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- PDB-3n99: Crystal structure of TM1086 -

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Basic information

Entry
Database: PDB / ID: 3n99
TitleCrystal structure of TM1086
Componentsuncharacterized protein TM1086
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


tm1086 (SG structure) fold / tm1086 (SG structure) domain / tm1086 fold / tm1086 domain / Protein of unknown function DUF4438 / TM_1086 superfamily / TM_1086, SG structure domain / : / Domain of unknown function (DUF4438), N-terminal / Domain of unknown function (DUF4438), C-terminal ...tm1086 (SG structure) fold / tm1086 (SG structure) domain / tm1086 fold / tm1086 domain / Protein of unknown function DUF4438 / TM_1086 superfamily / TM_1086, SG structure domain / : / Domain of unknown function (DUF4438), N-terminal / Domain of unknown function (DUF4438), C-terminal / Thrombin, subunit H - #170 / 3-layer Sandwich / Few Secondary Structures / Irregular / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DUF4438 domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsChruszcz, M. / Domagalski, M.J. / Wang, S. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of TM1086
Authors: Chruszcz, M. / Domagalski, M.J. / Wang, S. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein TM1086
B: uncharacterized protein TM1086
C: uncharacterized protein TM1086
D: uncharacterized protein TM1086
E: uncharacterized protein TM1086
G: uncharacterized protein TM1086
H: uncharacterized protein TM1086
I: uncharacterized protein TM1086
J: uncharacterized protein TM1086
K: uncharacterized protein TM1086
L: uncharacterized protein TM1086
M: uncharacterized protein TM1086
N: uncharacterized protein TM1086
O: uncharacterized protein TM1086
P: uncharacterized protein TM1086
S: uncharacterized protein TM1086
T: uncharacterized protein TM1086
U: uncharacterized protein TM1086
V: uncharacterized protein TM1086
X: uncharacterized protein TM1086
a: uncharacterized protein TM1086
b: uncharacterized protein TM1086
c: uncharacterized protein TM1086
d: uncharacterized protein TM1086
e: uncharacterized protein TM1086
g: uncharacterized protein TM1086
h: uncharacterized protein TM1086
i: uncharacterized protein TM1086
j: uncharacterized protein TM1086
k: uncharacterized protein TM1086
hetero molecules


Theoretical massNumber of molelcules
Total (without water)936,251116
Polymers933,20230
Non-polymers3,04986
Water91,0485054
1
A: uncharacterized protein TM1086
B: uncharacterized protein TM1086
C: uncharacterized protein TM1086
D: uncharacterized protein TM1086
E: uncharacterized protein TM1086
G: uncharacterized protein TM1086
H: uncharacterized protein TM1086
I: uncharacterized protein TM1086
J: uncharacterized protein TM1086
K: uncharacterized protein TM1086
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,02437
Polymers311,06710
Non-polymers95727
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: uncharacterized protein TM1086
M: uncharacterized protein TM1086
N: uncharacterized protein TM1086
O: uncharacterized protein TM1086
P: uncharacterized protein TM1086
S: uncharacterized protein TM1086
T: uncharacterized protein TM1086
U: uncharacterized protein TM1086
V: uncharacterized protein TM1086
X: uncharacterized protein TM1086
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,09539
Polymers311,06710
Non-polymers1,02829
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
a: uncharacterized protein TM1086
b: uncharacterized protein TM1086
c: uncharacterized protein TM1086
d: uncharacterized protein TM1086
e: uncharacterized protein TM1086
g: uncharacterized protein TM1086
h: uncharacterized protein TM1086
i: uncharacterized protein TM1086
j: uncharacterized protein TM1086
k: uncharacterized protein TM1086
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,13140
Polymers311,06710
Non-polymers1,06430
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)289.839, 299.521, 316.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61G
71H
81I
91J
101K
111L
121M
131N
141O
151P
Detailsdecamer

