[English] 日本語
Yorodumi
- PDB-3ld0: Crystal structure of B.licheniformis Anti-TRAP protein, an antago... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ld0
TitleCrystal structure of B.licheniformis Anti-TRAP protein, an antagonist of TRAP-RNA interactions
ComponentsInhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
KeywordsGENE REGULATION / Anti-TRAP / AT / TRAP / tryptophan RNA-binding attenuation protein / transcription attenuation / antitermination / transcription factors / tryptophan biosynthesis regulation
Function / homologyChaperone, DNAj Protein; Chain A / Chaperone, DNAj Protein; Chain A - #10 / Tryptophan RNA-binding attenuator protein inhibitory protein / Tryptophan RNA-binding attenuator protein inhibitory protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / Other non-globular / Special / metal ion binding / Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShevtsov, M.B. / Chen, Y. / Isupov, M.N. / Gollnick, P. / Antson, A.A.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Bacillus licheniformis Anti-TRAP can assemble into two types of dodecameric particles with the same symmetry but inverted orientation of trimers.
Authors: Shevtsov, M.B. / Chen, Y. / Isupov, M.N. / Leech, A. / Gollnick, P. / Antson, A.A.
History
DepositionJan 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
B: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
C: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
D: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
E: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
F: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
G: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
H: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
I: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
J: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
K: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
L: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
M: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
N: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
O: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
P: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
Q: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
R: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
S: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
T: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
U: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
V: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
W: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
X: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
Y: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
Z: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
1: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
2: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
3: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
4: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
5: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
6: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
7: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
8: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
9: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
a: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
b: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
c: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
d: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
e: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
f: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
g: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
h: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
i: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
j: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
k: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
l: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
m: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,126112
Polymers275,59848
Non-polymers3,52964
Water24,0501335
1
A: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
B: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
C: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
D: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
E: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
F: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
G: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
H: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
I: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
J: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
K: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
L: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,78228
Polymers68,89912
Non-polymers88216
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27590 Å2
ΔGint-209 kcal/mol
Surface area23940 Å2
MethodPISA
2
M: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
N: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
O: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
P: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
Q: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
R: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
S: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
T: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
U: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
V: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
W: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
X: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,78228
Polymers68,89912
Non-polymers88216
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27390 Å2
ΔGint-215 kcal/mol
Surface area24180 Å2
MethodPISA
3
Y: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
Z: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
1: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
2: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
3: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
4: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
5: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
6: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
7: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
8: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
9: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
a: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,78228
Polymers68,89912
Non-polymers88216
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27450 Å2
ΔGint-216 kcal/mol
Surface area24090 Å2
MethodPISA
4
b: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
c: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
d: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
e: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
f: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
g: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
h: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
i: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
j: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
k: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
l: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
m: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,78228
Polymers68,89912
Non-polymers88216
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27700 Å2
ΔGint-204 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.544, 99.865, 123.178
Angle α, β, γ (deg.)90.00, 117.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ...
Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA / YczA


Mass: 5741.617 Da / Num. of mol.: 48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: 5A32 / Gene: BL05022, BLi00308, rtpA, rtpA (YczA), yczA / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3) competent cells / References: UniProt: Q65NU7
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1335 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl pH 8.0-8.5 buffer, 0.2 M of MgCl2 salt and 20-25 % of poly(ethylene) glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→38.2 Å / Num. all: 128982 / Num. obs: 128724 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.4 / Num. unique all: 18742 / % possible all: 97

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.3.0008refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2bx9

