[English] 日本語
Yorodumi
- PDB-3iiq: Crystallographic analysis of bacterial signal peptidase in ternar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iiq
TitleCrystallographic analysis of bacterial signal peptidase in ternary complex with Arylomycin A2 and a beta-sultam inhibitor
Components
  • ARYLOMYCIN A2
  • SIGNAL PEPTIDASE I
KeywordsHYDROLASE/ANTIBIOTIC/INHIBITOR / SER/LYS DYAD / LIPOPEPTIDE / SERINE PROTEASE / BIARYL BRIDGE / MORPHOLINO BETA-SULTAM / ANTIBIOTIC / PEPTIDASE / HYDROLASE-ANTIBIOTIC-INHIBITOR COMPLEX
Function / homology
Function and homology information


signal peptidase I / signal peptide processing / protein processing / peptidase activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Signal Peptidase I; Chain: A, domain 2 / Signal Peptidase I; Chain: A, domain 2 - #10 / Signal peptidase I, all-beta subdomain / Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site ...Signal Peptidase I; Chain: A, domain 2 / Signal Peptidase I; Chain: A, domain 2 - #10 / Signal peptidase I, all-beta subdomain / Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA/Signal peptidase-like superfamily / Beta Complex / Ribbon / Mainly Beta
Similarity search - Domain/homology
ARYLOMYCIN A2 / ACETONITRILE / Chem-JZA / 10-METHYLUNDECANOIC ACID / : / Signal peptidase I
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
STREPTOMYCES SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPaetzel, M.
CitationJournal: Biochemistry / Year: 2009
Title: Crystallographic Analysis of Bacterial Signal Peptidase in Ternary Complex with Arylomycin A2 and a Beta-Sultam Inhibitor.
Authors: Luo, C. / Roussel, P. / Dreier, J. / Page, M.G. / Paetzel, M.
History
DepositionAug 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 2.0Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SIGNAL PEPTIDASE I
B: SIGNAL PEPTIDASE I
C: ARYLOMYCIN A2
D: ARYLOMYCIN A2
C: 10-METHYLUNDECANOIC ACID
D: 10-METHYLUNDECANOIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,21916
Polymers57,2234
Non-polymers1,99712
Water4,432246
1
B: SIGNAL PEPTIDASE I
D: ARYLOMYCIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3845
Polymers28,6112
Non-polymers7733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-4.4 kcal/mol
Surface area11380 Å2
MethodPISA
2
A: SIGNAL PEPTIDASE I
C: ARYLOMYCIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,83511
Polymers28,6112
Non-polymers1,2249
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint4.2 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.007, 70.007, 259.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein SIGNAL PEPTIDASE I / SPASE I / LEADER PEPTIDASE I


Mass: 27966.658 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 76-323, PERIPLASMIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Gene: LEPB / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P00803, signal peptidase I
#2: Protein/peptide ARYLOMYCIN A2


Type: Lipopeptide / Class: Antibiotic / Mass: 644.674 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ...Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ISO-C12 FATTY ACID IS LINKED TO RESIDUE 1.
Source: (natural) STREPTOMYCES SP. (bacteria) / References: NOR: NOR01115, ARYLOMYCIN A2

-
Non-polymers , 6 types, 258 molecules CD

#3: Chemical ChemComp-JZA / 4-[(1,1-dioxido-1,2-thiazetidin-2-yl)carbonyl]morpholine / beta-sultam


Mass: 220.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12N2O4S
#4: Chemical ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE


Mass: 352.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#7: Chemical
ChemComp-M12 / 10-METHYLUNDECANOIC ACID


Type: Lipopeptide / Class: Antibiotic / Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ...Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ISO-C12 FATTY ACID IS LINKED TO RESIDUE 1.
References: ARYLOMYCIN A2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsARYLOMYCIN A2 IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF THE ARYLOMYCIN FAMILY. ALL MEMBERS HAVE A ...ARYLOMYCIN A2 IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF THE ARYLOMYCIN FAMILY. ALL MEMBERS HAVE A FATTY ACID AT THE N-TERM AND A CORE STRUCTURE OF TRIPEPTIDE MACROCYCLE FORMED BY A C-C BIARYL LINKAGE BETWEEN RESIDUES 4 AND 6. HERE, ARYLOMYCIN A2 IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND ONE LIGAND (HET) M12.
Nonpolymer detailsLIGAND JZA, MORPHOLINO-BETA-SULTAM, IS A BETA-LACTAMSE TYPE INHIBITOR.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.61 %
Crystal growpH: 6.5
Details: 0.2M NH4 FORMATE, 25% PEG 2000, 0.1M NA CACODYLATE PH 6.5, AND 5% TERTIARY-AMYL ALCOHOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1217
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1217 Å / Relative weight: 1
ReflectionResolution: 2→67.4 Å / Num. obs: 40272 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.069 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.14 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.052 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T7D CHAIN A WITH LIGANDS REMOVED

