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- PDB-2jer: Agmatine deiminase of Enterococcus faecalis catalyzing its reaction. -

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Basic information

Entry
Database: PDB / ID: 2jer
TitleAgmatine deiminase of Enterococcus faecalis catalyzing its reaction.
ComponentsAGMATINE DEIMINASE
KeywordsHYDROLASE / AGMATINE DEIMINASE / TETRAMER / AGDI / 5- FOLD PSEUDOSYMMETRIC STRUCTURE / AGMATINE DEGRADATION PATHWAY / COVALENT AMIDINO ADDUCT / AGMATINE IMINOHYDROLASE
Function / homology
Function and homology information


agmatine deiminase / agmatine deiminase activity / putrescine biosynthetic process / protein-arginine deiminase activity
Similarity search - Function
Agmatine deiminase / Peptidyl-arginine deiminase, Porphyromonas-type / Porphyromonas-type peptidyl-arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
Putative agmatine deiminase
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTavarez, S. / Llacer, J.L. / Rubio, V.
CitationJournal: J.Bacteriol. / Year: 2007
Title: The Gene Cluster for Agmatine Catabolism of Enterococcus Faecalis: Study of Recombinant Putrescine Transcarbamylase and Agmatine Deiminase and a Snapshot of Agmatine Deiminase Catalyzing its Reaction.
Authors: Llacer, J.L. / Polo, L.M. / Tavarez, S. / Alarcon, B. / Hilario, R. / Rubio, V.
History
DepositionJan 19, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionJan 30, 2007ID: 2J2T
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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_validate_polymer_linkage / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGMATINE DEIMINASE
B: AGMATINE DEIMINASE
C: AGMATINE DEIMINASE
D: AGMATINE DEIMINASE
E: AGMATINE DEIMINASE
F: AGMATINE DEIMINASE
G: AGMATINE DEIMINASE
H: AGMATINE DEIMINASE


Theoretical massNumber of molelcules
Total (without water)351,6828
Polymers351,6828
Non-polymers00
Water39,1652174
1
A: AGMATINE DEIMINASE
B: AGMATINE DEIMINASE
E: AGMATINE DEIMINASE
F: AGMATINE DEIMINASE


Theoretical massNumber of molelcules
Total (without water)175,8414
Polymers175,8414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: AGMATINE DEIMINASE
D: AGMATINE DEIMINASE
G: AGMATINE DEIMINASE
H: AGMATINE DEIMINASE


Theoretical massNumber of molelcules
Total (without water)175,8414
Polymers175,8414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)107.727, 130.165, 126.726
Angle α, β, γ (deg.)90.00, 93.61, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12E
22G
32H
13A
23B
33C
43D
53F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 11
2116B1 - 11
3116C1 - 11
4116D1 - 11
5116E1 - 11
6116F1 - 11
7116G1 - 11
8116H1 - 11
1212A12 - 26
2212B12 - 26
3212C12 - 26
4212D12 - 26
5212E12 - 26
6212F12 - 26
7212G12 - 26
8212H12 - 26
1311A27 - 53
2311B27 - 53
3311C27 - 53
4311D27 - 53
5311E27 - 53
6311F27 - 53
7311G27 - 53
8311H27 - 53
1412A54 - 76
2412B54 - 76
3412C54 - 76
4412D54 - 76
5412E54 - 76
6412F54 - 76
7412G54 - 76
8412H54 - 76
1511A77 - 101
2511B77 - 101
3511C77 - 101
4511D77 - 101
5511E77 - 101
6511F77 - 101
7511G77 - 101
8511H77 - 101
1615A102 - 109
2615B102 - 109
3615C102 - 109
4615D102 - 109
5615E102 - 109
6615F102 - 109
7615G102 - 109
8615H102 - 109
1711A110 - 125
2711B110 - 125
3711C110 - 125
4711D110 - 125
5711E110 - 125
6711F110 - 125
7711G110 - 125
8711H110 - 125
1814A126 - 130
2814B126 - 130
3814C126 - 130
4814D126 - 130
5814E126 - 130
6814F126 - 130
7814G126 - 130
8814H126 - 130
1911A131 - 162
2911B131 - 162
3911C131 - 162
4911D131 - 162
5911E131 - 162
6911F131 - 162
7911G131 - 162
8911H131 - 162
11011A169 - 183
21011B169 - 183
31011C169 - 183
41011D169 - 183
51011E169 - 183
61011F169 - 183
71011G169 - 183
81011H169 - 183
11111A202 - 229
21111B202 - 229
31111C202 - 229
41111D202 - 229
51111E202 - 229
61111F202 - 229
71111G202 - 229
81111H202 - 229
11214A230 - 234
21214B230 - 234
31214C230 - 234
41214D230 - 234
51214E230 - 234
61214F230 - 234
71214G230 - 234
81214H230 - 234
11311A287 - 324
21311B287 - 324
31311C287 - 324
41311D287 - 324
51311E287 - 324
61311F287 - 324
71311G287 - 324
81311H287 - 324
11414A236 - 286
21414B236 - 286
31414C236 - 286
41414D236 - 286
51414E236 - 286
61414F236 - 286
71414G236 - 286
81414H236 - 286
11513A325
21513B325
31513C325
41513D325
51513E325
61513F325
71513G325
81513H325
11611A326 - 355
21611B326 - 355
31611C326 - 355
41611D326 - 355
51611E326 - 355
61611F326 - 355
71611G326 - 355
81611H326 - 355
11713A235
21713B235
31713C235
41713D235
51713E235
61713F235
71713G235
81713H235
11814A163 - 168
21814B163 - 168
31814C163 - 168
41814D163 - 168
51814E163 - 168
61814F163 - 168
71814G163 - 168
81814H163 - 168
11912A184 - 201
21912B184 - 201
31912C184 - 201
41912D184 - 201
51912E184 - 201
61912F184 - 201
71912G184 - 201
81912H184 - 201
1126E356 - 366
2126G356 - 366
3126H356 - 366
1136A356 - 366
2136B356 - 366
3136C356 - 366
4136D356 - 366
5136F356 - 366

