[English] 日本語
Yorodumi
- PDB-2xc1: Full-length Tailspike Protein Mutant Y108W of Bacteriophage P22 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xc1
TitleFull-length Tailspike Protein Mutant Y108W of Bacteriophage P22
ComponentsBIFUNCTIONAL TAIL PROTEIN
KeywordsHYDROLASE / ENDOGLYCOSIDASE / SALMONELLA PHAGE P22
Function / homology
Function and homology information


endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / metabolic process / virion attachment to host cell
Similarity search - Function
Tailspike Protein; Chain / Phage P22 tailspike-like, N-terminal domain / Pectate Lyase C-like - #20 / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectate Lyase C-like ...Tailspike Protein; Chain / Phage P22 tailspike-like, N-terminal domain / Pectate Lyase C-like - #20 / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectate Lyase C-like / Pectin lyase fold/virulence factor / 3 Solenoid / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesENTEROBACTERIA PHAGE P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMueller, J.J. / Seul, A. / Seckler, R. / Heinemann, U.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Bacteriophage P22 Tailspike: Structure of the Complete Protein and Function of the Interdomain Linker
Authors: Seul, A. / Mueller, J.J. / Andres, D. / Stettner, E. / Heinemann, U. / Seckler, R.
History
DepositionApr 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary / Version format compliance
Revision 1.2May 21, 2014Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BIFUNCTIONAL TAIL PROTEIN
B: BIFUNCTIONAL TAIL PROTEIN
C: BIFUNCTIONAL TAIL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,28722
Polymers215,5363
Non-polymers2,75119
Water40,8042265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39520 Å2
ΔGint-147.3 kcal/mol
Surface area63480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.358, 121.558, 208.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein BIFUNCTIONAL TAIL PROTEIN / FULL-LENGTH P22 TAILSPIKE PROTEIN / LATE PROTEIN GP9 / TAILSPIKE-PROTEIN / TSP / ENDORHAMNOSIDASE / ...FULL-LENGTH P22 TAILSPIKE PROTEIN / LATE PROTEIN GP9 / TAILSPIKE-PROTEIN / TSP / ENDORHAMNOSIDASE / ENDO-1 / 3-ALPHA-L-RHAMNOSIDASE


Mass: 71845.391 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-667 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE P22 (virus) / Plasmid: PTSP1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM83
References: UniProt: P12528, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

-
Non-polymers , 5 types, 2284 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2265 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 109 TO TRP ENGINEERED RESIDUE IN CHAIN B, TYR 109 TO TRP ...ENGINEERED RESIDUE IN CHAIN A, TYR 109 TO TRP ENGINEERED RESIDUE IN CHAIN B, TYR 109 TO TRP ENGINEERED RESIDUE IN CHAIN C, TYR 109 TO TRP
Sequence detailsSEQUENCE NUMBERING WITHOUT N-TERMINAL MET SHEETS AA,AB IN CHAIN A BELONG TO THE HEAD-BINDING DOMAIN ...SEQUENCE NUMBERING WITHOUT N-TERMINAL MET SHEETS AA,AB IN CHAIN A BELONG TO THE HEAD-BINDING DOMAIN SHEETS BA,BB IN CHAIN B BELONG TO THE HEAD-BINDING DOMAIN SHEETS CA,CB IN CHAIN C BELONG TO THE HEAD-BINDING DOMAIN SHEETS AC,AD,AE,AF,AG BELONG TO THE PARALLEL BETA-HELIX DOMAIN IN CHAIN A WITH, SHEETS AC AND AD ARE BIFURCATED SHEETS BC,BD,BE,BF,BG BELONG TO THE PARALLEL BETA-HELIX DOMAIN IN CHAIN B WITH, SHEETS BC AND BD ARE BIFURCATED SHEETS CC,CD,CE,CF,CG BELONG TO THE PARALLEL BETA-HELIX DOMAIN IN CHAIN C WITH, SHEETS CC AND CD ARE BIFURCATED SHEETS AH,BH,CH BELONG TO A PRISM IN THE C-TERMINAL DOMAIN SHEETS AI,BI,CI BELONG TO A BETA BARREL IN THE C-TERMINAL DOMAIN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.1 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PROTEIN- 15MG/ML IN 10MM HEPES PH7;RESERVOIR:750 ML 0.2M AMMONIUM ACETATE,0.1M TRI-SODIUM CITRATE DIHYDRATE PH 5.6, 30% W/V POLYETHYLENE GLYCOL 4000; HANGING DROPS:1.5MICROL RESERVOIR- 1. ...Details: PROTEIN- 15MG/ML IN 10MM HEPES PH7;RESERVOIR:750 ML 0.2M AMMONIUM ACETATE,0.1M TRI-SODIUM CITRATE DIHYDRATE PH 5.6, 30% W/V POLYETHYLENE GLYCOL 4000; HANGING DROPS:1.5MICROL RESERVOIR- 1.5MICROL PROTEIN SOLUTION; TEMPERATURE: 19 DEGR.; CRYO: 3% GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 28, 2008 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.65→48.3 Å / Num. obs: 237282 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5
Reflection shellResolution: 1.65→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / % possible all: 68.3

