[English] 日本語
Yorodumi
- PDB-5tdv: Intermediate O2 diiron complex in the Q228A variant of Toluene 4-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tdv
TitleIntermediate O2 diiron complex in the Q228A variant of Toluene 4-moonoxygenase (T4moHD)
Components(Toluene-4-monooxygenase system protein ...) x 4
KeywordsOXIDOREDUCTASE / diiron / oxygen activation / complex
Function / homology
Function and homology information


toluene 4-monooxygenase / toluene 4-monooxygenase activity / toluene catabolic process / 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
: / 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: 2.001 Å
AuthorsBailey, L.J. / Acheson, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

-
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
E: Toluene-4-monooxygenase system protein D
D: Toluene-4-monooxygenase system protein A
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)235,79214
Polymers235,5058
Non-polymers2876
Water27,1851509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33480 Å2
ΔGint-222 kcal/mol
Surface area62360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.293, 115.757, 181.654
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: 58099.242 Da / Num. of mol.: 2 / Mutation: Q228A
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: 38410.227 Da / Num. of mol.: 2
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: 11642.073 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 , 3 types, 1515 molecules

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


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Chemical
ChemComp-FE / FE (III) ION / Iron


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


Mass: 18.015 Da / Num. of mol.: 1509 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Bis-Tris pH 6.0, 20% PEG 3350, 200 mM Ammonium Chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2009
RadiationMonochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.001→42.28 Å / Num. obs: 140977 / % possible obs: 98.69 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.32
Reflection shellResolution: 2.001→2.03 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.67 / % possible all: 92

-
Processing

Software
NameVersionClassification
PHENIX(1.11rc1_2513)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DHH