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.946, -0.09155, 0.311), (-0.09266, -0.9956, -0.01125), (0.3107, -0.01818, -0.9503)-19.27, -41.12, 108.4
2given(-0.97521, -0.10871, -0.19274), (-0.11518, -0.49436, 0.86159), (-0.18894, 0.86243, 0.46959)86.06313, -82.88605, 59.77095
3given(-0.08604, -0.00912, -0.99625), (0.00519, 0.99994, -0.0096), (0.99628, -0.006, -0.08599)59.24129, -7.46982, 82.21975

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Components

#1: Protein
AGMATINE DEIMINASE / / AGMATINE IMINOHYDROLASE


Mass: 43960.301 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: CARBON ATOM OF THE GUANIDINIUM GROUP OF AGMATINE COVALENTLY LINKED WITH THE THIOL GROUP OF CYS357
Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: SD10 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q837U5, agmatine deiminase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2174 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE HIS325 OF UNIPROT DATABASE IS AN ARGININE IN THIS E. FAECALIS STRAIN. THE CRYSTAL STRUCTURE ...THE HIS325 OF UNIPROT DATABASE IS AN ARGININE IN THIS E. FAECALIS STRAIN. THE CRYSTAL STRUCTURE INCLUDE THE 24- AMINO ACID C-TERMINAL EXTENSION VGGKQNSSSVDKLAAALEHHHHHH