-
Processing

Software
NameVersionClassification
REFMAC5.5.0055refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2VNL AND 2VFM

2vnl

2vfm


Resolution: 1.65→49.45 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.888 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.21038 12041 5 %RANDOM
Rwork0.16532 ---
obs0.16756 228771 91.73 %-
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: 8.822 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15064 0 131 2265 17460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02215688
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210449
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.95821292
X-RAY DIFFRACTIONr_angle_other_deg0.8363.00125523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61951987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05924.841694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.303152542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4011573
X-RAY DIFFRACTIONr_chiral_restr0.0840.22388
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023072
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_it1.79129842
X-RAY DIFFRACTIONr_mcbond_other0.65824099
X-RAY DIFFRACTIONr_mcangle_it2.508315909
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.83445846
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.31565381
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 491 -
Rwork0.325 9322 -
obs--50.85 %
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)
10.910.0368-0.90861.31492.87387.39550.0736-0.12210.1121-0.0992-0.03670.0496-0.38460.0305-0.03690.24760.02540.01850.0863-0.0470.1322-71.38548.616-100.4
21.321-0.99770.14674.24821.15412.18020.03480.07790.04650.0471-0.01870.08810.17460.1056-0.01610.08870.0004-0.00790.0988-0.0460.0393-68.24639.862-113.799
31.315-1.3225-0.27653.89451.80563.28770.0382-0.0643-0.080.5718-0.08840.40940.7743-0.00210.05020.2952-0.05950.04180.0414-0.02980.0707-72.58631.903-104.144
41.0377-0.4179-0.72592.13150.99883.19660.037-0.18340.12840.2440.1564-0.16590.35220.3974-0.19330.11750.0206-0.01850.0995-0.0680.0562-63.73738.03-107.639
53.166-0.5163-0.31833.0071-0.96835.56790.10960.3671-0.0199-0.3381-0.0736-0.0085-0.0565-0.3811-0.0360.12770.0293-0.04620.1184-0.01410.0309-47.46542.85-86.167
60.78310.18540.06980.5605-0.51211.34150.01720.04-0.0091-0.07450.02310.10680.0268-0.0555-0.04030.0450.0012-0.04660.0072-0.00920.0812-51.16128.118-66.393
76.25961.8223-2.30223.2218-1.69274.28240.04880.0069-0.1535-0.1557-0.1333-0.16680.07520.14460.08450.15880.023-0.02450.1035-0.02010.1105-40.00224.162-68.785
80.95010.32260.37710.5484-0.05031.12540.0447-0.1989-0.02060.0725-0.01280.0416-0.0081-0.1494-0.03180.05010.01960.00180.0652-0.00680.0955-46.59227.554-37.93
90.79340.23430.12180.4594-0.2821.59170.0581-0.1544-0.12860.0648-0.01970.06130.1226-0.1682-0.03840.0653-0.0175-0.00270.04410.02230.1033-49.01318.576-36.406
101.2745-0.6459-1.04921.12660.69541.85360.00460.0278-0.0358-0.0967-0.00540.0350.03990.03890.00080.06410.0014-0.04610.0258-0.01290.0682-39.04623.245-59.639
110.6013-0.225-0.20150.80770.15820.53840.01510.01-0.0372-0.0727-0.00780.02960.01650.0181-0.00730.0436-0.0003-0.02710.0038-0.01010.0599-32.9821.848-53.07