2bx9


Resolution: 2.2→29.27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.811 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 1300 1 %RANDOM
Rwork0.19383 ---
obs0.19449 127405 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.288 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19034 0 64 1335 20433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02219706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.204226559
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.69352507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9526.06731
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.451153519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.7551548
X-RAY DIFFRACTIONr_chiral_restr0.0750.23079
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214356
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2620.39655
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.513813
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.51904
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.391
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3230.565
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8421.513081
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.705220605
X-RAY DIFFRACTIONr_scbond_it4.10237060
X-RAY DIFFRACTIONr_scangle_it6.3954.55945
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 88 -
Rwork0.227 9293 -
obs-9011 99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4581-0.1408-0.03730.4301-0.1050.7558-0.0307-0.0165-0.04220.0391-0.0101-0.0416-0.01140.010.0409-0.0498-0.0266-0.0234-0.0826-0.0214-0.0438-49.967311.697518.7544
20.2907-0.107-0.01790.3165-0.14240.5416-0.0134-0.0752-0.03670.10680.00920.01540.03760.00680.0042-0.12940.0020.0142-0.06230.0011-0.0735-69.60160.278511.028
30.6656-0.0925-0.06690.50790.03770.42440.02170.0010.05390.0997-0.0011-0.0290.01850.0549-0.0206-0.07480.0265-0.0179-0.07560.0273-0.0732-50.5809-12.385218.8402
40.3093-0.20450.18360.5755-0.06650.44870.0301-0.0260.10550.0891-0.0304-0.1049-0.04480.17510.0003-0.08550.01310.0123-0.01960.0032-0.0535-49.3894-0.2398-1.9568
50.3170.05290.15060.92040.1950.6570.02150.01520.06610.052-0.00840.05870.0019-0.057-0.0131-0.0242-0.01380.0333-0.0096-0.0055-0.0504-97.218636.944357.3221
60.4613-0.10130.05770.7517-0.07581.05530.0139-0.06320.04990.0421-0.01660.04920.0193-0.09860.0027-0.0661-0.0238-0.0071-0.0708-0.0183-0.0533-98.434624.645636.7364
70.24040.14670.01530.88560.14620.5765-0.00990.0323-0.0115-0.02720.0452-0.1501-0.08730.0742-0.0353-0.0803-0.00840.02940.045-0.01480.0233-78.29536.756942.4913
80.37480.14760.00640.72280.30821.0812-0.0140.04090.0098-0.0941-0.02890.0409-0.1189-0.02210.04290.0010.0152-0.0121-0.03910.0111-0.0145-98.309748.548536.2222
90.3883-0.1247-0.1330.593-0.1090.82730.0009-0.073-0.07070.1068-0.0261-0.0726-0.01180.0140.0251-0.0252-0.0478-0.0359-0.0673-0.003-0.05888.5512-1.023919.1179
100.3653-0.1182-0.00630.8612-0.1370.52660.004-0.0794-0.02670.1481-0.0330.0672-0.0423-0.00680.029-0.1375-0.01190.0137-0.0702-0.011-0.0542-10.7479-12.797210.8421
110.58480.14340.13170.63640.0870.55620.02740.02940.07830.0837-0.0483-0.1289-0.00120.12090.0209-0.03130.0223-0.02-0.05610.0332-0.03888.5861-25.031518.8946
120.1071-0.11680.16030.7868-0.00780.57530.0218-0.05570.0130.0685-0.0242-0.08720.0070.14230.0023-0.1060.00840.0159-0.04650.0139-0.05429.7498-12.9069-1.7115
130.34510.17260.0150.65840.15310.56210.0249-0.01220.09290.0377-0.00060.0598-0.0147-0.0704-0.02430.018-0.00630.02650.0187-0.0118-0.0339-38.036849.502257.1191
140.413-0.01950.02730.78940.02891.17910.0143-0.12910.01320.1280.0084-0.00170.0078-0.0976-0.0228-0.0808-0.0165-0.0189-0.0649-0.0267-0.0508-38.462737.378536.5059
150.20240.0059-0.05910.72150.24630.7574-0.0153-0.0161-0.00480.00750.0814-0.1108-0.09860.0933-0.0661-0.0613-0.0180.01560.0323-0.03650.0044-19.321750.604542.2207
160.23020.13140.07490.72140.29011.19570.0142-0.0160.0266-0.0261-0.03340.0329-0.1917-0.08580.01920.01470.04960.0058-0.01860.0116-0.0074-40.018561.384636.2592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 53
2X-RAY DIFFRACTION1C201 - 253
3X-RAY DIFFRACTION1B101 - 153
4X-RAY DIFFRACTION2E101 - 153
5X-RAY DIFFRACTION2D1 - 53
6X-RAY DIFFRACTION2F201 - 253
7X-RAY DIFFRACTION3I201 - 253
8X-RAY DIFFRACTION3H101 - 152
9X-RAY DIFFRACTION3G1 - 52
10X-RAY DIFFRACTION4K101 - 153
11X-RAY DIFFRACTION4J1 - 53
12X-RAY DIFFRACTION4L201 - 253
13X-RAY DIFFRACTION5M1 - 53
14X-RAY DIFFRACTION5O201 - 253
15X-RAY DIFFRACTION5N101 - 152
16X-RAY DIFFRACTION6Q101 - 153
17X-RAY DIFFRACTION6P1 - 53
18X-RAY DIFFRACTION6R201 - 253
19X-RAY DIFFRACTION7S1 - 53
20X-RAY DIFFRACTION7U201 - 253
21X-RAY DIFFRACTION7T101 - 153
22X-RAY DIFFRACTION8X201 - 253
23X-RAY DIFFRACTION8W101 - 153
24X-RAY DIFFRACTION8V1 - 53
25X-RAY DIFFRACTION9Y1 - 53
26X-RAY DIFFRACTION91201 - 253
27X-RAY DIFFRACTION9Z101 - 152
28X-RAY DIFFRACTION103101 - 153
29X-RAY DIFFRACTION1021 - 52
30X-RAY DIFFRACTION104201 - 252
31X-RAY DIFFRACTION1151 - 53
32X-RAY DIFFRACTION117201 - 253
33X-RAY DIFFRACTION116101 - 153
34X-RAY DIFFRACTION129101 - 153
35X-RAY DIFFRACTION1281 - 53
36X-RAY DIFFRACTION12a201 - 253
37X-RAY DIFFRACTION13c101 - 153
38X-RAY DIFFRACTION13b1 - 53
39X-RAY DIFFRACTION13d201 - 253
40X-RAY DIFFRACTION14e1 - 53
41X-RAY DIFFRACTION14g201 - 253
42X-RAY DIFFRACTION14f101 - 153
43X-RAY DIFFRACTION15i101 - 153
44X-RAY DIFFRACTION15h1 - 53
45X-RAY DIFFRACTION15j201 - 253
46X-RAY DIFFRACTION16k1 - 53
47X-RAY DIFFRACTION16m201 - 253
48X-RAY DIFFRACTION16l101 - 152

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • 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

-
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

Read more