[English] 日本語
Yorodumi
- PDB-5tdt: Oxygenated toluene intermediate in toluene 4-monooxygenase (T4moH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tdt
TitleOxygenated toluene intermediate in toluene 4-monooxygenase (T4moHD) after reaction in the crystal
Components(Toluene-4-monooxygenase system protein ...) x 4
KeywordsOXIDOREDUCTASE / Intermediate / diiron
Function / homology
Function and homology information


toluene 4-monooxygenase / toluene catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / monooxygenase activity / metal ion binding
Similarity search - Function
Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane/phenol monooxygenase, hydroxylase component ...Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / TOLUENE / PEROXIDE ION / Toluene-4-monooxygenase system, hydroxylase component subunit alpha / Toluene-4-monooxygenase system, hydroxylase component subunit gamma / Toluene-4-monooxygenase system, effector component / Toluene-4-monooxygenase system, hydroxylase component subunit beta
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.818 Å
AuthorsAcheson, J.F. / Fox, B.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0843239 United States
Department of Energy (DOE, United States)W-31-109-ENG-38 United States
CitationJournal: Nature / Year: 2017
Title: In-crystal reaction cycle of a toluene-bound diiron hydroxylase.
Authors: Acheson, J.F. / Bailey, L.J. / Brunold, T.C. / Fox, B.G.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toluene-4-monooxygenase system protein A
B: Toluene-4-monooxygenase system protein E
C: Toluene-4-monooxygenase system protein B
D: Toluene-4-monooxygenase system protein A
E: Toluene-4-monooxygenase system protein D
F: Toluene-4-monooxygenase system protein E
G: Toluene-4-monooxygenase system protein B
H: Toluene-4-monooxygenase system protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,43618
Polymers229,7208
Non-polymers71610
Water36,8952048
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34850 Å2
ΔGint-205 kcal/mol
Surface area62630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.898, 116.253, 181.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Toluene-4-monooxygenase system protein ... , 4 types, 8 molecules ADBFCGEH

#1: Protein Toluene-4-monooxygenase system protein A / Toluene-4-monooxygenase hydroxylase subunit / T4moH


Mass: 57453.438 Da / Num. of mol.: 2 / Fragment: residues 1-493 / Mutation: residues 1-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoA / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP
References: UniProt: Q00456, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Protein Toluene-4-monooxygenase system protein E / T4moE


Mass: 36176.645 Da / Num. of mol.: 2 / Fragment: residues 1-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoE / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP
References: UniProt: Q00460, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#3: Protein Toluene-4-monooxygenase system protein B / T4moB


Mass: 9600.989 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoB / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP
References: UniProt: Q00457, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#4: Protein Toluene-4-monooxygenase system protein D / T4mo effector protein D / T4moD / Toluene-4-monooxygenase effector protein


Mass: 11629.032 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoD / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP
References: UniProt: Q00459, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor

-
Non-polymers , 4 types, 2058 molecules

#5: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Chemical
ChemComp-MBN / TOLUENE / Toluene


Mass: 92.138 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H8
#7: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2048 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Bis-Tris pH 6.0, 18% PEG 3350, 200 mM Ammonuium Chloride, 5 mM Toluene

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98757 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2012
RadiationMonochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98757 Å / Relative weight: 1
ReflectionResolution: 1.818→30 Å / Num. obs: 169602 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.4
Reflection shellResolution: 1.818→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.57 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10pre_2124)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DHH