120.399-0.0927-0.07030.65910.46110.40980.0112-0.004-0.07880.0248-0.02180.0390.0424-0.04850.01060.0491-0.0034-0.02280.0150.00070.0701-30.44317.337-44.479
131.23730.15150.41742.81860.19072.2940.0782-0.0449-0.2908-0.0082-0.0702-0.21140.2370.0017-0.00810.05340.0168-0.01920.0213-0.00830.1268-21.5063.222-47.508
140.67-0.1417-0.18380.70370.14040.55350.0153-0.0183-0.05920.00490.00510.00740.0528-0.0064-0.02050.03330.0025-0.02950.0179-0.00020.0546-21.09721.862-37.076
151.4571-0.448-0.47431.69790.40421.10410.0254-0.15-0.09640.1108-0.01420.09190.1382-0.0235-0.01120.0553-0.0088-0.02670.04230.01380.0646-17.99620.137-29.485
161.0291-0.60270.15811.0709-0.56750.630.0774-0.2368-0.03170.1139-0.00580.083-0.0364-0.0478-0.07150.0802-0.0542-0.01080.1317-0.01210.0677-13.7520.294-24.486
171.4439-0.7622-0.79930.69040.59610.91020.0274-0.0357-0.0005-0.0126-0.01830.0035-0.05430.0172-0.00920.0379-0.0011-0.00480.05270.01130.0416-0.67535.067-21.129
180.42320.52060.17530.68110.32620.61450.0147-0.04340.01240.031-0.03170.0238-0.0009-0.0340.01710.0280.0056-0.01320.05280.01150.04820.24826.913-8.684
190.5816-0.44040.35589.0704-2.14181.65190.0053-0.05390.07720.0544-0.06090.0008-0.110.03990.05560.0290.0031-0.00890.0723-0.00570.04511.73129.464-0.156
200.64860.0065-0.12430.88220.22832.06910.03450.0424-0.0815-0.0099-0.03120.02350.1760.0431-0.00330.0370.0191-0.01680.03070.00660.054118.76412.5681.028
211.50820.1186-0.31443.86541.78091.46160.0002-0.06370.08410.0980.0439-0.15420.053-0.1818-0.04410.1117-0.00990.00740.105-0.04130.1092-68.10851.415-107.058
225.65082.56841.82042.45750.88392.4201-0.04490.1201-0.0169-0.11380.0077-0.1207-0.15320.10840.03720.1218-0.00480.02310.010.01990.0887-56.72663.602-108.314
232.62712.07160.40422.57240.06710.1422-0.04030.1822-0.5039-0.10180.0664-0.5713-0.01590.0462-0.0260.0761-0.00020.04260.0303-0.04210.1785-51.95254.437-111.934
244.58010.82581.26933.3269-0.10612.86720.08440.02680.24580.0842-0.2440.1890.0498-0.14920.15960.0882-0.00090.020.0356-0.00620.0833-60.34464.222-106.185
258.0629-4.78842.783310.5621-4.84929.63010.0536-0.0906-0.29060.3288-0.5018-0.60410.60110.3740.44830.1811-0.00270.02430.04560.06740.1357-59.88555.897-91.335
261.4747-0.3821-0.18530.64520.00920.47280.00510.1501-0.0125-0.1003-0.00730.059-0.00290.01320.00220.091-0.0012-0.03160.0323-0.00630.0163-33.47340.927-82.234
275.5395-0.7923-1.19231.91050.41944.7416-0.0024-0.0030.1799-0.03470.03190.0972-0.03790.0694-0.02950.09540.0109-0.0360.06510.00590.0875-26.21747.783-74.939
281.3654-0.25140.47810.599-0.08771.30410.10790.1581-0.2595-0.0694-0.02740.03550.15340.2721-0.08050.08060.0263-0.00620.0649-0.03620.0619-12.20819.963-70.494
290.7302-0.47870.16771.1528-0.04481.00880.04190.157-0.0171-0.1086-0.0454-0.03920.08240.23270.00350.04070.02150.00430.0898-0.02340.0285-9.75627.239-74.241
300.86640.2992-0.0581.56930.24430.48740.0190.10530.0814-0.1089-0.0171-0.0231-0.0630.0646-0.00190.0628-0.0081-0.00920.05470.00260.0274-15.11441.706-69.011
310.3820.13850.02030.71890.05020.44010.01440.07180.0118-0.0648-0.0037-0.0594-0.02270.1117-0.01070.0445-0.0065-0.00150.047-0.00070.0339-9.55438.191-61.66
