[English] 日本語
Yorodumi
- PDB-2h5n: Crystal Structure of Protein of Unknown Function PG1108 from Porp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h5n
TitleCrystal Structure of Protein of Unknown Function PG1108 from Porphyromonas gingivalis W83
ComponentsHypothetical protein PG_1108
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / SAD / MCSG / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyCo-chaperone DjlA, N-terminal / TerB-like / Tellurite resistance protein TerB / TerB-like / TerB-like / Orthogonal Bundle / Mainly Alpha / metal ion binding / Co-chaperone DjlA N-terminal domain-containing protein
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsNocek, B. / Bigelow, L. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein PG_1108 from Porphyromonas gingivalis W83
Authors: Nocek, B. / Bigelow, L. / Moy, S. / Joachimiak, A.
History
DepositionMay 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: 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_database_related / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _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.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_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein PG_1108
B: Hypothetical protein PG_1108
C: Hypothetical protein PG_1108
D: Hypothetical protein PG_1108
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6147
Polymers58,5414
Non-polymers733
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-75 kcal/mol
Surface area24600 Å2
MethodPISA
2
D: Hypothetical protein PG_1108

D: Hypothetical protein PG_1108

B: Hypothetical protein PG_1108
hetero molecules

B: Hypothetical protein PG_1108
hetero molecules

A: Hypothetical protein PG_1108
C: Hypothetical protein PG_1108
hetero molecules

A: Hypothetical protein PG_1108
C: Hypothetical protein PG_1108
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,22714
Polymers117,0818
Non-polymers1466
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area10800 Å2
ΔGint-122 kcal/mol
Surface area47340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.961, 84.826, 164.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1056-

HOH

21D-211-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ILEILEASNASNAA10 - 13210 - 132
2ILEILELYSLYSBB10 - 13110 - 131
3ILEILEASNASNCC10 - 13210 - 132
4METMETASNASNDD11 - 13211 - 132