3dhh


Resolution: 1.818→29.475 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.21
RfactorNum. reflection% reflectionSelection details
Rfree0.1872 1998 1.18 %Automatic
Rwork0.1528 ---
obs0.1532 169602 89.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.818→29.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16020 0 41 2048 18109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816580
X-RAY DIFFRACTIONf_angle_d0.8522507
X-RAY DIFFRACTIONf_dihedral_angle_d19.0169799
X-RAY DIFFRACTIONf_chiral_restr0.0522313
X-RAY DIFFRACTIONf_plane_restr0.0062935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8181-1.86350.2493650.21635445X-RAY DIFFRACTION41
1.8635-1.91390.2571080.19729035X-RAY DIFFRACTION68
1.9139-1.97020.22351330.183911180X-RAY DIFFRACTION84
1.9702-2.03380.2171460.173512281X-RAY DIFFRACTION92
2.0338-2.10640.22751520.165612801X-RAY DIFFRACTION96
2.1064-2.19080.20441550.164413000X-RAY DIFFRACTION98
2.1908-2.29040.19821560.156713043X-RAY DIFFRACTION98
2.2904-2.41110.20651560.152613042X-RAY DIFFRACTION98
2.4111-2.56210.20781550.150113071X-RAY DIFFRACTION98
2.5621-2.75980.18381540.149713007X-RAY DIFFRACTION97
2.7598-3.03730.22861540.156312968X-RAY DIFFRACTION97
3.0373-3.47620.17031550.151812951X-RAY DIFFRACTION96
3.4762-4.37730.14681540.127912879X-RAY DIFFRACTION95
4.3773-29.47860.15011550.145912901X-RAY DIFFRACTION92
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)
10.1555-0.0078-0.18360.15760.12850.27780.006-0.0072-0.0229-0.0533-0.01820.023-0.1274-0.0333-0.00280.10940.0322-0.02250.06430.00110.062229.01413.713722.8772
20.12360.0193-0.06540.0225-0.05740.15040.12970.07190.034-0.1168-0.05450.084-0.1938-0.07380.13630.3070.1179-0.04970.1329-0.00770.141216.709229.873917.8302
30.0181-0.00420.02610.0462-0.00410.0345-0.04890.00080.0395-0.0338-0.0147-0.0422-0.0445-0.0261-0.07130.35330.0971-0.00630.07450.01430.090128.425128.5855-2.3798
4-0.0015-0.00130.00360.01370.02870.03650.01230.01170.122-0.0085-0.00240.0046-0.17070.0095-0.01260.3737-0.02250.03470.0098-0.00890.12942.452730.531114.5161
50.0060.00170.00220.0020.00150.0009-0.01450.0204-0.02580.00430.01520.00320.00560.0323-00.1537-0.01270.00880.1176-0.0050.085257.88642.98994.7253
60.0075-0.0134-0.00330.02730.00710.00310.0464-0.0071-0.0055-0.0027-0.0192-0.03840.0220.07370.00020.1335-0.03010.00740.2501-0.01580.228378.4911.773513.7756
70.05620.0112-0.11770.0367-0.00110.27720.0085-0.06290.0209-0.01610.0382-0.0629-0.23660.32020.03610.192-0.1140.00680.1219-0.02460.101262.602716.287519.3673
80.080.02790.09790.06910.00930.1430.00510.0429-0.0416-0.05370.0583-0.0607-0.11980.17860.09540.255-0.12570.06360.1487-0.00330.111666.85218.11586.3692
90.01240.01590.00350.0240.01990.02720.02490.02980.0019-0.03310.0239-0.0514-0.12330.11360.05940.3276-0.20380.02980.1558-0.00810.213469.07330.919214.82
100.00020.00010.00040.00110.00820.0609-0.0155-0.01360.00340.0102-0.00980.0034-0.0496-0.0195-0.00790.14690.087-0.02070.1379-0.03950.15216.285231.585632.2311
110.00010.00080.00030.0045-0.00080.00010.0158-0.00120.04670.0079-0.00790.0254-0.027-0.0073-0.01340.19580.1543-0.01660.1027-0.05010.21675.476840.440432.2091