3dhh


Resolution: 2.001→42.276 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.04
RfactorNum. reflection% reflection
Rfree0.195 7077 5.02 %
Rwork0.1529 --
obs0.155 140909 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→42.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16001 0 8 1509 17518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716663
X-RAY DIFFRACTIONf_angle_d0.8522657
X-RAY DIFFRACTIONf_dihedral_angle_d7.86413542
X-RAY DIFFRACTIONf_chiral_restr0.0522337
X-RAY DIFFRACTIONf_plane_restr0.0062964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0006-2.02330.27042310.20754082X-RAY DIFFRACTION92
2.0233-2.04710.23992310.20344333X-RAY DIFFRACTION96
2.0471-2.07210.24292140.19174351X-RAY DIFFRACTION97
2.0721-2.09830.2522770.18984326X-RAY DIFFRACTION97
2.0983-2.1260.24461940.17924396X-RAY DIFFRACTION98
2.126-2.15510.24122330.17624383X-RAY DIFFRACTION98
2.1551-2.18590.23412440.17194439X-RAY DIFFRACTION98
2.1859-2.21850.22112370.17324409X-RAY DIFFRACTION98
2.2185-2.25320.21752580.16434362X-RAY DIFFRACTION98
2.2532-2.29010.20962230.164423X-RAY DIFFRACTION99
2.2901-2.32960.21872010.15754483X-RAY DIFFRACTION99
2.3296-2.37190.20752390.15784415X-RAY DIFFRACTION99
2.3719-2.41750.21532330.15674411X-RAY DIFFRACTION98
2.4175-2.46690.19672310.15134447X-RAY DIFFRACTION99
2.4669-2.52050.21842490.15364410X-RAY DIFFRACTION99
2.5205-2.57910.1972340.15114448X-RAY DIFFRACTION99
2.5791-2.64360.19592480.1554430X-RAY DIFFRACTION99
2.6436-2.71510.21482440.15644449X-RAY DIFFRACTION99
2.7151-2.7950.21362560.15334492X-RAY DIFFRACTION100
2.795-2.88520.20232190.15864517X-RAY DIFFRACTION100
2.8852-2.98830.20652540.15864456X-RAY DIFFRACTION100
2.9883-3.10790.19142400.15534558X-RAY DIFFRACTION100
3.1079-3.24930.20612280.15244542X-RAY DIFFRACTION100
3.2493-3.42050.18792100.15194589X-RAY DIFFRACTION100
3.4205-3.63470.19632160.1424561X-RAY DIFFRACTION100
3.6347-3.91520.1622700.13174530X-RAY DIFFRACTION100
3.9152-4.30880.13742200.12664599X-RAY DIFFRACTION100
4.3088-4.93150.14982570.12274592X-RAY DIFFRACTION100
4.9315-6.210.18812500.15194637X-RAY DIFFRACTION100
6.21-42.28590.17732360.16014762X-RAY DIFFRACTION98
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)
11.3849-0.63080.1230.36340.30071.1849-0.1028-0.3106-0.03510.09440.14630.01810.0655-0.41310.00860.1283-0.03590.00240.24310.00810.1701-9.1273-11.899327.2303
20.7289-0.2104-0.11530.6633-0.54261.51780.0729-0.10740.11860.0382-00.0660.00140.0761-0.06630.1433-0.03460.0030.1208-0.03180.17428.5221-6.665114.8039
30.9626-0.27080.28140.0853-0.11920.72650.0470.0033-0.0031-0.0607-0.0178-0.00060.21180.1352-0.01490.17640.02920.00030.0809-0.01030.143115.3271-18.15916.0497
40.64110.182-0.38560.7088-0.80612.8027-0.0382-0.04770.0130.1004-0.055-0.04130.06020.12240.04680.14140.0035-0.00780.1173-0.02090.178416.0752-6.101421.1998
55.9730.2654-2.07531.01650.12782.21820.0631-0.11320.10880.07230.02090.00230.0571-0.0346-0.0430.15710.0684-0.00930.16860.00510.123620.8319-14.064932.4762
60.6179-0.64730.15741.83730.01620.11470.08240.09570.0117-0.0079-0.0561-0.0464-0.17920.0181-0.00450.11250.0227-0.0090.19370.00280.142326.6194-4.154428.5236
70.94120.0677-0.15841.20130.09410.82390.00240.06680.0127-0.068-0.0237-0.24660.10730.3088-0.03820.15090.11090.02160.26320.02030.207342.3601-16.545522.8086
80.57240.02940.27910.74410.12621.15560.07710.0508-0.063-0.1115-0.0617-0.1250.2780.2270.0110.25350.12680.01630.16930.00640.177631.8065-28.237426.4089
90.9183-0.4132-0.07290.7426-0.02070.26180.10010.1316-0.1704-0.2343-0.09920.00810.69620.28530.11470.3880.0844-0.00940.1678-0.03940.201316.3608-28.69137.1978
100.0473-0.01550.04730.8658-0.0094-0.01020.04010.0312-0.1611-0.35180.0730.08870.7485-0.2176-0.06020.4104-0.058-0.00830.11880.00660.2473.3324-31.80714.0484