-
Components

#1: Protein
Hypothetical protein PG_1108


Mass: 14635.183 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7MVF6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% 1,4 butanediol, 0.1 imidazole pH 8.0, 0.1 M Zn(oAC)2, 0.1M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.01→40 Å / Num. all: 35653 / Num. obs: 35476 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.1
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Cootmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.443 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.184 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24365 1869 5 %RANDOM
Rwork0.18825 ---
obs0.19094 35476 99.5 %-
all-37345 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.528 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å20 Å2
2--2.12 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.01→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 3 331 4156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223942
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9875306
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39925.973149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35815792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6951518
X-RAY DIFFRACTIONr_chiral_restr0.1150.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022798
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21939
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.22857
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.2285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3120.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8511.52655
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16124087
X-RAY DIFFRACTIONr_scbond_it2.02731478
X-RAY DIFFRACTIONr_scangle_it3.1294.51219
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 836 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.70.5
2Bmedium positional0.70.5
3Cmedium positional0.480.5
4Dmedium positional0.570.5
1Amedium thermal1.152
2Bmedium thermal1.332
3Cmedium thermal0.952
4Dmedium thermal1.112
LS refinement shellResolution: 2.01→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 119 -
Rwork0.223 2492 -
obs--95.99 %
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)
152.3657-9.3812-5.8151.87061.6192.3999-0.0682-0.49130.638-0.00460.0964-0.035-0.02830.2351-0.02830.0535-0.0258-0.054-0.01470.04940.0869-4.596718.716644.1471
20.3968-0.2046-0.0271.91831.30580.9226-0.01530.03760.102-0.05410.0598-0.0830.03540.1271-0.04450.05020.028-0.01240.01930.02180.055722.380811.54333.3357
36.7635-10.44040.648725.1364-6.21243.07270.72980.12270.322-1.4354-0.6568-0.40790.44650.4244-0.07290.1519-0.00480.040.08160.0353-0.01928.29077.184915.7309
44.9783-1.2767-4.42841.6028-1.52939.50780.0302-0.1045-0.1424-0.3295-0.04410.1653-0.10660.1510.01390.0383-0.0023-0.01210.04860.07380.066221.465615.055818.9871
57.567-4.3328-8.7275.01656.370310.8085-0.15610.54460.51020.0822-0.06940.3972-0.3840.10310.2255-0.02850.0214-0.02650.05830.06430.132315.308217.900127.7171
619.8412-7.4947-2.996811.31181.36780.91040.76530.50091.3507-0.8647-0.3058-0.8303-0.65060.1124-0.45950.15730.01050.07160.04710.06080.114224.86822.096631.4028
73.64441.90781.531124.7386-8.302210.78890.1197-0.16830.42120.2357-0.3719-1.5307-0.1070.41030.25220.00370.0380.0162-0.0109-0.0080.211332.38778.729434.1406