120.0076-0.00130.00410.0038-0.00290.00390.00320.00240.0029-0.02050.00240.00450.0018-0.0086-0.00090.20630.1342-0.03020.1802-0.03350.2434-0.932536.763130.9543
130.00050.00310.00090.00370.00180.0005-0.0139-0.01430.00990.0270.00730.053-0.0326-0.070500.17730.0826-0.02510.2137-0.03080.2025-3.030128.471232.7534
140.0007-0.00040.00150.00030.00040.001-0.0454-0.02160.00410.0042-0.04730.02220.00520.0278-00.27340.09990.03470.2707-0.06750.20541.565234.93844.2204
150.0033-0.0017-0.00440.0045-0.00060.0065-0.0303-0.0844-0.00950.027-0.01770.0312-0.0462-0.013-00.19180.0842-0.04840.194-0.07230.20295.5436.522139.8111
160.00140.0016-0.00110.0279-0.07360.1910.01660.1056-0.04850.0133-0.0256-0.0154-0.00730.15-0.02250.06240.01950.00330.1435-0.03280.157959.5946-10.841-27.3737
170.0308-0.0110.03810.05020.01340.04430.01290.03780.04590.0221-0.0165-0.0252-0.0215-0.0353-0.00020.0802-0.00070.01010.09940.0040.090341.726-7.0062-14.7064
180.02580.00580.03170.03290.02360.0360.01630.039-0.00710.0174-0.01090.03010.0562-0.02260.00040.0712-0.00640.00540.0855-0.00450.081638.2705-15.571-14.1097
190.015-0.00580.0029-0.0021-0.0018-0.00010.03430.0033-0.0084-0.0159-0.01270.03950.0044-0.007100.0844-0.0143-0.00780.09070.00090.099831.9816-24.1219-18.4714
200.01140.01030.01370.01130.0090.0141-0.0316-0.01670.0279-0.0129-0.01980.02280.0177-0.0047-00.0694-0.0077-0.00170.09550.0040.111933.775-6.9022-20.6122
210.02490.0060.03050.0363-0.01680.0376-0.00730.0102-0.0156-0.0074-0.00460.0578-0.01-0.020400.0732-0.01130.00540.1235-0.00530.110626.1932-9.8891-29.952
220.00780.0180.00570.050.03740.02930.0311-0.010.0018-0.03120.030.1239-0.051-0.07360.01630.0675-0.01310.01410.1369-0.0060.13911.134-15.6838-23.511
230.0101-0.0042-0.00860.0077-0.00440.03940.00510.0159-0.0372-0.0291-0.0040.05290.0313-0.058300.0831-0.0180.00750.1322-0.00680.13213.6883-27.1517-29.634
240.0231-0.01640.02420.021-0.00470.02610.0154-0.0232-0.03770.04430.0081-0.00460.0733-0.026800.1093-0.01790.01210.1102-0.00070.124119.9039-32.801-18.0553
250.0021-0.0001-0.0020.00180.00080.0012-0.0104-0.02760.00710.0530.00990.0452-0.0106-0.0074-00.12790.01180.03120.1372-0.01470.180224.1745-4.26136.7427
260.0035-0.00040.00450.0012-0.00120.00350.00880.0105-0.03880.0020.0041-0.01330.0127-0.006-00.07850.00390.0170.0958-0.01070.121534.1236-12.24216.153
270.0002-0.0005-0.00070.00210.00280.0039-0.0144-0.01-0.00560.0016-0.001-0.0093-0.00450.0001-0.00230.17160.06340.01660.0830.03190.174733.0119-19.267727.5368
280.007-0.00350.00130.0053-0.00150.002-0.0139-0.0251-0.02140.01380.00260.0343-0.0032-0.00030.00040.11480.01380.01110.09810.01620.082626.7613-8.253321.3361
290.00490.00060.00270.0015-0.00120.0046-0.0038-0.0224-0.01890.01970.068-0.04520.01510.02690.00020.08020.01440.01990.126-0.00110.132342.8694-15.041915.4154
300.0012-0.00060.0010.0005-0.00160.0023-0.00890.0132-0.0110.00290.00940.01780.00810.008100.0856-0.0008-0.00580.0929-0.00830.126640.3144-3.750517.0641
310.002-0.0007-0.00020.0024-0.00160.001-0.0217-0.0064-0.00640.02120.0173-0.0305-0.02380.018-0.00020.09920.0172-0.0080.1265-0.03010.132944.6779-8.330426.4557