116.7888-4.7093-0.41993.76760.5171.42990.08470.05010.2188-0.1427-0.0229-0.0436-0.2462-0.1836-0.06730.16840.00190.00510.14860.00850.1624-7.7749-2.93194.7542
123.53380.33860.06393.5116-2.25463.39750.2071-0.07440.28420.10340.10420.7828-0.3074-0.7184-0.22660.21370.1024-0.02440.4627-0.00620.3235-28.0132-0.931313.063
131.2258-0.573-0.05151.06390.13451.33280.0489-0.1123-0.0184-0.0519-0.00610.10510.1092-0.2602-0.03330.1172-0.0637-0.00370.14560.00690.1379-8.8457-13.600416.2076
140.8368-0.59050.66872.4165-1.18422.2876-0.05-0.517-0.0270.45360.19980.5571-0.3209-0.8394-0.0560.17560.02530.05920.5460.00610.2585-23.4249-7.165926.8325
150.2473-0.6396-0.04371.7943-0.18431.20960.0886-0.1404-0.14-0.17970.0510.27270.2709-0.5105-0.11330.2042-0.1391-0.02790.28330.04040.2771-18.2378-20.944915.1859
160.72150.1942-0.03390.8596-0.30461.0830.11190.2137-0.2859-0.4257-0.00310.25530.5544-0.88060.21050.2883-0.2986-0.09680.1884-0.02410.2942-14.9236-25.88259.853
172.1745-0.77050.53740.4643-0.1481.05530.0607-0.0438-0.5845-0.1526-0.1702-0.24170.53470.3233-0.02050.3660.18650.02630.28890.0370.397243.9322-35.267232.2863
182.1024-1.21580.48613.3366-1.05612.6362-0.0960.0574-0.5621-0.0887-0.0947-0.19430.33340.2991-0.17440.36270.25590.00120.39930.04460.43950.8335-36.686531.1593
190.7262-0.52180.93331.6279-0.8911.2521-0.0492-0.049-0.39180.1284-0.1186-0.33910.44180.78250.06090.31150.185-0.02560.45260.04360.367952.9331-28.360532.804
204.5168-4.24540.58124.3728-0.88660.368-0.271-0.8340.17920.58610.2434-0.65080.03390.1160.01540.50050.2283-0.13960.51630.04060.460747.9206-34.670144.327
211.34440.5740.89912.42190.07051.90490.0272-0.8109-0.3370.4079-0.2674-0.63420.46160.20680.05460.40920.1816-0.01680.37640.11750.383544.3781-36.391439.8915
222.5065-4.20741.72978.299-1.0274.9962-0.3227-0.60970.26080.95160.2836-0.79610.33260.15680.07740.3110.0224-0.08170.3540.0240.293925.18654.52836.393
232.7899-3.4715-2.36496.16542.29366.04240.16610.19620.1564-0.3695-0.2688-0.0465-0.5723-0.17730.06390.1177-0.0231-0.03330.11970.02540.163415.886212.30616.1936
246.1798-4.544-1.59746.78153.2562.4001-0.2875-0.17110.65540.19190.3016-0.617-0.41770.3784-0.16210.2398-0.0351-0.02190.13120.02540.201922.785912.017521.1627
253.6276-2.02590.28722.65751.61012.8043-0.0319-0.16440.2259-0.01690.1114-0.1214-0.33010.3182-0.34110.1784-0.02760.01660.10350.01930.14620.23938.618224.4268
264.1011-0.16282.36232.4403-2.41947.3878-0.16170.08930.0995-0.14020.29770.2325-0.4123-0.5374-0.15210.15950.0039-0.020.10730.02210.18957.16415.17115.343
274.2344-1.84591.5952.47610.15777.2539-0.01790.1729-0.0396-0.17390.0342-0.0468-0.2139-0.2292-0.04030.1739-0.0127-0.00830.09130.02050.15279.16814.254917.0839
284.3818-0.76091.87625.5738-1.37258.2191-0.0529-0.6665-0.04740.16730.28990.50910.0428-0.7156-0.13450.14070.0350.02950.1625-0.00830.16237.87827.807329.8443
290.99270.3532-0.10250.44040.3270.8762-0.04830.23020.0585-0.06980.0593-0.0048-0.0928-0.2745-0.01020.12560.0364-0.00840.21810.0210.1829-9.469310.9127-27.3954
300.56250.2598-0.27070.9773-0.60821.0890.13830.0852-0.1101-0.0271-0.03390.04020.03110.0966-0.09750.1030.0325-0.00410.1182-0.02290.15918.30776.9228-14.7046
310.74850.2233-0.12210.397-0.16770.8470.0060.0001-0.00490.0462-0.0209-0.049-0.26590.20010.00670.1559-0.0488-0.00110.1076-0.00110.135214.428818.897-15.9309
320.4864-0.02760.50570.7282-0.94872.8241-0.03840.0661-0.034-0.0727-0.0905-0.03460.01590.15710.10620.1254-0.00640.00170.1347-0.01140.152715.75936.83-21.2103
335.21930.07681.73870.84180.37621.5571-0.01210.11620.0504-0.0503-0.026-0.0299-0.10210.14010.07660.1225-0.04830.01630.1750.02440.11820.264415.0449-32.2851