810.07051.0867-4.06751.4197-0.39051.64460.0391-0.14660.22020.25070.06770.00630.0408-0.0254-0.10690.07870.059-0.00170.03450.03750.048521.3124.901839.0562
92.9348-0.45934.68438.93753.23799.2727-0.0425-0.0835-0.15920.2519-0.15060.8230.2372-0.6180.19310.02420.04020.04880.01580.00430.097210.945.801236.2903
103.80891.6055-3.91161.6127-4.148110.6907-0.11420.04630.3141-0.1977-0.04440.5465-0.1012-0.05950.15850.03880.0345-0.05130.04360.02490.072615.22438.809925.6811
1123.5069-7.5564-19.006823.79028.368815.60710.13521.02760.4539-1.176-1.0290.9581-0.21210.03720.89370.1667-0.0011-0.2590.06350.05870.018512.90376.027213.451
122.9049-1.41240.58142.8393-0.18524.62080.06070.2735-0.1446-0.1067-0.17580.066-0.092-0.05610.11510.04230.0251-0.05620.054-0.0170.038418.7358-0.949821.928
1310.6895-1.84456.38116.9847-5.75497.0580.2499-0.3079-0.4763-0.020.35260.490.2369-0.3319-0.60250.00740.0187-0.02950.0289-0.02790.046114.0723-0.217429.4575
140.09221.0923-0.050213.00540.0095.8602-0.12450.12160.2305-0.3490.15451.124-0.4404-0.7444-0.03-0.08980.0859-0.07830.15840.08490.21426.12939.116623.82
152.0169-0.69491.58810.6105-0.48272.43970.1430.0568-0.20280.04530.0339-0.0007-0.0301-0.0122-0.17680.0251-0.0223-0.03460.0213-0.01370.058529.92-13.746934.1435
161.2037-3.9631-1.226417.70194.76661.36360.0943-0.0129-0.1025-0.373-0.2370.505-0.1219-0.04620.14260.04390.0031-0.0810.0581-0.00550.012720.0285-13.918919.3043
179.46622.0654.74340.45041.03472.37680.12640.0310.4087-0.18490.0998-0.27070.27080.0731-0.22620.0538-0.0236-0.01080.0268-0.02170.022829.5427-20.975623.3752
181.84765.1987-2.118814.628-5.96192.42990.1589-0.2452-0.3135-0.1079-0.3406-0.80440.09420.4210.18170.0329-0.0192-0.05320.1285-0.02120.017334.3549-22.119531.7615
194.047-6.0687-1.903411.21135.09574.1385-0.0087-0.0008-0.184-0.0270.03180.38180.186-0.0821-0.02320.0463-0.0324-0.0252-0.01820.0081-0.025424.2964-22.899834.2836
200.0308-0.6649-0.046215.9404-1.66124.502-0.1749-0.08960.12670.70770.42290.6587-0.3994-0.4823-0.2481-0.00190.01540.0010.0260.02930.044420.3118-9.631238.4106
217.21365.99362.93685.66161.30313.0918-0.015-0.22840.06280.0058-0.2337-0.20190.0248-0.39590.24870.07640.0066-0.03580.0239-0.00860.032327.7488-5.895838.763
226.0236-2.4808-3.15041.5331.80172.14490.0615-0.09730.1248-0.27260.1122-0.1698-0.1095-0.0675-0.17370.0242-0.0032-0.04490.00680.00690.061137.9847-4.962638.0644
232.83410.79234.1071.41270.46256.34630.34860.0462-0.2157-0.3381-0.134-0.13770.12880.3575-0.2145-0.00720.0404-0.0170.04040.00640.079341.248-9.649132.6827
243.23023.03243.17723.4233.57333.7305-0.04970.089-0.026-0.0733-0.0597-0.2089-0.08720.00510.10950.01680.0021-0.03340.0613-0.00590.020833.0883-12.157824.4965
2531.8308-15.62718.704615.1823-4.072710.19680.55391.6795-0.3999-1.5112-0.8629-0.38320.18590.38290.3090.066-0.01240.02740.128-0.0903-0.163432.7503-11.457712.5
262.43970.4290.68094.2161.75113.62820.01730.15620.1683-0.2257-0.07930.0077-0.1195-0.10730.0620.07880.0287-0.01690.01930.01350.009329.5432-3.463820.6483
276.2544-1.7048-4.2724.84544.39095.29420.06620.33040.30980.01350.084-0.1296-0.2180.0323-0.15010.0340.007-0.04070.01470.0360.007336.1331-2.785726.7337
284.620.81853.749915.2982-6.249116.4721-0.02580.5759-0.5283-0.43980.1775-1.00480.37810.7329-0.1517-0.10240.00050.04850.1141-0.08180.052741.9411-12.947120.7028