320.0056-0.00040.00130.0013-0.00070.0030.0159-0.01360.00670.02230.0058-0.00610.0099-0.0018-00.19970.03490.00910.24880.02530.100835.5874-6.114638.9554
330.0433-0.00610.00490.03340.01040.00530.0307-0.029-0.12530.0766-0.0135-0.04340.1315-0.06970.00360.1113-0.0177-0.01260.08440.0060.128840.825-30.4382-9.9595
340.0066-0.00260.00750.0032-0.00310.0136-0.00540.00730.0110.00560.0270.0103-0.06070.04-00.0874-0.00740.0010.08840.00390.076658.1557-1.8491-4.6809
350.00070.0059-0.00320.036-0.02580.02090.0153-0.01370.06170.02450.0044-0.0367-0.06280.09650.00380.0795-0.0378-0.00230.2452-0.01340.186678.18650.9073-14.1639
360.1161-0.01070.0610.0332-0.01210.15830.03340.0398-0.0552-0.005-0.0116-0.0350.03910.13590.04480.05980.03040.00460.1171-0.01560.094663.6024-14.7598-19.7093
370.0152-0.02260.01360.0311-0.00090.06360.0387-0.039-0.05150.0213-0.003-0.06010.08260.12970.01990.08640.0227-0.0310.15920.00220.15567.8697-16.3874-6.6375
380.01150.00780.0310.00730.02160.07410.07570.0471-0.09680.0317-0.0126-0.03190.13210.1044-0.00150.10940.0669-0.02960.1684-0.02220.243371.4226-28.7136-15.3933
390.0003-0.001-0.00420.00320.0070.0184-0.00270.0407-0.074-0.00750.00920.02620.1232-0.0689-0.00020.108-0.0351-0.00760.1337-0.01860.18646.4681-38.9554-31.5565
400.0054-0.00340.00060.0125-0.00170.0026-0.03220.0041-0.0148-0.03170.03330.03230.0242-0.01060.00440.0681-0.0350.0020.16750.00330.1611-0.9662-32.2722-32.3135
410.0046-0.00140.00410.0016-0.00080.0034-0.04210.0191-0.0006-0.0068-0.0051-0.0018-0.0313-0.0075-00.1782-0.0846-0.05040.2252-0.01760.20464.0875-38.1374-43.9464
420.00090.00160.00130.00260.0040.0044-0.0280.08450.0032-0.04160.04460.01580.0293-0.005700.1215-0.04550.01150.1973-0.05580.14598.1672-39.4304-39.5875
430.00300.00180.00070.00020.00090.01560.02650.0147-0.02930.01580.0368-0.0129-0.009700.10410.0137-0.02510.18410.03450.180723.78793.1613-36.1148
440.00860.0013-0.00540.00230.00050.0030.0203-0.0409-0.0293-0.0187-0.00380.0394-0.0648-0.0674-00.13770.03210.00880.11160.00280.116233.160411.4299-15.8999
450.01270.0043-0.00380.0027-0.0010.0015-0.02890.0140.0043-0.0041-0.02420.0134-0.0086-0.0061-0.00010.23950.0079-0.00510.10990.06540.155431.454418.2779-27.3405
460.00230.0001-0.00040.00590.0010.0001-0.02940.010.0687-0.04330.01050.0166-0.0391-0.0085-00.11640.02310.00710.11560.00780.125325.96766.8169-20.9996
470.01360.003-0.01360.002400.0176-0.00690.03170.0380.05740.0171-0.013-0.0341-0.00780.00040.1915-0.0305-0.01190.08970.00160.141340.788815.826-17.5615
480.0064-0.0014-0.0040.00230.00150.00480.02670.0130.0010.0050.02190.00620.00190.017100.1871-0.0060.00480.1238-0.02290.152243.94212.1409-8.9166
490.0024-0.0004-0.00020.00020.00110.00460.0118-0.01070.00760.0010.0017-0.0119-0.0377-0.001600.09640.01230.00730.0996-0.02180.10739.84683.3582-16.8779
500.00410.00150.00630.00410.00610.01380.0023-0.00530.01040.01160.034-0.0423-0.05160.02560.00020.1512-0.03510.01840.1517-0.00430.170443.85818.139-26.1301
510.0154-0.0025-0.00260.0015-0.00040.00450.0030.00520.0164-0.0183-0.00760.0066-0.00610.01410.00010.18150.0019-0.02580.20750.03090.117434.67735.5121-38.682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 439 )