340.85720.94730.34471.89820.57060.49720.00190.0303-0.0352-0.0067-0.0409-0.11140.13380.2850.03890.1116-0.02170.0060.25630.0290.142227.7616.7584-29.8313
351.67250.0240.64111.08790.37070.9638-0.01510.07070.03410.03450.0483-0.2546-0.04450.3221-0.06790.1518-0.0865-0.00640.31550.0420.219342.834420.6226-20.2336
360.5959-0.05170.19340.4152-0.19451.5919-0.0018-0.0130.06030.0362-0.0303-0.1148-0.28620.26640.04960.2262-0.1085-0.00410.21460.01690.204330.406329.7598-25.9358
373.65392.35780.88963.6334-0.10940.45660.2634-0.290.52770.4817-0.15070.0697-0.73050.216-0.09130.4775-0.2015-0.01910.2877-0.04110.219719.736729.61742.4616
380.6635-0.13560.07050.9883-0.2530.60310.0727-0.03240.17340.19090.00510.0522-0.47320.0613-0.08270.3296-0.0380.00230.1195-0.00890.21635.823730.7749-14.7921
396.3784.85370.79834.22850.52170.9512-0.0048-0.1124-0.0473-0.0349-0.00770.03260.0805-0.1393-0.01580.14570.0092-0.0060.1521-0.00320.1553-7.78492.1875-4.8116
403.9970.51390.054.0492-1.99032.6136-0.01740.0151-0.2872-0.0730.19880.46550.2738-0.7948-0.140.1461-0.05770.02140.3714-0.01120.258-27.7591-1.2092-13.5657
411.04940.49940.05771.1318-0.10321.32590.02020.08240.02190.05250.03480.0905-0.1139-0.2045-0.0640.09820.05560.00090.1210.00450.1367-9.324312.8984-16.3327
420.2661-0.67850.15922.5367-1.93862.7683-0.03930.25730.0857-0.57390.10850.59120.3394-0.6236-0.08320.12780.0159-0.07980.42610.0610.2452-23.44195.2152-27.1526
431.6390.59220.24051.15760.08830.65610.04070.14290.2870.06150.02840.2976-0.3087-0.2588-0.00720.22120.1370.0190.19750.03280.2745-15.903424.0306-18.7909
440.60210.91540.01172.58380.44311.25310.145-0.1050.17910.2186-0.03350.2157-0.2381-0.36320.00820.19230.0910.06880.1933-0.00560.2271-16.68916.5321-5.5171
451.91541.49350.13791.69360.03020.60570.1152-0.12390.78610.0676-0.13960.8494-0.4529-0.43790.08080.26690.15970.07980.26910.05790.4971-21.160828.9371-15.7516
462.86140.6876-0.56372.9811-1.50362.52270.06110.13420.34590.1847-0.1060.1114-0.55690.31380.01420.2853-0.11610.01540.28920.03520.279541.594237.9519-31.9508
472.16661.7648-1.69427.264-5.35134.07720.1358-0.10470.1179-0.0111-0.2868-0.076-0.54990.64840.1710.3203-0.1636-0.00210.4083-0.01920.348648.298440.0128-30.7437
480.99481.34610.58745.2592-2.08962.94040.06780.3573-0.1971-0.0707-0.4208-0.6733-0.00530.51220.12150.2092-0.10940.02250.50770.02750.345152.453629.841-28.1778
492.23932.0852-0.28683.20350.8014.2-0.50341.1288-0.3101-0.47780.19750.15460.4537-0.19560.3910.3574-0.33590.09480.7287-0.01280.376944.55833.2697-42.78
506.54-5.9869-1.42255.49691.3650.6247-0.19720.43480.4784-0.45610.2553-0.12430.0134-0.2381-0.0610.3967-0.2206-0.01610.56980.12970.330847.496544.2354-42.7194
510.9191-1.56361.71774.873-2.51823.32210.07870.84240.5202-0.5081-0.0948-0.2869-0.10440.3092-0.03760.4202-0.1804-0.0360.4430.10890.257441.892237.1512-39.2216
521.69762.6254-0.50367.6245-0.37995.8582-0.50740.8422-0.458-0.99530.3806-1.18840.12930.95630.20850.35720.0480.07670.5426-0.02640.33626.5674-3.0921-36.4077
533.71222.99631.96334.80251.49764.32150.0734-0.3508-0.24910.3319-0.2088-0.07150.7670.16830.02530.16850.08820.01560.1960.02930.153916.7401-11.624-16.0534
546.47794.30612.38244.72023.77224.34010.00580.5303-0.559-0.10590.2734-0.70650.50490.7073-0.2930.31450.1419-0.01170.23210.04760.187323.1331-11.5102-22.006
556.462.82154.24217.30681.80494.4269-0.05480.2112-0.394-0.37170.0759-0.08910.23670.5562-0.08640.11580.06820.02060.16420.00010.118921.0882-7.5803-23.7053
565.21070.4324-0.92963.2807-1.05754.77360.0234-0.0787-0.25690.05990.12330.40270.9086-0.251-0.18080.2481-0.01150.00380.0944-0.02150.19039.059-15.9933-17.5293
574.3283-4.54753.72469.4301-6.07954.2130.1252-0.38340.26640.17710.27090.2209-0.1132-0.2527-0.25050.20330.0095-0.00720.1940.02660.24536.0382-12.3042-8.8501
