.2042-1.89445.96410.15290.00770.6240.0097-0.07470.0478-0.7471-0.2099-0.06140.76170.0860.01210.7281-0.10690.60523.973861.705719.1217
177.73410.95450.30316.59710.11116.07590.2056-0.6131-0.8570.4095-0.24210.20750.5611-0.34720.01930.73140.0049-0.03720.6493-0.02160.512530.499643.049422.4585
186.05611.0433-5.37711.0696-0.48048.88150.2288-0.1316-1.1264-0.0606-0.42380.23590.73960.19850.17181.03630.0217-0.34090.96970.02051.244627.795834.99926.1782
191.7781-1.69730.47176.6542-1.49014.97210.12680.0377-0.0916-0.2361-0.0778-0.1668-0.3070.6015-0.09830.71060.0075-0.09650.7531-0.09360.52133.310549.6110.2914
202.991-1.2831-2.09266.47070.34737.49770.37480.79250.0218-0.543-0.07190.4515-0.56860.1668-0.33660.9180.0342-0.13070.769-0.05960.59830.190556.5353-4.752
214.94272.13870.2996.4642-1.11364.26680.1596-0.7426-0.47880.3141-0.4539-0.85840.06920.48210.19360.65970.06390.03240.4844-0.03330.6332-19.602160.31387.8483
225.08592.6732.45048.73182.39857.18960.0104-0.16780.5384-0.32640.01060.1631-0.56050.06850.11710.7424-0.06860.09510.6773-0.01540.6223-21.623368.075211.7811
237.9096-1.1721.31954.5522-1.41143.57880.23530.5148-0.4119-0.31540.0787-0.01280.1471-0.1441-0.23060.8061-0.0357-0.00550.6657-0.06160.7263-31.52649.23728.9647
242.30360.1120.4322.05510.16945.69050.05270.086-0.08460.0745-0.1114-0.28020.2817-0.120.16410.74060.0106-0.04770.5523-0.00280.7539-23.980546.664121.7171
253.5535-0.25-1.12936.50040.72217.32770.3514-0.3965-0.21090.2644-0.22860.2815-0.04260.20490.00810.7516-0.0506-0.04570.6574-0.02940.5675-28.734661.656833.1613
266.00711.13193.29935.45632.2567.1326-0.41360.4796-0.71040.20040.7999-0.32120.19510.5628-0.43430.89640.05370.19520.67060.03120.6548-21.44297.6543-14.6054
275.8247-0.19522.02434.8716-0.62646.72860.1403-0.0662-0.19720.9541-0.1703-0.81370.20640.76410.06240.91390.00650.08350.7002-0.04680.886-15.855493.1041-7.6614
285.678-0.18273.33692.8602-2.10867.3790.0132-0.7083-0.18390.69140.23980.3411-0.0444-0.8609-0.24330.9050.05150.14370.81340.02080.8272-32.738794.6195-9.6764
294.6397-0.15571.13623.3108-0.17192.7838-0.13290.49130.3928-0.27160.112-0.3806-0.320.36340.06360.7403-0.06940.08580.68950.06150.6002-26.039792.4914-28.9289
303.68460.5373.16384.2246-1.14047.02570.26440.1249-0.44720.0504-0.00880.12150.13110.0395-0.32410.81160.05440.12080.5599-0.0050.7764-29.865773.0842-17.0112
315.0931.9841-1.23744.3933-1.88123.64770.7323-0.14240.13180.7821-0.5945-0.0057-0.00780.3091-0.03580.7442-0.0143-0.07960.5475-0.0640.7444-9.017329.2169-10.3297
322.6769-0.76141.30957.4020.39686.9945-0.3009-0.572-0.68880.82870.01490.13580.16890.34680.21560.58720.0085-0.01950.68150.14140.8545-3.633922.6788-5.6478
336.7041-2.3420.75896.9848-0.71044.75-0.1280.6719-1.2307-0.7064-0.00190.33980.9141-0.21550.10650.7028-0.0037-0.0220.6894-0.07570.8676-5.821520.7908-21.471
344.14131.4070.38335.12720.40296.96670.0235-0.1360.32990.0918-0.12950.5279-0.4987-0.33450.12850.48410.0490.00520.5503-0.03960.6493-8.878340.7272-17.7339
353.61582.006-4.00742.6289-1.38275.14330.9470.74320.33220.7583-0.83710.149-1.4723-0.291-0.46411.19290.2579-0.08991.0143-0.02960.77173.717950.466-12.0199
365.6808-0.4298-1.45977.5708-1.59173.20650.04270.4319-0.4979-0.1137-0.1489-0.21440.10330.00460.13080.4873-0.0352-0.06410.6577-0.0290.700415.600133.6822-20.547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 21 )A-1 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 74 )A22 - 74
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 90 )A75 - 90
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 117 )A91 - 117
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 189 )A118 - 189
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 213 )A190 - 213
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 315 )A214 - 315
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 21 )B0 - 21
9X-RAY DIFFRACTION9chain 'B' and (resid 22 through 75 )B22 - 75
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 134 )B76 - 134
11X-RAY DIFFRACTION11chain 'B' and (resid 135 through 189 )B135 - 189
12X-RAY DIFFRACTION12chain 'B' and (resid 190 through 213 )B190 - 213
13X-RAY DIFFRACTION13chain 'B' and (resid 214 through 280 )B214 - 280
14X-RAY DIFFRACTION14chain 'B' and (resid 281 through 315 )B281 - 315
15X-RAY DIFFRACTION15chain 'C' and (resid 0 through 21 )C0 - 21
16X-RAY DIFFRACTION16chain 'C' and (resid 22 through 117 )C22 - 117
17X-RAY DIFFRACTION17chain 'C' and (resid 118 through 189 )C118 - 189
18X-RAY DIFFRACTION18chain 'C' and (resid 190 through 213 )C190 - 213
19X-RAY DIFFRACTION19chain 'C' and (resid 214 through 280 )C214 - 280
20X-RAY DIFFRACTION20chain 'C' and (resid 281 through 315 )C281 - 315
21X-RAY DIFFRACTION21chain 'D' and (resid 0 through 21 )D0 - 21
22X-RAY DIFFRACTION22chain 'D' and (resid 22 through 117 )D22 - 117
23X-RAY DIFFRACTION23chain 'D' and (resid 118 through 164 )D118 - 164
24X-RAY DIFFRACTION24chain 'D' and (resid 165 through 248 )D165 - 248
25X-RAY DIFFRACTION25chain 'D' and (resid 249 through 315 )D249 - 315
26X-RAY DIFFRACTION26chain 'E' and (resid 0 through 21 )E0 - 21
27X-RAY DIFFRACTION27chain 'E' and (resid 22 through 75 )E22 - 75
28X-RAY DIFFRACTION28chain 'E' and (resid 76 through 134 )E76 - 134
29X-RAY DIFFRACTION29chain 'E' and (resid 135 through 213 )E135 - 213
30X-RAY DIFFRACTION30chain 'E' and (resid 214 through 315 )E214 - 315
31X-RAY DIFFRACTION31chain 'F' and (resid -1 through 21 )F-1 - 21
32X-RAY DIFFRACTION32chain 'F' and (resid 22 through 75 )F22 - 75
33X-RAY DIFFRACTION33chain 'F' and (resid 76 through 117 )F76 - 117
34X-RAY DIFFRACTION34chain 'F' and (resid 118 through 189 )F118 - 189
35X-RAY DIFFRACTION35chain 'F' and (resid 190 through 208 )F190 - 208
36X-RAY DIFFRACTION36chain 'F' and (resid 209 through 315 )F209 - 315

+
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