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- PDB-3glb: Crystal structure of the effector binding domain of a CATM varian... -

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Basic information

Entry
Database: PDB / ID: 3glb
TitleCrystal structure of the effector binding domain of a CATM variant (R156H)
ComponentsHTH-type transcriptional regulator catM
KeywordsTRANSCRIPTION / LTTR / BENM / CATM / TRANSCRIPTIONAL ACTIVATOR / LYSR-TYPE TRANSCRIPTIONAL REGULATOR / Activator / Aromatic hydrocarbons catabolism / DNA-binding / Repressor / Transcription regulation
Function / homology
Function and homology information


: / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2Z,4Z)-HEXA-2,4-DIENEDIOIC ACID / HTH-type transcriptional regulator CatM
Similarity search - Component
Biological speciesAcinetobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsEzezika, O.C. / Craven, S.H. / Neidle, E.L. / Momany, C.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1.
Authors: Craven, S.H. / Ezezika, O.C. / Haddad, S. / Hall, R.A. / Momany, C. / Neidle, E.L.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionMay 19, 2009ID: 2H9Q
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator catM
B: HTH-type transcriptional regulator catM
C: HTH-type transcriptional regulator catM
D: HTH-type transcriptional regulator catM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,66316
Polymers101,3464
Non-polymers1,31712
Water4,432246
1
A: HTH-type transcriptional regulator catM
B: HTH-type transcriptional regulator catM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4309
Polymers50,6732
Non-polymers7577
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-37 kcal/mol
Surface area18530 Å2
MethodPISA
2
C: HTH-type transcriptional regulator catM
D: HTH-type transcriptional regulator catM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2347
Polymers50,6732
Non-polymers5605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-3 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.689, 115.410, 76.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
34C
44D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNARGARGAA90 - 1552 - 67
21GLNGLNARGARGBB90 - 1552 - 67
31GLNGLNARGARGCC90 - 1552 - 67
41GLNGLNARGARGDD90 - 1552 - 67
12ILEILESERSERAA157 - 21969 - 131
22ILEILESERSERBB157 - 21969 - 131
32ILEILESERSERCC157 - 21969 - 131
42ILEILESERSERDD157 - 21969 - 131
13ASPASPHISHISAA277 - 296189 - 208
23ASPASPHISHISBB277 - 296189 - 208
33ASPASPHISHISCC277 - 296189 - 208
43ASPASPHISHISDD277 - 296189 - 208
14LEULEUASNASNAA221 - 275133 - 187
24LEULEUASNASNBB221 - 275133 - 187
34LEULEUASNASNCC221 - 275133 - 187
44LEULEUASNASNDD221 - 275133 - 187

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
HTH-type transcriptional regulator catM / Cat operon transcriptional regulator


Mass: 25336.521 Da / Num. of mol.: 4 / Mutation: R156H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Gene: catM, catR, ACIAD1445 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07774
#2: Chemical
ChemComp-CCU / (2Z,4Z)-HEXA-2,4-DIENEDIOIC ACID / CIS,CIS-MUCONIC ACID / Muconic acid