326.2654-2.8128-0.90912.244-1.987511.3035-0.2438-0.0984-0.4229-0.442-0.0147-0.19881.5860.67320.25840.33030.02630.18570.3488-0.04340.465710.13441.33-65.473
333.10760.21220.36942.6737-0.34190.99780.01060.0330.10990.0953-0.0766-0.0844-0.07480.2650.0660.0436-0.0525-0.00190.10110.01170.05895.67250.711-59.448
340.59290.14360.14560.59690.00970.29170.01810.05610.0109-0.0149-0.021-0.0215-0.01050.13430.00290.0328-0.0055-0.00620.0630.00230.0334-3.75534.001-49.815
351.22550.4503-0.0221.6894-0.0990.9862-0.03660.1372-0.0693-0.17330.0415-0.11420.05960.127-0.00490.02430.00660.00020.0728-0.00520.04272.56929.31-45.248
364.03881.816-2.91617.10862.435210.1264-0.10050.293-0.3069-0.32850.01570.07140.18860.1620.08490.0740.052-0.00640.0858-0.02910.06654.38816.908-45.113
370.80680.4203-0.59961.4473-0.15521.2159-0.03480.0882-0.0588-0.04870.0408-0.12070.10260.1277-0.0060.02250.0126-0.01890.0802-0.00550.04655.92329.933-38.309
380.4109-1.16030.50325.08120.41172.4872-0.01980.03770.0314-0.0351-0.0602-0.0781-0.15370.08550.080.04890.0142-0.02250.06970.00280.089-2.86832.848-21.166
390.4721-0.0105-0.22170.104-0.18370.71550.05060.0482-0.0528-0.0357-0.02480.02530.12030.0954-0.02590.04960.0205-0.01390.0625-0.00340.04888.79217.96-19.203
401.01210.1930.2351.077-0.0670.8626-0.01030.06680.0159-0.04550.0011-0.10340.02080.19520.00920.01050.0127-0.00370.0870.01130.046327.74424.848-4.987
411.3142-0.0129-0.28741.23440.74342.443-0.018-0.0373-0.17370.1703-0.1014-0.00780.2601-0.21520.11940.0823-0.0072-0.00140.0328-0.01210.0535-76.55753.936-95.317
4211.111-0.4001-1.3885.23310.81233.30550.0323-0.03850.74430.02930.2328-0.5296-0.34990.6366-0.26510.1364-0.0307-0.02080.1499-0.05570.112-69.6865.916-88.116
433.0866-0.8371-0.44222.00591.28012.80060.11530.13060.13810.045-0.0191-0.12080.11250.0598-0.09630.02950.0183-0.01510.0239-0.02260.065-75.10363.212-97.313
443.8758-1.73810.28977.99330.44444.94070.1076-0.0281-0.32280.43330.0227-0.28121.0497-0.1072-0.13030.2527-0.0351-0.03190.0223-0.0210.091-77.61548.083-93.357
4512.46831.3366-0.76998.6646-1.00813.5797-0.01961.1476-0.0281-0.79440.07871.0010.129-0.5008-0.0590.1388-0.0107-0.0920.1649-0.01120.1216-55.90239.307-82.132
460.54450.26980.00431.10640.16190.5851-0.01280.06310.0278-0.08480.01090.0164-0.0493-0.02450.00190.05860.007-0.03790.00950.00250.0657-45.0356.06-65.308
473.5664-0.61090.38294.3599-0.30015.0433-0.0331-0.0858-0.2464-0.0491-0.01840.00640.0379-0.03320.05150.0638-0.0082-0.02670.04540.00750.0832-47.11848.429-56.36
480.5473-0.34440.17771.06310.05630.375-0.0827-0.01320.20790.02910.015-0.1693-0.08950.05740.06770.0536-0.011-0.0230.01460.00140.1028-21.55867.769-49.231
491.93730.8647-0.85421.3534-0.26071.148-0.0399-0.04560.0329-0.0372-0.01190.07740.04460.00770.05180.05520.0095-0.03730.01020.00690.0665-38.86652.001-52.976
500.72630.2909-0.23470.57250.02810.8002-0.013-0.00680.0261-0.015-0.01860.0458-0.0312-0.0370.03160.0450.0109-0.02420.00690.00120.0646-33.85151.586-46.89
510.82390.1048-0.27090.5599-0.0780.5687-0.022-0.04850.07130.0120.01980.0276-0.0218-0.0260.00220.0440.0178-0.02080.014-0.00220.0556-28.80649.576-39.678
5210.0196-1.4028-1.554210.0421-0.83044.76670.1887-0.50091.17430.3525-0.0802-0.8924-0.6030.3989-0.10850.1455-0.0123-0.02070.1117-0.09610.2422-32.08159.706-24.413
