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- PDB-2f4i: Crystal structure of an ob-fold protein (tm0957) from thermotoga ... -

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Basic information

Entry
Database: PDB / ID: 2f4i
TitleCrystal structure of an ob-fold protein (tm0957) from thermotoga maritima msb8 at 1.90 A resolution
Componentshypothetical protein TM0957Hypothesis
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Envelope glycoprotein gp160, DUF2291, helical domain / Envelope glycoprotein gp160, DUF2291, alpha/beta domain / Uncharacterised conserved protein UCP033535, periplasmic lipoprotein / TM0957-like superfamily / Predicted periplasmic lipoprotein (DUF2291) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (tm0957) from THERMOTOGA MARITIMA at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE 1. THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] ...SEQUENCE 1. THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED BY RESIDUES 33-217 OF THE PREDICTED TM0957 GENE PRODUCT. RESIDUES 1-32 WERE OMITTED TO REMOVE A PREDICTED TRANSMEMBRANE HELIX. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION. MASS SPECTROMETRIC ANALYSIS SUGGESTS THAT 70-88 % OF THE AVAILABLE SITES ARE METHYLATED.
Remark 300BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TM0957
B: hypothetical protein TM0957
C: hypothetical protein TM0957
D: hypothetical protein TM0957
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7758
Polymers92,6444
Non-polymers1314
Water8,719484
1
A: hypothetical protein TM0957
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2323
Polymers23,1611
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein TM0957
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1962
Polymers23,1611
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hypothetical protein TM0957
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1852
Polymers23,1611
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: hypothetical protein TM0957


Theoretical massNumber of molelcules
Total (without water)23,1611
Polymers23,1611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: hypothetical protein TM0957
hetero molecules

B: hypothetical protein TM0957
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4285
Polymers46,3222
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y+1/2,-z1
Buried area1690 Å2
ΔGint-44 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.677, 78.075, 82.487
Angle α, β, γ (deg.)90.00, 93.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31B
41D
12C
22A
32B
42D
13C
23A
33B
43D
14C
24A
34B
44D
15C
25A
35B
45D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHELEUCC39 - 6019 - 40
21PHELEUAA39 - 6019 - 40
31PHELEUBB39 - 6019 - 40
41PHELEUDD39 - 6019 - 40
12GLYVALCC61 - 8641 - 66
22GLYVALAA61 - 8641 - 66
32GLYVALBB61 - 8641 - 66
42GLYVALDD61 - 8641 - 66
13ARGHISCC92 - 12872 - 108
23ARGHISAA92 - 12872 - 108
33ARGHISBB92 - 12872 - 108
43ARGHISDD92 - 12872 - 108
14GLYALACC133 - 156113 - 136
24GLYALAAA133 - 156113 - 136
34GLYALABB133 - 156113 - 136
44GLYALADD133 - 156113 - 136
15THRGLNCC157 - 214137 - 194
25THRGLNAA157 - 214137 - 194
35THRGLNBB157 - 214137 - 194
45THRGLNDD157 - 214137 - 194

NCS ensembles :
ID
1
2
3
4
5
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Components

