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- PDB-2xr1: DIMERIC ARCHAEAL CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR ... -

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Basic information

Entry
Database: PDB / ID: 2xr1
TitleDIMERIC ARCHAEAL CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR WITH N-TERMINAL KH DOMAINS (KH-CPSF) FROM METHANOSARCINA MAZEI
ComponentsCLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 100 KD SUBUNIT
KeywordsHYDROLASE / METALLO-BETA-LACTAMASE / BETA-CASP / RNA PROCESSING
Function / homology
Function and homology information


RNA binding / metal ion binding
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #230 / Transcription termination factor CPSF1, archaea / KH domain, archaeal / KH domain / Rossmann fold - #10890 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain ...GMP Synthetase; Chain A, domain 3 - #230 / Transcription termination factor CPSF1, archaea / KH domain, archaeal / KH domain / Rossmann fold - #10890 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / K Homology domain / K homology RNA-binding domain / K Homology domain, type 2 / KH domain / K homology domain superfamily, prokaryotic type / 4-Layer Sandwich / K homology domain-like, alpha/beta / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cleavage and polyadenylation specificity factor 100 kD subunit
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMir-Montazeri, B. / Ammelburg, M. / Forouzan, D. / Lupas, A.N. / Hartmann, M.D.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal Structure of a Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor.
Authors: Mir-Montazeri, B. / Ammelburg, M. / Forouzan, D. / Lupas, A.N. / Hartmann, M.D.
History
DepositionSep 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 100 KD SUBUNIT
B: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 100 KD SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,5246
Polymers144,2622
Non-polymers2624
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 100 KD SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2623
Polymers72,1311
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 100 KD SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2623
Polymers72,1311
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.660, 97.720, 90.720
Angle α, β, γ (deg.)90.00, 98.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110A
210B
111A
211B
112A
212B
113A
213B
114A
214B
115A
215B
116A
216B
117A
217B
118A
218B
119A
219B
120A
220B
121A
221B
122A
222B
123A
223B
124A
224B
125A
225B
126A
226B
127A
227B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 9
2111B1 - 9
1125A10 - 16
2125B10 - 16
1131A18 - 50
2131B18 - 50
1145A52 - 56
2145B52 - 56
1155A57 - 60
2155B57 - 60
1161A62 - 70
2161B62 - 70
1171A72 - 87
2171B72 - 87
1181A89 - 98
2181B89 - 98
1191A100 - 101
2191B100 - 101
11101A103 - 115
21101B103 - 115
11111A117 - 139
21111B117 - 139
11121A141 - 311
21121B141 - 311
11131A313 - 353
21131B313 - 353
11141A355 - 358
21141B355 - 358
11151A360 - 38
21151B360 - 38
11161A390 - 40
21161B390 - 40
11171A411 - 433
21171B411 - 433
11181A441 - 470
21181B441 - 470
11191A477 - 487
21191B477 - 487
11201A489 - 495
21201B489 - 495
11211A500 - 511
21211B500 - 511
11221A513 - 527
21221B513 - 527
11231A530 - 544
21231B530 - 544
11241A546 - 550
21241B546 - 550
11251A551 - 552
21251B551 - 552
11261A570 - 591
21261B570 - 591
11271A593 - 637
21271B593 - 637

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27

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Components

#1: Protein CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 100 KD SUBUNIT / ARCHAEAL CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR WITH N-TERMINAL KH DOMAINS / KH-CPSF


Mass: 72131.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA MAZEI (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8PZ03
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL CLEAVABLE HEXA-HIS TAG