Mass: 142.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 296.4 K / Method: microbatch under oil
Details: precipitant: 1.6 M Ammonium Sulfate, 0.1 m Citric Acid, ph 4, 0.1 m Cis,Cis-Muconate. protein: 20 mM Tris HCL, 0.5 M NACL, ph 7.9, 250 mM Imdizale, 10% Glycerol protein and preicipitant ...Details: precipitant: 1.6 M Ammonium Sulfate, 0.1 m Citric Acid, ph 4, 0.1 m Cis,Cis-Muconate. protein: 20 mM Tris HCL, 0.5 M NACL, ph 7.9, 250 mM Imdizale, 10% Glycerol protein and preicipitant mixed in a ratio of 3:1 , MICROBATCH UNDER OIL, temperature 296.4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2005 / Details: Bending magnet
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7.8 % / Av σ(I) over netI: 31.1 / Number: 194071 / Rmerge(I) obs: 0.072 / Χ2: 1.14 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 24741 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.035099.910.031.1677.4
4.796.0310010.0531.447.8
4.184.7910010.0531.5017.9
3.84.1810010.0681.3147.9
3.533.810010.0921.1668
3.323.5310010.1331.088
3.153.3210010.1910.978
3.023.1510010.2710.928
2.93.0210010.3560.8958
2.82.998.610.4620.9257.5
ReflectionResolution: 2.8→50 Å / Num. obs: 24741 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 73.8 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.14 / Net I/σ(I): 31.098
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2405 / Χ2: 0.925 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F7B
Resolution: 2.8→45.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.757 / SU B: 33.364 / SU ML: 0.375 / SU Rfree: 0.437 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1221 4.9 %RANDOM
Rwork0.205 ---
obs0.209 24719 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 146.85 Å2 / Biso mean: 53.208 Å2 / Biso min: 27.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--1.65 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6759 0 85 246 7090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226986
X-RAY DIFFRACTIONr_bond_other_d0.0040.024669
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9889475
X-RAY DIFFRACTIONr_angle_other_deg0.884311518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64724.583288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.426151234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1191528
X-RAY DIFFRACTIONr_chiral_restr0.0550.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027568
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021292
X-RAY DIFFRACTIONr_nbd_refined0.190.21491
X-RAY DIFFRACTIONr_nbd_other0.1710.24778
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23371
X-RAY DIFFRACTIONr_nbtor_other0.0810.23587
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.210
X-RAY DIFFRACTIONr_mcbond_it0.43325577
X-RAY DIFFRACTIONr_mcbond_other0.06121714
X-RAY DIFFRACTIONr_mcangle_it0.58346986
X-RAY DIFFRACTIONr_scbond_it1.59982999
X-RAY DIFFRACTIONr_scangle_it2.324102489
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A895MEDIUM POSITIONAL0.50.5
12B895MEDIUM POSITIONAL0.380.5
13C895MEDIUM POSITIONAL0.440.5
11D895MEDIUM POSITIONAL0.430.5
11A895MEDIUM THERMAL0.232
12B895MEDIUM THERMAL0.212
13C895MEDIUM THERMAL0.172
11D895MEDIUM THERMAL0.192
21A845MEDIUM POSITIONAL0.530.5
22B845MEDIUM POSITIONAL0.430.5
23C845MEDIUM POSITIONAL0.380.5
21D845MEDIUM POSITIONAL0.410.5
21A845MEDIUM THERMAL0.22
22B845MEDIUM THERMAL0.262
23C845MEDIUM THERMAL0.192
21D845MEDIUM THERMAL0.162
31A262MEDIUM POSITIONAL0.520.5
32B262MEDIUM POSITIONAL0.340.5
33C262MEDIUM POSITIONAL0.470.5
31D262MEDIUM POSITIONAL0.430.5
31A262MEDIUM THERMAL0.242
32B262MEDIUM THERMAL0.232
33C262MEDIUM THERMAL0.182
31D262MEDIUM THERMAL0.252
41A667MEDIUM POSITIONAL0.420.5
42B667MEDIUM POSITIONAL0.420.5
43C667MEDIUM POSITIONAL0.360.5
41D667MEDIUM POSITIONAL0.340.5
41A667MEDIUM THERMAL0.232
42B667MEDIUM THERMAL0.262
43C667MEDIUM THERMAL0.232
41D667MEDIUM THERMAL0.192
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 85 -
Rwork0.288 1665 -
all-1750 -
obs--97.82 %
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)
13.7373-1.8081-0.011.5905-1.83794.74430.10040.4038-0.3178-0.1525-0.01640.07610.3044-0.2668-0.0841-0.01-0.0059-0.0835-0.0413-0.053-0.245817.541-38.277-1.699
27.23113.6191-0.93253.11873.558812.5158-0.35670.75630.2551-0.46730.1427-0.0701-0.3847-0.17010.21390.01160.1176-0.10620.0697-0.0313-0.196917.335-36.319-14.065