#1: Protein
hypothetical protein TM0957 / Hypothesis


Mass: 23160.959 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0957 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X052
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.41 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 0.2M MgCl2, 30.0% PEG-4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942, 0.95372
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2005 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.953721
ReflectionResolution: 2.25→29.83 Å / Num. obs: 39599 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 5.8
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→29.83 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.66 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. MG AND CL WERE ADDED BASED ON CRYSTALLIZATION CONDITIONS. 4. TLS GROUPS WERE ASSIGNED WITH THE AID OF TLSMD.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1987 5 %RANDOM
Rwork0.19 ---
all0.193 ---
obs0.19279 37581 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å2-0.16 Å2
2--0.79 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5639 0 4 484 6127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225866
X-RAY DIFFRACTIONr_bond_other_d0.0020.023947
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9717942
X-RAY DIFFRACTIONr_angle_other_deg1.03939686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9125705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04125.122287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48515.0781086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2951529
X-RAY DIFFRACTIONr_chiral_restr0.0950.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026408
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021153
X-RAY DIFFRACTIONr_nbd_refined0.20.21022
X-RAY DIFFRACTIONr_nbd_other0.190.23962
X-RAY DIFFRACTIONr_nbtor_refined0.180.22775
X-RAY DIFFRACTIONr_nbtor_other0.0890.23173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0910.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.216
X-RAY DIFFRACTIONr_mcbond_it1.70733715
X-RAY DIFFRACTIONr_mcbond_other0.3831442
X-RAY DIFFRACTIONr_mcangle_it2.33655748
X-RAY DIFFRACTIONr_scbond_it1.16922526
X-RAY DIFFRACTIONr_scangle_it1.61132194
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11C123tight positional0.040.05
12A123tight positional0.070.05
13B123tight positional0.070.05
14D123tight positional0.060.05
21C154tight positional0.040.05
22A154tight positional0.060.05
23B154tight positional0.050.05
24D154tight positional0.060.05
31C218tight positional0.050.05
32A218tight positional0.060.05
33B218tight positional0.070.05
34D218tight positional0.050.05
41C142tight positional0.070.05
42A142tight positional0.090.05
43B142tight positional0.120.05
44D142tight positional0.050.05
51C341tight positional0.050.05
52A341tight positional0.060.05
53B341tight positional0.060.05
54D341tight positional0.060.05
11C184medium positional0.560.5
12A184medium positional0.280.5
13B184medium positional0.420.5
14D184medium positional0.370.5
21C140medium positional0.20.5
22A140medium positional0.330.5
23B140medium positional0.340.5
24D140medium positional0.380.5
31C266medium positional0.350.5
32A266medium positional0.420.5
33B266medium positional0.40.5
34D266medium positional0.420.5
41C110medium positional0.680.5
42A110medium positional0.840.5
43B110medium positional0.760.5
44D110medium positional0.70.5
51C357medium positional0.50.5
52A357medium positional0.720.5
53B357medium positional0.580.5
54D357medium positional0.560.5
11C123tight thermal0.180.5
12A123tight thermal0.20.5
13B123tight thermal0.160.5
14D123tight thermal0.170.5
21C154tight thermal0.160.5
22A154tight thermal0.180.5
23B154tight thermal0.180.5
24D154tight thermal0.130.5
31C218tight thermal0.170.5
32A218tight thermal0.160.5
33B218tight thermal0.170.5
34D218tight thermal0.180.5
41C142tight thermal0.20.5
42A142tight thermal0.190.5
43B142tight thermal0.180.5
44D142tight thermal0.140.5
51C341tight thermal0.180.5
52A341tight thermal0.170.5
53B341tight thermal0.170.5
54D341tight thermal0.140.5
11C184medium thermal0.742
12A184medium thermal0.962
13B184medium thermal0.772
14D184medium thermal0.682
21C140medium thermal0.542
22A140medium thermal0.992
23B140medium thermal0.862
24D140medium thermal0.782
31C266medium thermal0.612
32A266medium thermal0.62
33B266medium thermal0.562
34D266medium thermal0.742
41C110medium thermal1.042
42A110medium thermal1.032
43B110medium thermal1.042
44D110medium thermal0.52
51C357medium thermal0.732
52A357medium thermal0.742
53B357medium thermal0.682
54D357medium thermal0.682
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 159 -
Rwork0.221 2705 -
obs--98.39 %
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)
10.6503-0.28280.66671.10250.78077.05960.05730.0689-0.1076-0.1418-0.02970.02240.20080.0081-0.0275-0.0721-0.01520.0012-0.0506-0.0112-0.019866.225639.85859.1012
20.714-0.04670.03752.266-0.75262.1978-0.0409-0.05760.02250.16480.0322-0.0519-0.0552-0.05060.0087-0.05120.02370.0081-0.0389-0.0116-0.025462.820345.201622.18
30.89740.4888-0.37532.0598-0.60552.62650.02290.1157-0.0038-0.0917-0.0494-0.0087-0.02790.0270.0264-0.12670.0285-0.0076-0.0310.0116-0.026765.4347.46748.7446
40.8443-0.5468-0.35240.86720.08337.0929-0.05880.0170.1221-0.0290.0044-0.0242-0.2623-0.22520.0544-0.0425-0.01660.0186-0.0462-0.0068-0.004669.319235.2425-18.1919
51.9964-0.48610.281.04680.05622.362-0.06830.1796-0.0799-0.07050.0219-0.07-0.00740.16540.04640.0154-0.00640.0378-0.00990.0068-0.020274.972627.1232-32.5697
61.0575-0.31880.38430.8778-0.32072.8413-0.01570.0832-0.0118-0.04140.0130.0478-0.07080.00030.0027-0.038-0.00150.0109-0.0481-0.0058-0.00767.001728.8189-19.4437
70.76490.37480.2071.1349-0.17657.5821-0.0309-0.0015-0.1279-0.0166-0.0355-0.0584-0.09580.00620.0665-0.0656-0.0166-0.02990.02580.00970.041834.438942.695817.792
82.93760.775-0.22850.94560.18430.65410.0968-0.4181-0.16670.1728-0.0935-0.161-0.01370.0512-0.0033-0.0016-0.0216-0.05410.09670.03450.005736.765644.729434.414
93.7010.8006-0.61170.4139-0.14970.78850.00450.08720.07690.01280.0332-0.0772-0.0434-0.0753-0.0377-0.041-0.0043-0.009-0.04410.02080.01832.401547.976519.904
100.83270.0982-0.6690.7698-0.838514.37990.041-0.0071-0.0992-0.0370.0207-0.10480.52-0.39-0.06170.0252-0.0251-0.01680.0565-0.00180.080433.200138.5611-6.1171
112.05340.4694-0.30161.99550.27364.1779-0.07050.1789-0.1222-0.06330.1482-0.13560.0343-0.0532-0.07780.0282-0.038-0.02470.0969-0.01580.046632.511740.1129-23.1575
122.38820.66780.6452.458-0.18756.40290.1334-0.0352-0.1383-0.04660.0915-0.02290.2345-0.4408-0.2248-0.0216-0.0293-0.01920.066-0.00130.0527.704639.7486-11.447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA39 - 8219 - 62
2X-RAY DIFFRACTION2AA83 - 15663 - 136
3X-RAY DIFFRACTION3AA157 - 214137 - 194
4X-RAY DIFFRACTION4BB37 - 8217 - 62
5X-RAY DIFFRACTION5BB83 - 14363 - 123
6X-RAY DIFFRACTION6BB144 - 214124 - 194
7X-RAY DIFFRACTION7CC38 - 8118 - 61
8X-RAY DIFFRACTION8CC82 - 14362 - 123
9X-RAY DIFFRACTION9CC144 - 214124 - 194
10X-RAY DIFFRACTION10DD39 - 8019 - 60
11X-RAY DIFFRACTION11DD81 - 14461 - 124
12X-RAY DIFFRACTION12DD145 - 214125 - 194

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