1t7d


Resolution: 2→67.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.239 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2035 5.1 %RANDOM
Rwork0.207 ---
obs0.21 38237 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2--1.17 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 2→67.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 114 246 3933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0223770
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3482.0145115
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3835431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36524165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88215577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2291522
X-RAY DIFFRACTIONr_chiral_restr0.3210.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022873
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.21663
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.22426
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8241.52255
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33423542
X-RAY DIFFRACTIONr_scbond_it3.30131762
X-RAY DIFFRACTIONr_scangle_it4.3684.51569
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 113 -
Rwork0.266 1741 -
obs--60.77 %
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)
131.0406-11.79487.646743.0687-5.66594.43930.6596-1.67251.18411.4435-1.6351-4.6309-1.4652-0.46940.97550.0838-0.136-0.23540.0988-0.04750.19737.484421.964-7.4643
21.09610.48280.0073.00680.8291.78140.02660.1207-0.12520.3484-0.0244-0.18450.1058-0.0562-0.0023-0.0199-0.0086-0.01210.2388-0.01330.0158-3.412211.8379-14.8828
321.8851-10.181111.20811.7696-11.075613.846-0.416-0.38221.18450.68250.3913-0.9353-0.7251-0.12920.02470.06150.01490.03370.14930.01820.0157-0.385929.0444-12.9678
41.4260.5352-0.30023.1456-1.95295.28650.10380.23020.12620.37860.0840.1687-0.1424-0.4678-0.18780.03350.01390.01390.22230.01830.0083-9.874522.1636-10.4581
51.12842.5643-0.06338.72371.98511.5686-0.05710.39520.2438-0.09790.17320.3956-0.1625-0.4738-0.1161-0.10930.0573-0.01690.39080.15590.0661-20.129927.7514-24.1147
61.40071.21151.07489.1683-0.54431.0923-0.26580.48970.17120.12820.45680.4585-0.0401-0.3118-0.191-0.0699-0.0010.06250.50840.02920.0424-15.49119.7669-27.4731
72.1901-0.7792-3.117117.43691.48485.6903-0.02790.1228-0.21190.20220.6382-0.45260.83770.1793-0.6103-0.1869-0.1133-0.07730.35-0.150.0758-11.44771.2802-24.7457
82.3891-0.7479-0.05544.9963-0.16153.3899-0.2774-0.1153-0.3495-0.21960.1536-0.29020.47330.17180.1237-0.0863-0.08380.00350.4865-0.0567-0.012-17.0548-0.703-28.0131
94.39632.1315-0.74562.757-0.10180.16560.00290.52320.0085-0.26340.06370.2473-0.0333-0.0881-0.0666-0.0686-0.047-0.02830.44880.0237-0.0181-14.086217.563-27.5193
1028.4464-1.457-2.803612.8139-4.049144.8897-0.31180.0785-1.56370.3377-0.7880.14290.7579-1.23991.0998-0.10490.05860.15260.50580.01670.322-28.724619.3224-15.6738
115.70934.8882.971727.5398-6.29624.8930.3315-0.31880.34750.39850.27381.7815-0.593-0.9548-0.6053-0.01530.19090.21170.36160.11880.118-26.824330.7231-12.1948
1248.31542.370122.321242.984927.659421.527-0.96470.64532.33780.13450.21582.3335-1.5175-1.87920.74880.00890.0990.10290.66550.37160.2458-26.569228.6704-18.2243
131.3780.2393-0.7381.46820.38570.71520.03610.25680.20340.32750.06620.2242-0.1492-0.2541-0.1023-0.01790.04960.03310.30930.0685-0.0041-16.655323.7842-14.8124
142.9014-2.6197-1.99116.16782.22144.09140.06160.2497-0.08420.2198-0.0036-0.13260.0268-0.0795-0.0580.0357-0.0364-0.0580.27180.0210.0778-1.405217.2662-12.645
15135.6967-42.4202-40.177640.63559.997712.1357-1.4872-3.7451-0.40290.72731.8581-1.64511.2374-0.0847-0.37090.3839-0.34670.11480.3291-0.13790.2451-5.3397-1.1229-11.8291