297.3981.86433.226219.7753-2.95782.1435-0.12850.08260.1945-0.585-0.21090.3004-0.1063-0.08360.33940.09540.0384-0.02770.15110.071-0.019434.237825.8681-3.0456
303.2546-1.07613.13130.714-0.00265.99080.09780.0658-0.29590.0094-0.10570.10860.0567-0.22570.00790.01560.0056-0.00870.0270.03430.098135.885417.47618.0962
319.1033-3.594-4.06883.2929-2.23939.7099-0.0748-0.8792-0.28660.14870.20060.4589-0.45020.5085-0.1258-0.0367-0.03120.02830.09580.06450.113935.250913.926321.3015
328.1991-3.35452.375613.8271-7.11743.72070.2633-0.04650.12580.28810.21460.3842-0.1484-0.0574-0.47790.02020.01430.01490.07590.00780.032429.306221.221918.4468
336.3866-2.67831.27355.2644-4.8884.8316-0.21150.1550.27230.2464-0.1557-0.0372-0.0945-0.19090.36720.01150.023-0.02710.010.01990.053628.377726.45778.4065
3413.2745-2.47825.313730.2899-2.68022.22260.07020.0211-0.58250.5530.28060.98240.2569-0.2232-0.35080.01830.0281-0.01210.06620.01880.015824.18218.76593.5626
3527.9438-9.1396-6.80973.93485.454712.67690.51230.531-2.45220.1429-0.540.44750.3524-0.04540.02770.0071-0.014-0.143-0.05190.00930.38434.88919.66153.0222
366.36092.9177-2.397815.0487-8.06564.44290.12350.546-0.2518-0.2714-0.19340.0580.01650.19160.06980.03690.0284-0.02950.1090.0337-0.013343.381318.25420.2301
3721.69465.9262-11.02117.67421.26918.62370.09120.27491.017-0.45270.2648-0.0071-0.2045-0.1919-0.3560.09460.02880.00240.0120.07550.059342.733430.4450.366
385.19981.9815-3.73931.3858-2.55914.72860.10160.16390.40860.11320.09410.0705-0.2311-0.2729-0.19570.06960.0093-0.00620.00590.06030.062337.486828.27299.9975
394.804-2.70553.533610.8713-2.07743.4359-0.3134-1.07990.29130.84980.2890.563-0.1106-0.28050.02440.08150.03290.03020.1033-0.0826-0.008638.555927.337623.8245
401.9517-1.2452-3.29971.98130.72787.1779-0.0082-0.08350.05620.11560.0032-0.01540.11390.27480.00510.0185-0.0159-0.01610.04270.03730.048945.537522.414414.3722
417.1882.5501-3.71861.8588-2.62113.70020.1944-0.02630.42210.2818-0.194-0.1702-0.62670.5268-0.00040.05220.0111-0.0440.00410.02250.095644.816131.040812.4786
426.1629-5.49858.19519.1026-2.373316.7077-0.119-0.19290.47890.42220.17920.7527-0.99660.0113-0.06020.15670.04550.0958-0.0720.05120.147435.773636.168911.6951
432.60150.1236-0.94331.18770.56450.6561-0.1530.077-0.20320.0070.0698-0.0210.070.02560.08320.033-0.0197-0.01080.09370.05350.066760.87119.72816.0743
443.68621.46521.56253.76021.50130.90610.0105-0.1177-0.0642-0.0729-0.14180.11280.0203-0.01370.13120.0224-0.0177-0.02570.04610.0510.026554.435820.145318.8431
452.1186-0.15630.02932.2012-0.06160.0020.0528-0.2554-0.12750.03040.0731-0.05640.095-0.0538-0.12580.0656-0.0173-0.05870.06290.01070.000360.214617.952225.0003
469.9678-3.2201-4.50141.68042.70134.4624-0.08550.04670.11410.19360.1595-0.14780.04810.4325-0.0740.05450.0035-0.02540.06040.07040.043464.80469.116717.9808
4738.248530.6276-15.670428.16-8.071511.9335-0.5081-0.1207-2.18790.0972-0.2107-0.68530.75421.0080.71880.03620.0859-0.02930.01820.04470.169668.39386.274713.901
489.5122-2.25570.75793.4697-2.99868.1121-0.0916-0.16230.3333-0.1799-0.06290.0247-0.01570.49130.1545-0.0283-0.01620.00640.04520.02040.002869.063216.217210.7686
498.60845.82572.41810.3062-3.12924.248-0.2445-0.65850.5124-0.26340.07810.3175-0.3193-0.19010.16640.0238-0.00010.04610.0910.01830.011958.872121.55225.4567
504.86682.87874.657912.52393.11664.470.17070.4877-0.2301-0.1863-0.2446-0.0629-0.13120.25140.07390.01520.00470.02630.09160.05680.042152.855513.45042.7961