583.70711.2306-1.88251.6280.76225.29910.0733-0.03770.12070.1150.01760.18660.2879-0.1202-0.08470.20690.0237-0.02140.11720.01570.202310.1192-3.4852-16.9055
593.9492-0.0873-2.10654.73-1.07031.7806-0.02880.6724-0.0235-0.51420.28910.5140.5458-0.6329-0.1710.2021-0.034-0.08360.202-0.01980.17078.6523-7.5425-29.7692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 191 )
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 247 )
5X-RAY DIFFRACTION5chain 'A' and (resid 248 through 278 )
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 316 )
7X-RAY DIFFRACTION7chain 'A' and (resid 317 through 398 )
8X-RAY DIFFRACTION8chain 'A' and (resid 399 through 492 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 48 )
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 78 )
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 102 )
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 121 )
13X-RAY DIFFRACTION13chain 'B' and (resid 122 through 175 )
14X-RAY DIFFRACTION14chain 'B' and (resid 176 through 192 )
15X-RAY DIFFRACTION15chain 'B' and (resid 193 through 244 )
16X-RAY DIFFRACTION16chain 'B' and (resid 245 through 306 )
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 26 )
18X-RAY DIFFRACTION18chain 'C' and (resid 27 through 37 )
19X-RAY DIFFRACTION19chain 'C' and (resid 38 through 54 )
20X-RAY DIFFRACTION20chain 'C' and (resid 55 through 66 )
21X-RAY DIFFRACTION21chain 'C' and (resid 67 through 83 )
22X-RAY DIFFRACTION22chain 'E' and (resid 2 through 13 )
23X-RAY DIFFRACTION23chain 'E' and (resid 14 through 33 )
24X-RAY DIFFRACTION24chain 'E' and (resid 34 through 46 )
25X-RAY DIFFRACTION25chain 'E' and (resid 47 through 54 )
26X-RAY DIFFRACTION26chain 'E' and (resid 55 through 72 )
27X-RAY DIFFRACTION27chain 'E' and (resid 73 through 84 )
28X-RAY DIFFRACTION28chain 'E' and (resid 85 through 102 )
29X-RAY DIFFRACTION29chain 'D' and (resid 2 through 34 )
30X-RAY DIFFRACTION30chain 'D' and (resid 35 through 86 )
31X-RAY DIFFRACTION31chain 'D' and (resid 87 through 191 )
32X-RAY DIFFRACTION32chain 'D' and (resid 192 through 247 )
33X-RAY DIFFRACTION33chain 'D' and (resid 248 through 278 )
34X-RAY DIFFRACTION34chain 'D' and (resid 279 through 326 )
35X-RAY DIFFRACTION35chain 'D' and (resid 327 through 398 )
36X-RAY DIFFRACTION36chain 'D' and (resid 399 through 492 )
37X-RAY DIFFRACTION37chain 'F' and (resid 1 through 22 )
38X-RAY DIFFRACTION38chain 'F' and (resid 23 through 78 )
39X-RAY DIFFRACTION39chain 'F' and (resid 79 through 102 )
40X-RAY DIFFRACTION40chain 'F' and (resid 103 through 121 )
41X-RAY DIFFRACTION41chain 'F' and (resid 122 through 175 )
42X-RAY DIFFRACTION42chain 'F' and (resid 176 through 192 )
43X-RAY DIFFRACTION43chain 'F' and (resid 193 through 230 )
44X-RAY DIFFRACTION44chain 'F' and (resid 231 through 274 )
45X-RAY DIFFRACTION45chain 'F' and (resid 275 through 305 )
46X-RAY DIFFRACTION46chain 'G' and (resid 2 through 26 )
47X-RAY DIFFRACTION47chain 'G' and (resid 27 through 37 )
48X-RAY DIFFRACTION48chain 'G' and (resid 38 through 49 )
49X-RAY DIFFRACTION49chain 'G' and (resid 50 through 59 )
50X-RAY DIFFRACTION50chain 'G' and (resid 60 through 69 )
51X-RAY DIFFRACTION51chain 'G' and (resid 70 through 83 )
52X-RAY DIFFRACTION52chain 'H' and (resid 1 through 13 )
53X-RAY DIFFRACTION53chain 'H' and (resid 14 through 33 )
54X-RAY DIFFRACTION54chain 'H' and (resid 34 through 46 )
55X-RAY DIFFRACTION55chain 'H' and (resid 47 through 54 )
56X-RAY DIFFRACTION56chain 'H' and (resid 55 through 67 )
57X-RAY DIFFRACTION57chain 'H' and (resid 68 through 72 )
58X-RAY DIFFRACTION58chain 'H' and (resid 73 through 84 )
59X-RAY DIFFRACTION59chain 'H' and (resid 85 through 102 )

+
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