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Components

#1: Protein ...
uncharacterized protein TM1086


Mass: 31106.725 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1086 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q9X0H2
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5054 / 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: 3.67 Å3/Da / Density % sol: 66.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.6
Details: 60% Tacsimate, 0.1M Na citrate, pH 5.6, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 13, 2006 / Details: MIRRORS
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. all: 537068 / Num. obs: 537068 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 19.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.4 / Num. unique all: 26709 / Rsym value: 0.55 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0109refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DCL
Resolution: 2.38→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.28 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 26930 5 %RANDOM
Rwork0.1514 ---
all0.15338 509826 --
obs0.15338 509826 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.764 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms63060 0 86 5054 68200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02264640
X-RAY DIFFRACTIONr_bond_other_d00.0243441
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.96787470
X-RAY DIFFRACTIONr_angle_other_deg4.2933106940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67958554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4624.3512450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5141511415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.19415343
X-RAY DIFFRACTIONr_chiral_restr0.0980.210043
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02172135
X-RAY DIFFRACTIONr_gen_planes_other0.0070.0211776
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_it0.9281.541799
X-RAY DIFFRACTIONr_mcbond_other01.517639
X-RAY DIFFRACTIONr_mcangle_it1.907267437
X-RAY DIFFRACTIONr_scbond_it3.256322841
X-RAY DIFFRACTIONr_scangle_it5.7444.519977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3391 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.320.5
Bmedium positional0.310.5
Cmedium positional0.310.5
Dmedium positional0.290.5
Emedium positional0.290.5
Gmedium positional0.460.5
Hmedium positional0.350.5
Imedium positional0.470.5
Jmedium positional0.340.5
Kmedium positional0.320.5
Lmedium positional0.30.5
Mmedium positional0.270.5
Nmedium positional0.290.5
Omedium positional0.320.5
Pmedium positional0.30.5
Smedium positional0.360.5
Tmedium positional0.290.5
Umedium positional0.290.5
Vmedium positional0.320.5
Xmedium positional0.420.5
amedium positional0.260.5
bmedium positional0.340.5
cmedium positional0.30.5
dmedium positional0.30.5
emedium positional0.390.5
gmedium positional0.490.5
hmedium positional0.370.5
imedium positional0.30.5
jmedium positional0.370.5
kmedium positional0.460.5
Amedium thermal1.682
Bmedium thermal1.992
Cmedium thermal3.412
Dmedium thermal2.722
Emedium thermal2.772
Gmedium thermal2.542
Hmedium thermal2.542
Imedium thermal1.582
Jmedium thermal4.912
Kmedium thermal3.592
Lmedium thermal2.62
Mmedium thermal2.182
Nmedium thermal1.942
Omedium thermal2.312
Pmedium thermal2.462
Smedium thermal3.432
Tmedium thermal2.222
Umedium thermal3.512
Vmedium thermal1.752
Xmedium thermal1.72
amedium thermal3.032
bmedium thermal3.772
cmedium thermal2.462
dmedium thermal2.262
emedium thermal1.692
gmedium thermal3.532
hmedium thermal3.492
imedium thermal2.822
jmedium thermal3.52
kmedium thermal1.912
LS refinement shellResolution: 2.381→2.443 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 1794 -
Rwork0.219 33670 -
obs--89.04 %
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)
10.2073-0.0084-0.01630.102-0.17640.31340.0097-0.0059-0.0098-0.0029-0.00290.0105-0.00110.0048-0.00690.012-0.0123-0.01370.0568-0.00310.0225-22.01486.74824.595
20.31940.0073-0.01850.103-0.10720.1181-0.01610.00830.0019-0.01270.01520.00690.0077-0.00710.00090.0089-0.0122-0.00750.0570.00170.011616.31288.81721.248
30.2087-0.00740.07320.0942-0.09080.109-0.01490.0098-0.02780.00130.0223-0.0019-0.0074-0.0165-0.00730.0064-0.0027-0.00260.0236-0.00340.040231.78969.92551.002
40.35740.02340.05220.0213-0.0270.1019-0.0180.01050.00390.0071-0.0131-0.0029-0.0044-0.00010.03110.0117-0.0177-0.00470.044-0.00020.032-30.11666.70356.465
50.23770.0874-0.09970.0966-0.11690.2038-0.00030.00740.00430.00680.00660.00240.01110.0049-0.00630.0107-0.0045-0.00610.02390.00970.04833.18856.472.897
60.32250.10670.16180.1696-0.00920.37150.0015-0.06480.046-0.0063-0.03170.0281-0.0053-0.0390.03020.0137-0.0010.01350.0699-0.03420.0328-26.61691.48379.025