514.6884-3.4264-1.19916.10376.5679.3032-0.11250.4889-0.6236-0.0866-0.09370.05440.32740.18740.20620.0366-0.025-0.05610.0206-0.00840.151252.89131.58283.4407
523.43072.34072.98442.5542.08368.565-0.0233-0.1325-0.53160.01240.0898-0.10760.09860.0895-0.06650.0262-0.0051-0.0118-0.02330.07020.112755.49014.543713.6791
535.3786-6.76470.225210.236-2.499112.53850.4398-0.4495-0.07450.302-0.32210.0530.09490.0624-0.11770.05-0.0514-0.00770.12990.1205-0.057550.111710.868227.3151
541.6435-0.48551.43811.61711.03715.23190.067-0.1875-0.1708-0.0735-0.02650.0260.0961-0.2909-0.04050.0064-0.0215-0.01610.03240.07940.100146.442711.003714.8224
558.94121.53740.72490.6491-1.39369.15970.1362-0.2076-0.7740.05040.51080.3730.076-0.4904-0.647-0.0027-0.012-0.0127-0.0010.10750.152147.95072.668316.7196
5628.1953-1.1062-10.95715.52243.10025.5595-0.1991-0.7354-1.93030.2624-0.0692-0.21660.35980.2760.26840.0646-0.0116-0.09890.02850.20820.179957.0327-1.663120.0238
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 101 - 10
2X-RAY DIFFRACTION2AA11 - 2911 - 29
3X-RAY DIFFRACTION3AA30 - 3630 - 36
4X-RAY DIFFRACTION4AA37 - 4437 - 44
5X-RAY DIFFRACTION5AA45 - 5145 - 51
6X-RAY DIFFRACTION6AA52 - 6452 - 64
7X-RAY DIFFRACTION7AA65 - 7065 - 70
8X-RAY DIFFRACTION8AA71 - 8071 - 80
9X-RAY DIFFRACTION9AA81 - 8581 - 85
10X-RAY DIFFRACTION10AA86 - 9586 - 95
11X-RAY DIFFRACTION11AA96 - 10296 - 102
12X-RAY DIFFRACTION12AA103 - 114103 - 114
13X-RAY DIFFRACTION13AA115 - 122115 - 122
14X-RAY DIFFRACTION14AA123 - 132123 - 132
15X-RAY DIFFRACTION15BB10 - 2910 - 29
16X-RAY DIFFRACTION16BB30 - 3830 - 38
17X-RAY DIFFRACTION17BB39 - 4639 - 46
18X-RAY DIFFRACTION18BB47 - 5347 - 53
19X-RAY DIFFRACTION19BB54 - 6454 - 64
20X-RAY DIFFRACTION20BB65 - 7065 - 70
21X-RAY DIFFRACTION21BB71 - 7671 - 76
22X-RAY DIFFRACTION22BB77 - 8177 - 81
23X-RAY DIFFRACTION23BB82 - 8682 - 86
24X-RAY DIFFRACTION24BB87 - 9587 - 95
25X-RAY DIFFRACTION25BB96 - 10296 - 102
26X-RAY DIFFRACTION26BB103 - 114103 - 114
27X-RAY DIFFRACTION27BB115 - 122115 - 122
28X-RAY DIFFRACTION28BB123 - 131123 - 131
29X-RAY DIFFRACTION29CC10 - 1710 - 17
30X-RAY DIFFRACTION30CC18 - 2918 - 29
31X-RAY DIFFRACTION31CC30 - 3630 - 36
32X-RAY DIFFRACTION32CC37 - 4237 - 42
33X-RAY DIFFRACTION33CC43 - 5143 - 51
34X-RAY DIFFRACTION34CC52 - 6252 - 62
35X-RAY DIFFRACTION35CC63 - 6863 - 68
36X-RAY DIFFRACTION36CC69 - 7969 - 79
37X-RAY DIFFRACTION37CC80 - 8480 - 84
38X-RAY DIFFRACTION38CC85 - 9485 - 94
39X-RAY DIFFRACTION39CC95 - 10495 - 104
40X-RAY DIFFRACTION40CC105 - 117105 - 117
41X-RAY DIFFRACTION41CC118 - 123118 - 123
42X-RAY DIFFRACTION42CC124 - 133124 - 133
43X-RAY DIFFRACTION43DD11 - 2411 - 24
44X-RAY DIFFRACTION44DD25 - 3425 - 34
45X-RAY DIFFRACTION45DD35 - 4235 - 42
46X-RAY DIFFRACTION46DD43 - 4843 - 48
47X-RAY DIFFRACTION47DD49 - 5449 - 54
48X-RAY DIFFRACTION48DD55 - 6355 - 63
49X-RAY DIFFRACTION49DD64 - 6964 - 69
50X-RAY DIFFRACTION50DD70 - 7770 - 77
51X-RAY DIFFRACTION51DD78 - 8278 - 82
52X-RAY DIFFRACTION52DD83 - 9483 - 94
53X-RAY DIFFRACTION53DD95 - 10595 - 105
54X-RAY DIFFRACTION54DD106 - 117106 - 117
55X-RAY DIFFRACTION55DD118 - 123118 - 123
56X-RAY DIFFRACTION56DD124 - 133124 - 133

+
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://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