35.57560.72341.16481.28-0.93091.2304-0.14920.77290.5473-0.4210.02510.05080.16590.26620.12410.2295-0.017-0.07290.240.0899-0.135628.157-17.833-14.507
48.5111-2.88572.2697.1529-1.10931.8241-0.17750.3340.2846-0.16850.16790.1459-0.1686-0.12030.00960.162-0.0938-0.02070.0340.0266-0.187932.887-18.458-7.047
51.66431.2973-2.11777.76452.60455.3758-0.26860.36290.3692-0.4058-0.17110.54260.2677-0.47960.4396-0.1360.1125-0.14210.1404-0.0348-0.19868.963-33.257-6.345
613.90815.30558.330816.84359.1684.9901-0.96151.13893.1735-0.16-0.7340.9908-2.3445-0.98231.69550.14770.24510.06250.70590.1214-0.007210.535-22.3962.556
74.2312-1.7508-0.14386.6731-0.52130.06160.08860.59020.0416-0.4999-0.150.3047-0.5656-0.21480.06140.0562-0.10720.05870.1404-0.0197-0.245448.106-28.456-9.397
83.01231.3294-1.17393.342.29523.5077-0.10930.351-0.2007-0.3374-0.02110.1265-0.00630.13060.1304-0.0116-0.07140.04320.1848-0.028-0.120151.934-36.459-12.229
93.0426-0.9079-1.19133.23250.61993.80980.0002-0.0511-0.497-0.0994-0.02740.0218-0.01410.09130.0272-0.1971-0.0491-0.0129-0.03630.0456-0.237834.836-45.9535.675
101.20262.26482.73394.48434.87366.5595-0.2340.1204-0.0321-0.28940.0596-0.1486-0.13570.40120.1743-0.0277-0.05710.07730.1437-0.0275-0.232958.68-32.877-8.636
11176.06-30.6767-4.360252.64169.80611.8383-4.2177-8.2632.45046.67343.78621.22260.6917-0.97250.43150.81530.09180.17761.1505-0.3896-0.077751.139-22.2918.53
124.0624-0.8765-0.51379.7349-3.63081.53160.3410.4697-0.94870.2395-0.2431-0.31990.6548-0.0715-0.09790.4151-0.0161-0.19870.1844-0.1596-0.118817.63-23.114-44.095
137.25313.7166.88846.01495.38557.8852-0.02990.41710.145-0.30310.07170.7372-0.1665-0.3166-0.04180.06640.0214-0.05510.1803-0.0243-0.2759.448-11.367-47.447
142.01430.95392.21472.87751.53332.53170.19080.00220.20330.253-0.22770.33310.1851-0.14720.03690.1282-0.04950.04380.1019-0.0468-0.294116.237-0.312-32.531
154.1656-2.0265-0.54452.6033-0.12946.31750.05550.10970.19290.2498-0.34640.14520.4893-0.2560.29080.1708-0.09780.009-0.0179-0.0722-0.271820.5091.333-32.846
168.55520.58842.05973.80930.85392.43380.4220.1733-1.13120.70180.04730.42580.7071-0.4112-0.46930.3331-0.0626-0.03610.2116-0.0438-0.2037.105-22.395-40.008
1721.1993-0.14078.832920.932.372932.8008-0.0860.2250.53383.83020.33610.776-0.0791-0.5964-0.25011.0058-0.1303-0.06490.19990.09140.186412.823-19.279-24.893
182.3830.01881.40852.31934.34938.94780.02640.20270.33230.5401-0.064-0.05120.18510.49730.03760.03060.0731-0.07320.16730.0818-0.320336.9743.4-41.984
195.06922.8381.60778.22461.68486.99630.29790.26640.1228-0.2955-0.2090.0946-0.0374-0.0939-0.0889-0.0940.1375-0.01330.14890.0924-0.285937.2824.889-49.608
201.32930.1143-0.10123.7649-0.12962.27610.22150.2276-0.7474-0.246-0.0884-0.67910.69720.3789-0.13310.24690.252-0.16030.3611-0.09430.054240.459-18.604-49.819
218.2482-0.87380.26883.68490.80294.93970.50970.3465-0.39050.2664-0.2887-0.49470.52790.1975-0.2210.30540.1419-0.2210.1223-0.0281-0.078834.117-19.451-44.895
222.9362-1.92870.86998.2379-4.06097.50140.01730.05920.11690.2471-0.1517-0.2612-0.36680.75260.1344-0.11790.0488-0.0410.33260.1094-0.252146.6814.996-44.896
234.67750.34731.5470.02580.11480.51170.324-1.75740.5138-1.1689-0.74850.43383.74264.60730.42450.49520.1907-0.04460.48-0.01450.130355.573-4.905-49.278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A89 - 118
2X-RAY DIFFRACTION2A119 - 148
3X-RAY DIFFRACTION3A149 - 228
4X-RAY DIFFRACTION4A229 - 266
5X-RAY DIFFRACTION5A267 - 294
6X-RAY DIFFRACTION6A295 - 303
7X-RAY DIFFRACTION7B90 - 112
8X-RAY DIFFRACTION8B113 - 162
9X-RAY DIFFRACTION9B163 - 206
10X-RAY DIFFRACTION10B268 - 294
11X-RAY DIFFRACTION11B295 - 301
12X-RAY DIFFRACTION12C89 - 124
13X-RAY DIFFRACTION13C125 - 148
14X-RAY DIFFRACTION14C149 - 206
15X-RAY DIFFRACTION15C207 - 267
16X-RAY DIFFRACTION16C268 - 295
17X-RAY DIFFRACTION17C296 - 300
18X-RAY DIFFRACTION18D89 - 112
19X-RAY DIFFRACTION19D113 - 148
20X-RAY DIFFRACTION20D149 - 217
21X-RAY DIFFRACTION21D218 - 266
22X-RAY DIFFRACTION22D267 - 297
23X-RAY DIFFRACTION23D298 - 307

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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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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

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