70.40610.0786-0.03830.346-0.17130.08730.0164-0.05840.02420.0597-0.0259-0.0148-0.0250.00760.00940.0252-0.0192-0.0090.0646-0.02290.02399.93785.30689.226
80.2580.0485-0.08570.1558-0.03310.1112-0.00970.00180.0120.0050.00570.01260.0024-0.01540.00410.0161-0.0165-0.0110.0298-0.00590.041732.465101.61862.68
90.32920.12190.04540.0817-0.01450.5403-0.0186-0.01130.060.0053-0.0010.0312-0.0852-0.07330.01960.0240.0284-0.00650.0439-0.02060.0742-26.673112.20846.432
100.3932-0.10890.0660.0729-0.04480.33280.01320.00250.0936-0.0251-0.00310.0014-0.0487-0.002-0.01010.0333-0.0078-0.01920.01090.01020.068510.01118.50136.324
110.01150.01040.00010.1426-0.06030.3686-0.01650.00070.01180.00040.0225-0.00580.01380.0013-0.0060.0339-0.0125-0.02130.03450.00430.017-66.84456.69729.897
120.06810.13430.00270.28560.0020.1632-0.0139-0.00730.002-0.01590.00340.0105-0.0080.01620.01040.0495-0.0021-0.00490.02280.00560.0183-86.76524.69821.889
130.0870.0810.0030.16330.08210.32840.0107-0.0012-0.01170.01310.00550.00220.00150.0054-0.01620.0436-0.01360.0040.0133-0.00920.0165-88.74921.362-16.395
140.08380.11280.07170.24030.03140.2341-0.0072-0.01380.0097-0.0062-0.0194-0.00680.0094-0.00250.02660.0159-0.0183-0.00780.03880.00490.0203-56.61473.263-3.317
150.1070.1165-0.06170.1319-0.08510.1957-0.00110.00060.0050.0043-0.01030.0050.0220.00620.01140.0293-0.01940.00110.0335-0.00330.0066-70.03351.278-31.905
160.36940.07430.06370.08630.02680.4188-0.01370.01550.0666-0.0092-0.00930.0213-0.0442-0.01210.02310.0560.0108-0.03150.01660.00580.0354-85.54289.459-10.137
170.21160.1331-0.01540.14640.04380.2673-0.01450.01350.0312-0.00630.02640.0069-0.0112-0.0422-0.01180.0302-0.0091-0.02730.05220.0120.0287-101.81962.799-32.743
180.128-0.0293-0.13680.33220.00850.4105-0.0161-0.0014-0.017-0.0154-0.01270.07290.0061-0.06810.02880.0091-0.0105-0.00920.0682-0.00510.0439-118.48836.336-10.219
190.14980.03390.07350.2786-0.10150.2576-0.015-0.0135-0.00340.02160.00630.0199-0.0432-0.03060.00870.0580.0145-0.00330.0219-0.02160.0281-91.87479.17626.399
200.2152-0.06740.08210.305-0.04560.0339-0.00330.006-0.01080.00030.0069-0.01470-0.0024-0.00360.03130.0072-0.01310.0191-0.00350.0234-73.161-3.43756.395
210.14850.02930.04010.28270.04660.04040.01970.0058-0.0094-0.0014-0.0146-0.02150.0016-0.0039-0.00510.01690.01110.00380.01820.00960.0358-56.62829.83866.527
220.24940.01610.17950.14830.03590.1337-0.0023-0.0044-0.0181-0.01520.01360.0008-0.00380.0027-0.01130.00350.0058-0.00180.02770.00280.0569-24.65221.8386.414
230.1590.07170.12150.19280.07290.1-0.0139-0.02120.0133-0.01170.0014-0.0213-0.0012-0.01050.01250.03320.0142-0.00630.0087-0.00430.034-51.151-32.03569.776
240.0774-0.08210.06390.312-0.02590.0729-0.0109-0.00450.0205-0.01080.00260.0039-0.00130.0120.00830.01440.0173-0.00980.0253-0.00560.0536-21.24-16.43488.384
250.1721-0.08920.16270.36510.10690.34760.0154-0.00390.00690.0647-0.01490.01320.0644-0.0335-0.00050.05610.00280.01090.02420.02690.0357-62.456-32.926101.529
260.3854-0.0229-0.01520.3930.10040.061-0.0148-0.0560.00180.06330.0212-0.00430.0220.0226-0.00640.05980.0273-0.00850.04340.00890.0124-36.08-10.328118.222
270.48620.02840.030.3126-0.12640.05620.002-0.07610.05070.04190.0004-0.0002-0.014-0.0013-0.00240.04250.02840.00060.0416-0.02310.0353-46.2726.365112.048
280.0783-0.06650.14810.338-0.00770.3888-0.0069-0.0291-0.02960.02380.01940.05320.0288-0.0804-0.01240.0182-0.0090.02490.03610.01640.0655-89.237-10.32585.403
290.2872-0.02970.07750.1783-0.1210.1321-0.0121-0.0103-0.01840.01680.0089-0.00380.00170.00740.00310.02130.0210.01180.0303-0.0050.0403-78.89526.23191.619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 280
2X-RAY DIFFRACTION2B1 - 280
3X-RAY DIFFRACTION3C1 - 280
4X-RAY DIFFRACTION4D1 - 280
5X-RAY DIFFRACTION5E1 - 280
6X-RAY DIFFRACTION6G1 - 280
7X-RAY DIFFRACTION7H1 - 280
8X-RAY DIFFRACTION8I1 - 280
9X-RAY DIFFRACTION9J1 - 280
10X-RAY DIFFRACTION10K1 - 280
11X-RAY DIFFRACTION11L1 - 280
12X-RAY DIFFRACTION12M1 - 280
13X-RAY DIFFRACTION13N1 - 280
14X-RAY DIFFRACTION14O1 - 280
15X-RAY DIFFRACTION15P1 - 280
16X-RAY DIFFRACTION16S1 - 280
17X-RAY DIFFRACTION17T1 - 280
18X-RAY DIFFRACTION18U1 - 280
19X-RAY DIFFRACTION19V1 - 280
20X-RAY DIFFRACTION20a1 - 280
21X-RAY DIFFRACTION21b1 - 280
22X-RAY DIFFRACTION22c1 - 280
23X-RAY DIFFRACTION23d1 - 280
24X-RAY DIFFRACTION24e1 - 280
25X-RAY DIFFRACTION25g1 - 280
26X-RAY DIFFRACTION26h1 - 280
27X-RAY DIFFRACTION27i1 - 280
28X-RAY DIFFRACTION28j1 - 280
29X-RAY DIFFRACTION29k1 - 280

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Major update of PDB

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  • 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

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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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