2X-RAY DIFFRACTION2chain 'A' and (resid 440 through 490 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 23 )
4X-RAY DIFFRACTION4chain 'B' and (resid 24 through 79 )
5X-RAY DIFFRACTION5chain 'B' and (resid 80 through 103 )
6X-RAY DIFFRACTION6chain 'B' and (resid 104 through 122 )
7X-RAY DIFFRACTION7chain 'B' and (resid 123 through 221 )
8X-RAY DIFFRACTION8chain 'B' and (resid 222 through 274 )
9X-RAY DIFFRACTION9chain 'B' and (resid 275 through 307 )
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 15 )
11X-RAY DIFFRACTION11chain 'C' and (resid 16 through 26 )
12X-RAY DIFFRACTION12chain 'C' and (resid 27 through 37 )
13X-RAY DIFFRACTION13chain 'C' and (resid 38 through 54 )
14X-RAY DIFFRACTION14chain 'C' and (resid 55 through 66 )
15X-RAY DIFFRACTION15chain 'C' and (resid 67 through 83 )
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 34 )
17X-RAY DIFFRACTION17chain 'D' and (resid 35 through 86 )
18X-RAY DIFFRACTION18chain 'D' and (resid 87 through 150 )
19X-RAY DIFFRACTION19chain 'D' and (resid 151 through 191 )
20X-RAY DIFFRACTION20chain 'D' and (resid 192 through 247 )
21X-RAY DIFFRACTION21chain 'D' and (resid 248 through 316 )
22X-RAY DIFFRACTION22chain 'D' and (resid 317 through 368 )
23X-RAY DIFFRACTION23chain 'D' and (resid 369 through 439 )
24X-RAY DIFFRACTION24chain 'D' and (resid 440 through 491 )
25X-RAY DIFFRACTION25chain 'E' and (resid 2 through 14 )
26X-RAY DIFFRACTION26chain 'E' and (resid 15 through 34 )
27X-RAY DIFFRACTION27chain 'E' and (resid 35 through 40 )
28X-RAY DIFFRACTION28chain 'E' and (resid 41 through 55 )
29X-RAY DIFFRACTION29chain 'E' and (resid 56 through 73 )
30X-RAY DIFFRACTION30chain 'E' and (resid 74 through 85 )
31X-RAY DIFFRACTION31chain 'E' and (resid 86 through 98 )
32X-RAY DIFFRACTION32chain 'E' and (resid 99 through 103 )
33X-RAY DIFFRACTION33chain 'F' and (resid 3 through 79 )
34X-RAY DIFFRACTION34chain 'F' and (resid 80 through 103 )
35X-RAY DIFFRACTION35chain 'F' and (resid 104 through 122 )
36X-RAY DIFFRACTION36chain 'F' and (resid 123 through 221 )
37X-RAY DIFFRACTION37chain 'F' and (resid 222 through 274 )
38X-RAY DIFFRACTION38chain 'F' and (resid 275 through 307 )
39X-RAY DIFFRACTION39chain 'G' and (resid 2 through 37 )
40X-RAY DIFFRACTION40chain 'G' and (resid 38 through 54 )
41X-RAY DIFFRACTION41chain 'G' and (resid 55 through 66 )
42X-RAY DIFFRACTION42chain 'G' and (resid 67 through 83 )
43X-RAY DIFFRACTION43chain 'H' and (resid 3 through 14 )
44X-RAY DIFFRACTION44chain 'H' and (resid 15 through 34 )
45X-RAY DIFFRACTION45chain 'H' and (resid 35 through 40 )
46X-RAY DIFFRACTION46chain 'H' and (resid 41 through 55 )
47X-RAY DIFFRACTION47chain 'H' and (resid 56 through 68 )
48X-RAY DIFFRACTION48chain 'H' and (resid 69 through 73 )
49X-RAY DIFFRACTION49chain 'H' and (resid 74 through 85 )
50X-RAY DIFFRACTION50chain 'H' and (resid 86 through 98 )
51X-RAY DIFFRACTION51chain 'H' and (resid 99 through 103 )

+
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