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8 / Details: 20%(W/V) PEG3350, 200MM SODIUM NITRATE, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→38.6 Å / Num. obs: 41154 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.43 % / Biso Wilson estimate: 64.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.59
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.09 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I7V
Resolution: 2.59→38.43 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 27.302 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.366 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.26678 2023 4.9 %RANDOM
Rwork0.20919 ---
obs0.21203 39130 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.886 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å2-1.77 Å2
2--1.38 Å20 Å2
3----3.37 Å2
Refinement stepCycle: LAST / Resolution: 2.59→38.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9329 0 4 42 9375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229540
X-RAY DIFFRACTIONr_bond_other_d0.0020.026358
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9712973
X-RAY DIFFRACTIONr_angle_other_deg0.958315568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20151203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21224.055402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.607151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2751557
X-RAY DIFFRACTIONr_chiral_restr0.0860.21502
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110571
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021838
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4741.56069
X-RAY DIFFRACTIONr_mcbond_other0.1171.52432
X-RAY DIFFRACTIONr_mcangle_it0.93629809
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.68633471
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8364.53164
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A76tight positional0.030.05
12B76tight positional0.030.05
31A411tight positional0.050.05
32B411tight positional0.050.05
61A98tight positional0.040.05
62B98tight positional0.040.05
71A91tight positional0.030.05
72B91tight positional0.030.05
81A125tight positional0.050.05
82B125tight positional0.050.05
91A17tight positional0.050.05
92B17tight positional0.050.05
101A137tight positional0.030.05
102B137tight positional0.030.05
111A224tight positional0.040.05
112B224tight positional0.040.05
121A2254tight positional0.040.05
122B2254tight positional0.040.05
131A505tight positional0.040.05
132B505tight positional0.040.05
141A52tight positional0.030.05
142B52tight positional0.030.05
151A370tight positional0.040.05
152B370tight positional0.040.05
161A128tight positional0.030.05
162B128tight positional0.030.05
171A288tight positional0.030.05
172B288tight positional0.030.05
181A367tight positional0.040.05
182B367tight positional0.040.05
191A137tight positional0.040.05
192B137tight positional0.040.05
201A74tight positional0.030.05
202B74tight positional0.030.05
211A129tight positional0.030.05
212B129tight positional0.030.05
221A163tight positional0.020.05
222B163tight positional0.020.05
231A185tight positional0.030.05
232B185tight positional0.030.05
241A78tight positional0.030.05
242B78tight positional0.030.05
251A14tight positional0.020.05
252B14tight positional0.020.05
261A294tight positional0.030.05
262B294tight positional0.030.05
271A577tight positional0.040.05
272B577tight positional0.040.05
21A42medium positional0.150.5
22B42medium positional0.150.5
41A30medium positional0.190.5
42B30medium positional0.190.5
51A24medium positional0.210.5
52B24medium positional0.210.5
21A72loose positional0.685
22B72loose positional0.685
41A16loose positional0.555
42B16loose positional0.555
51A21loose positional0.75
52B21loose positional0.75
11A76tight thermal0.080.5
12B76tight thermal0.080.5
31A411tight thermal0.10.5
32B411tight thermal0.10.5
61A98tight thermal0.10.5