530.8414-0.0297-0.12820.2581-0.05520.4924-0.0182-0.1084-0.00680.071-0.0016-0.0162-0.02210.00510.01990.04750.0069-0.01560.0238-0.00230.0423-23.42145.825-31.245
541.15690.3408-0.67051.5156-0.57832.09720.1199-0.05140.16180.1035-0.0594-0.1011-0.31740.1096-0.06050.074-0.0059-0.02480.0359-0.01210.089-11.73851.149-29.039
550.47160.3007-0.13430.5584-0.15670.7395-0.0162-0.05630.05170.0035-0.0066-0.0834-0.08910.10040.02280.0266-0.0115-0.01640.0293-0.00330.0573-6.52144.324-26.731
561.4097-0.03470.38450.42690.07030.1265-0.0459-0.03830.08830.00660.023-0.0136-0.01340.02080.02290.0503-0.0061-0.01730.11030.00310.05766.43430.524-26.468
571.0385-0.66280.02871.03360.10170.45190.04160.08740.0874-0.0222-0.0751-0.0741-0.02840.10790.03350.0354-0.001-0.00780.06540.01450.041213.24335.232-16.312
580.90440.0413-0.00060.9568-0.14081.4720.0022-0.0620.05950.0377-0.02680.03-0.1077-0.01360.02460.04230.0102-0.01730.04760.00510.050916.03431.192.025
597.15860.47132.1254.43840.12245.1607-0.0968-0.41770.12980.2-0.0269-0.2377-0.13690.08570.12370.02930.0029-0.04080.0453-0.02310.084227.04533.8437.783
603.77971.015-0.26980.9209-0.441.3518-0.0502-0.1804-0.01230.07520.02550.04010.038-0.05220.02460.05060.01-0.00950.05750.00530.033815.61925.4479.763
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 17
2X-RAY DIFFRACTION2A18 - 36
3X-RAY DIFFRACTION3A37 - 77
4X-RAY DIFFRACTION4A78 - 110
5X-RAY DIFFRACTION5A111 - 123
6X-RAY DIFFRACTION6A124 - 180
7X-RAY DIFFRACTION7A181 - 189
8X-RAY DIFFRACTION8A190 - 216
9X-RAY DIFFRACTION9A217 - 263
10X-RAY DIFFRACTION10A264 - 290
11X-RAY DIFFRACTION11A291 - 353
12X-RAY DIFFRACTION12A354 - 402
13X-RAY DIFFRACTION13A403 - 426
14X-RAY DIFFRACTION14A427 - 483
15X-RAY DIFFRACTION15A484 - 506
16X-RAY DIFFRACTION16A507 - 542
17X-RAY DIFFRACTION17A543 - 555
18X-RAY DIFFRACTION18A556 - 610
19X-RAY DIFFRACTION19A611 - 621
20X-RAY DIFFRACTION20A622 - 666
21X-RAY DIFFRACTION21B6 - 23
22X-RAY DIFFRACTION22B24 - 38
23X-RAY DIFFRACTION23B39 - 85
24X-RAY DIFFRACTION24B86 - 106
25X-RAY DIFFRACTION25B107 - 112
26X-RAY DIFFRACTION26B113 - 180
27X-RAY DIFFRACTION27B181 - 189
28X-RAY DIFFRACTION28B190 - 217
29X-RAY DIFFRACTION29B218 - 284
30X-RAY DIFFRACTION30B285 - 317
31X-RAY DIFFRACTION31B318 - 400
32X-RAY DIFFRACTION32B401 - 407
33X-RAY DIFFRACTION33B408 - 423
34X-RAY DIFFRACTION34B424 - 483
35X-RAY DIFFRACTION35B484 - 506
36X-RAY DIFFRACTION36B507 - 513
37X-RAY DIFFRACTION37B514 - 542
38X-RAY DIFFRACTION38B543 - 549
39X-RAY DIFFRACTION39B550 - 613
40X-RAY DIFFRACTION40B614 - 666
41X-RAY DIFFRACTION41C6 - 50
42X-RAY DIFFRACTION42C51 - 62
43X-RAY DIFFRACTION43C63 - 83
44X-RAY DIFFRACTION44C84 - 110
45X-RAY DIFFRACTION45C111 - 121
46X-RAY DIFFRACTION46C122 - 180
47X-RAY DIFFRACTION47C181 - 189
48X-RAY DIFFRACTION48C190 - 263
49X-RAY DIFFRACTION49C264 - 288
50X-RAY DIFFRACTION50C289 - 339
51X-RAY DIFFRACTION51C340 - 399
52X-RAY DIFFRACTION52C400 - 408
53X-RAY DIFFRACTION53C409 - 478
54X-RAY DIFFRACTION54C479 - 497
55X-RAY DIFFRACTION55C498 - 541
56X-RAY DIFFRACTION56C542 - 561
57X-RAY DIFFRACTION57C562 - 613
58X-RAY DIFFRACTION58C614 - 641
59X-RAY DIFFRACTION59C642 - 648
60X-RAY DIFFRACTION60C649 - 666

+
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