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.5M SODIUM CHLORIDE, 1.6M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, 5MM AGMATINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9765
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.65→45.36 Å / Num. obs: 417377 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.4
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EWO
Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.364 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 20970 5 %RANDOM
Rwork0.167 ---
obs0.168 396242 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20.44 Å2
2---0.62 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23234 0 0 2174 25408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02223752
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.94632208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47352911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83925.4311217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.389153935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.17315119
X-RAY DIFFRACTIONr_chiral_restr0.1540.23442
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218451
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.212051
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.216425
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.21916
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8551.514925
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.236223579
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.045310059
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1974.58629
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
11A1874tight positional0.060.05
12B1874tight positional0.050.05
13C1874tight positional0.060.05
14D1874tight positional0.060.05
15E1874tight positional0.040.05
16F1874tight positional0.050.05
17G1874tight positional0.040.05
18H1874tight positional0.040.05
11A793medium positional0.450.5
12B793medium positional0.550.5
13C793medium positional0.480.5
14D793medium positional0.510.5
15E793medium positional0.530.5
16F793medium positional0.510.5
17G793medium positional0.450.5
18H793medium positional0.420.5
11A103loose positional0.545
12B103loose positional0.65
13C103loose positional0.645
14D103loose positional1.335
15E103loose positional0.465
16F103loose positional0.45
17G103loose positional0.545
18H103loose positional0.55
21E100loose positional0.265
22G100loose positional0.445
23H100loose positional0.475
31A93loose positional0.235
32B93loose positional0.245
33C93loose positional0.235
34D93loose positional0.445
35F93loose positional0.165
11A1874tight thermal0.170.5
12B1874tight thermal0.160.5
13C1874tight thermal0.160.5
14D1874tight thermal0.150.5
15E1874tight thermal0.140.5
16F1874tight thermal0.140.5
17G1874tight thermal0.120.5
18H1874tight thermal0.130.5
11A793medium thermal0.862
12B793medium thermal0.882
13C793medium thermal0.822
14D793medium thermal0.862
15E793medium thermal0.792
16F793medium thermal0.732
17G793medium thermal0.642
18H793medium thermal0.652
11A103loose thermal1.7810
12B103loose thermal1.9310
13C103loose thermal2.0310
14D103loose thermal1.9210
15E103loose thermal2.2610
16F103loose thermal1.5710
17G103loose thermal1.4810
18H103loose thermal1.4910
21E100loose thermal2.2910
22G100loose thermal1.6310
23H100loose thermal1.8310
31A93loose thermal1.1710
32B93loose thermal1.6410
33C93loose thermal1.1910
34D93loose thermal3.310
35F93loose thermal1.4510
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 1485 -
Rwork0.202 29288 -
obs--99.88 %
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)
10.5808-0.1871-0.15620.9274-0.04530.672-0.01520.0433-0.0018-0.05590.03640.05240.0226-0.0756-0.0211-0.1503-0.0115-0.0161-0.11380.0023-0.123621.637-10.12660.278
20.72470.2198-0.12970.9761-0.11230.7947-0.04490.05810.02480.00960.05910.07060.012-0.0936-0.0142-0.1375-0.0196-0.0084-0.1128-0.0112-0.126220.943-33.72457.986
30.66470.0892-0.00011.00540.02460.8344-0.03440.03550.00250.01750.02920.01980.03660.00350.0052-0.13780.0245-0.0059-0.11950.0071-0.1390.014-41.54998.239
40.57020.0029-0.13641.2173-0.15450.7566-0.00230.02460.01530.05580.0498-0.0139-0.04730.0006-0.0476-0.12390.0319-0.0039-0.11750.007-0.1265-2.26-18.10997.64
50.7982-0.32510.0031.0475-0.06460.4786-0.0481-0.02550.04120.04180.0519-0.2032-0.00290.0687-0.0038-0.13790.007-0.0358-0.0954-0.0226-0.075354.513-28.53575.14
60.6660.0862-0.0420.8627-0.1610.614-0.0311-0.01260.0021-0.03320.0195-0.2174-0.02580.05190.0115-0.1343-0.02250.0162-0.1037-0.019-0.041557.832-18.70753.906
70.62570.19440.03051.1425-0.48810.75180.0677-0.06170.05450.42720.05630.2137-0.125-0.0622-0.12410.08770.05490.1221-0.07030.0241-0.0565-20.176-36.251130.034
80.90820.3128-0.20331.1689-0.3070.81080.1255-0.09890.07280.5768-0.03940.0998-0.15750.0203-0.0860.20780.01020.0214-0.0764-0.0139-0.12830.831-26.45135.478
90.7049-0.26780.03310.9072-0.29990.997-0.0433-0.05110.15440.07850.0454-0.0565-0.1869-0.0156-0.002-0.10660.0001-0.0263-0.102-0.0037-0.071822.028.25865.031
100.96590.5374-0.250.8968-0.18390.816-0.12330.1599-0.223-0.08630.0708-0.06240.1789-0.02430.0526-0.0646-0.03340.0188-0.084-0.0395-0.055321.018-52.09253.275
110.8449-0.0380.06430.80280.05530.9013-0.0126-0.0165-0.18450.04840.008-0.02390.30550.07720.0045-0.01010.04110.0015-0.09060.0093-0.08244.931-59.83898.745
120.81280.1566-0.06661.1005-0.24150.79780.0516-0.0190.19060.1530.04940.101-0.2438-0.0968-0.1011-0.020.05560.0443-0.08890.01-0.0554-7.5690.13398.346
130.8176-0.5124-0.00271.43770.04270.5165-0.1978-0.3311-0.01590.38750.194-0.08720.05830.03840.0037-0.01310.0847-0.05380.0245-0.0096-0.062851.26-33.44993.229
140.94770.3249-0.25241.24420.02120.4689-0.07530.19070.008-0.32160.0822-0.2327-0.04270.0096-0.0069-0.0302-0.04730.0726-0.0492-0.0078-0.003660.997-13.68335.922
150.49670.368-0.31251.888-0.72851.15370.07230.08940.10350.33640.19390.6444-0.0782-0.4025-0.26620.04730.06690.18230.07560.10760.1695-37.792-41.563125.49
160.47570.24260.27051.98680.13241.03090.1646-0.09890.02760.6419-0.075-0.2858-0.15530.2773-0.08970.3051-0.0579-0.10630.0326-0.0116-0.062918.491-21.196139.967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 151
2X-RAY DIFFRACTION1A360 - 367
3X-RAY DIFFRACTION2B1 - 151
4X-RAY DIFFRACTION2B360 - 366
5X-RAY DIFFRACTION3C1 - 151
6X-RAY DIFFRACTION3C360 - 368
7X-RAY DIFFRACTION4D1 - 151
8X-RAY DIFFRACTION4D360 - 373
9X-RAY DIFFRACTION5E1 - 151
10X-RAY DIFFRACTION5E360 - 368
11X-RAY DIFFRACTION6F1 - 151
12X-RAY DIFFRACTION6F360 - 366
13X-RAY DIFFRACTION7G1 - 151
14X-RAY DIFFRACTION7G360 - 367
15X-RAY DIFFRACTION8H1 - 151
16X-RAY DIFFRACTION8H360 - 366
17X-RAY DIFFRACTION9A160 - 354
18X-RAY DIFFRACTION10B160 - 354
19X-RAY DIFFRACTION11C160 - 354
20X-RAY DIFFRACTION12D160 - 354
21X-RAY DIFFRACTION13E160 - 354
22X-RAY DIFFRACTION14F160 - 354
23X-RAY DIFFRACTION15G160 - 354
24X-RAY DIFFRACTION16H160 - 354

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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