62B98tight thermal0.10.5
71A91tight thermal0.110.5
72B91tight thermal0.110.5
81A125tight thermal0.090.5
82B125tight thermal0.090.5
91A17tight thermal0.060.5
92B17tight thermal0.060.5
101A137tight thermal0.060.5
102B137tight thermal0.060.5
111A224tight thermal0.060.5
112B224tight thermal0.060.5
121A2254tight thermal0.110.5
122B2254tight thermal0.110.5
131A505tight thermal0.120.5
132B505tight thermal0.120.5
141A52tight thermal0.10.5
142B52tight thermal0.10.5
151A370tight thermal0.130.5
152B370tight thermal0.130.5
161A128tight thermal0.090.5
162B128tight thermal0.090.5
171A288tight thermal0.090.5
172B288tight thermal0.090.5
181A367tight thermal0.10.5
182B367tight thermal0.10.5
191A137tight thermal0.080.5
192B137tight thermal0.080.5
201A74tight thermal0.060.5
202B74tight thermal0.060.5
211A129tight thermal0.080.5
212B129tight thermal0.080.5
221A163tight thermal0.070.5
222B163tight thermal0.070.5
231A185tight thermal0.080.5
232B185tight thermal0.080.5
241A78tight thermal0.060.5
242B78tight thermal0.060.5
251A14tight thermal0.10.5
252B14tight thermal0.10.5
261A294tight thermal0.110.5
262B294tight thermal0.110.5
271A577tight thermal0.120.5
272B577tight thermal0.120.5
21A42medium thermal0.162
22B42medium thermal0.162
41A30medium thermal0.352
42B30medium thermal0.352
51A24medium thermal0.142
52B24medium thermal0.142
21A72loose thermal0.3110
22B72loose thermal0.3110
41A16loose thermal0.4610
42B16loose thermal0.4610
51A21loose thermal0.2210
52B21loose thermal0.2210
LS refinement shellResolution: 2.595→2.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 145 -
Rwork0.321 2629 -
obs--91.31 %
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)
16.8465-2.23991.91913.9409-1.131411.6815-0.1256-0.1993-0.0718-0.2544-0.1091-0.67961.00831.12910.23460.4994-0.00590.13370.22810.04080.23174.51659.9577-32.6801
23.58371.1121-0.23151.65741.80167.35070.02010.2137-0.5008-0.0570.26250.04340.4767-0.6531-0.28260.5513-0.0545-0.08950.36390.07140.4004-18.30513.8986-38.9115
33.0051-0.33720.21953.1587-1.04584.3655-0.11440.25830.2614-0.01820.18560.27950.3837-0.5195-0.07130.2015-0.144-0.00390.20990.0370.0537-16.68186.1005-9.7154
46.25990.4715-2.16362.4477-1.03335.3104-0.12660.69890.12460.00660.29990.95030.0208-1.8989-0.17330.2746-0.2324-0.14171.30890.19120.4992-41.66035.4154-15.0748
52.11430.05210.28152.3974-0.18232.78930.0305-0.283-0.67960.01240.12380.28860.9388-0.8299-0.15430.5974-0.31760.02180.39130.07650.2755-22.7495-8.1501-1.0029
65.12190.9443-3.698910.902413.685321.9296-0.02610.04530.2251-0.3913-0.39970.5146-0.449-0.60430.42580.42850.097-0.00490.14020.03920.2793-5.48935.568836.6124
74.0933-1.8747-1.45292.57610.97752.60360.1017-0.92881.05080.23750.3038-0.4282-0.2636-0.0172-0.40550.518-0.14010.02590.4367-0.15010.801311.46625.433942.7579
82.68180.3650.6142.94990.08672.70060.0010.12340.1959-0.2780.0154-0.2354-0.26780.1544-0.01650.1093-0.02890.03780.059-0.01660.05042.98719.491522.3979
92.4008-0.30570.09112.94750.45231.0899-0.1096-0.226-0.11180.47620.2907-0.75670.14390.2043-0.18110.2070.0152-0.15520.2595-0.14320.275820.4475-6.571839.4711
104.12630.26691.3675.07910.53363.48860.00520.5631-0.2367-0.3630.4112-1.2665-0.06620.8432-0.41640.0707-0.0431-0.00460.3554-0.17850.592926.729-8.170728.2416
111.5504-0.37710.6882.37790.12592.08550.134-0.0108-0.5135-0.12650.09170.10320.1956-0.21-0.22570.1303-0.0342-0.02120.1033-0.00660.1755-3.2707-8.220524.2844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 73
2X-RAY DIFFRACTION2A74 - 158
3X-RAY DIFFRACTION3A159 - 401
4X-RAY DIFFRACTION4A410 - 564
5X-RAY DIFFRACTION5A565 - 637
6X-RAY DIFFRACTION6B1 - 49
7X-RAY DIFFRACTION7B50 - 158
8X-RAY DIFFRACTION8B159 - 387
9X-RAY DIFFRACTION9B388 - 465
10X-RAY DIFFRACTION10B466 - 567
11X-RAY DIFFRACTION11B568 - 637

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  • 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

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