164.295-1.4959-1.52736.2051-1.26274.1240.0230.5144-0.303-0.0109-0.2066-0.25910.12520.10930.1836-0.0745-0.0098-0.00740.3129-0.03520.06662.99329.4707-21.7008
173.9601-0.0094-1.45282.55990.94024.354-0.0741-0.09380.1639-0.29850.0032-0.20030.06470.25710.07090.02160.01-0.02530.1980.0180.047515.252435.9121-48.8929
1814.087117.1875-6.726225.2374-0.974615.4679-0.75840.108-0.5933-1.44010.6841-0.96172.01320.39830.0743-0.03650.2528-0.05610.21710.05030.017120.653420.8459-51.1883
192.0989-0.4507-0.67432.5916-1.36386.9447-0.078-0.0834-0.0456-0.13040.05480.140.344-0.15250.02320.0842-0.00840.01780.17380.0240.012810.062826.4056-53.8963
208.3269-3.8757-5.88242.54794.29457.4125-0.2212-0.3479-0.4972-0.0992-0.01430.12080.6643-0.31270.23540.0591-0.05270.05030.17230.1055-0.01331.427416.9824-41.7493
2145.7228-28.326-31.686344.508117.148425.19910.04220.0601-2.4986-1.1833-1.17921.11591.8554-0.86341.1370.32880.0670.03810.41470.27090.06846.36829.333-42.0772
224.4116-4.93222.60468.39451.1427.24390.7253-0.2355-1.05760.687-1.43850.04043.3708-1.79840.71320.557-0.11490.29960.1904-0.0130.04296.98337.9548-39.7575
232.1887-2.3979-0.35696.9636-0.84271.96880.14030.07180.2198-0.30.00530.0747-0.1563-0.1562-0.1455-0.0660.0005-0.02040.3608-0.0250.0461-0.017839.3835-38.2956
247.3974-6.97660.76899.5408-1.53941.2729-0.3891-0.570.51250.62620.332-0.3268-0.2475-0.35560.0571-0.03460.0581-0.03180.4464-0.06990.029-0.852540.7269-31.852
254.8775-0.98131.04114.7724-1.79612.7199-0.0461-0.3129-0.0693-0.09550.001-0.38470.32390.33650.04510.00820.0586-0.00550.38980.0253-0.05757.704625.6625-35.8282
262.8502-3.1422-3.067113.6319.94869.40010.22220.2073-0.4942-0.5014-0.48220.40580.5103-1.36750.260.0743-0.0918-0.03790.25430.0065-0.0178-6.530819.8563-48.9172
2740.9657-19.9292-12.792510.32576.015638.24680.0870.1876-2.4193-0.3763-0.21471.39991.042-1.70430.12770.2084-0.1351-0.05350.21440.12830.1448-3.84913.5797-47.4077
281.5435-1.4029-0.48372.70112.02473.1772-0.1566-0.1699-0.2614-0.1490.13830.10730.5338-0.03120.01830.0898-0.03670.03360.18210.0714-0.00485.701520.8634-48.2507
292.38030.63550.47210.6990.51222.5658-0.0459-0.0851-0.0187-0.06040.0419-0.08610.27050.05970.00410.14230.00860.00020.22630.04490.047611.11926.4627-51.7443
3047.1171-16.909216.377114.3838-9.12528.358-0.3959-0.27590.2357-0.51550.32760.9841-1.2567-2.28990.0682-0.09990.076-0.09720.1201-0.02350.02179.802246.2807-47.1978
3110.4247-4.74545.046835.0323-15.716916.348-0.30160.38381.1737-1.26620.80832.5315-2.1038-1.4189-0.50670.14750.1742-0.20560.155-0.0290.087713.487149.2604-45.0337
3219.95663.39274.00797.84658.44779.10170.4069-1.1662-0.86460.4063-0.0721-0.20620.6501-0.4539-0.3348-0.0285-0.0088-0.05110.35720.07870.102319.369636.6726-39.9678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 82
2X-RAY DIFFRACTION2A83 - 103
3X-RAY DIFFRACTION3A104 - 126
4X-RAY DIFFRACTION4A127 - 150
5X-RAY DIFFRACTION5A151 - 168
6X-RAY DIFFRACTION6A169 - 197
7X-RAY DIFFRACTION7A206 - 213
8X-RAY DIFFRACTION8A214 - 224
9X-RAY DIFFRACTION9A225 - 245
10X-RAY DIFFRACTION10A246 - 250
11X-RAY DIFFRACTION11A251 - 256
12X-RAY DIFFRACTION12A257 - 261
13X-RAY DIFFRACTION13A262 - 286
14X-RAY DIFFRACTION14A287 - 305
15X-RAY DIFFRACTION15A306 - 312
16X-RAY DIFFRACTION16A313 - 323
17X-RAY DIFFRACTION17B80 - 104
18X-RAY DIFFRACTION18B105 - 126
19X-RAY DIFFRACTION19B127 - 148
20X-RAY DIFFRACTION20B149 - 164
21X-RAY DIFFRACTION21B165 - 170
22X-RAY DIFFRACTION22B171 - 183
23X-RAY DIFFRACTION23B184 - 212
24X-RAY DIFFRACTION24B213 - 226
25X-RAY DIFFRACTION25B227 - 241
26X-RAY DIFFRACTION26B242 - 256
27X-RAY DIFFRACTION27B257 - 261
28X-RAY DIFFRACTION28B262 - 277
29X-RAY DIFFRACTION29B278 - 301
30X-RAY DIFFRACTION30B302 - 308
31X-RAY DIFFRACTION31B309 - 317
32X-RAY DIFFRACTION32B318 - 323

+
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