[English] 日本語
Yorodumi
- PDB-3pg9: Thermotoga maritima DAH7P synthase in complex with inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pg9
TitleThermotoga maritima DAH7P synthase in complex with inhibitor
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTransferase/Transferase inhibitor / Thermotoga maritima / DAH7PS / Shikimate pathway / aromatic biosynthesis / Tyr-bound / Tim barrel / act domain / ferredoxin-like domain / Transferase / Transferase-Transferase inhibitor complex / allosteric regulation
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1 / DAHP synthase ferredoxin-like domain / DAHP synthase ferredoxin-like domain / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / Alpha-Beta Plaits / TIM Barrel ...Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1 / DAHP synthase ferredoxin-like domain / DAHP synthase ferredoxin-like domain / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / NITRATE ION / TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCross, P.J. / Dobson, R.C.J. / Patchett, M.L. / Parker, E.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Tyrosine latching of a regulatory gate affords allosteric control of aromatic amino acid biosynthesis
Authors: Cross, P.J. / Dobson, R.C.J. / Patchett, M.L. / Parker, E.J.
History
DepositionOct 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 22, 2012Group: Database references
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Phospho-2-dehydro-3-deoxyheptonate aldolase
B: Phospho-2-dehydro-3-deoxyheptonate aldolase
C: Phospho-2-dehydro-3-deoxyheptonate aldolase
D: Phospho-2-dehydro-3-deoxyheptonate aldolase
E: Phospho-2-dehydro-3-deoxyheptonate aldolase
F: Phospho-2-dehydro-3-deoxyheptonate aldolase
G: Phospho-2-dehydro-3-deoxyheptonate aldolase
H: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,25823
Polymers299,4418
Non-polymers1,81715
Water10,178565
1
A: Phospho-2-dehydro-3-deoxyheptonate aldolase
B: Phospho-2-dehydro-3-deoxyheptonate aldolase
F: Phospho-2-dehydro-3-deoxyheptonate aldolase
G: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,68913
Polymers149,7214
Non-polymers9689
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15930 Å2
ΔGint-73 kcal/mol
Surface area44590 Å2
MethodPISA
2
C: Phospho-2-dehydro-3-deoxyheptonate aldolase
D: Phospho-2-dehydro-3-deoxyheptonate aldolase
E: Phospho-2-dehydro-3-deoxyheptonate aldolase
H: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,56910
Polymers149,7214
Non-polymers8496
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15560 Å2
ΔGint-73 kcal/mol
Surface area44750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.610, 121.002, 133.379
Angle α, β, γ (deg.)90.00, 92.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Phospho-2-dehydro-3-deoxyheptonate aldolase / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3- ...3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3-deoxyheptonate aldolase


Mass: 37430.137 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 (DSM3109) / Gene: aroF / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9WYH8, 3-deoxy-7-phosphoheptulonate synthase

-
Non-polymers , 5 types, 580 molecules

#2: Chemical
ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 20%(w/v) polyethylene glycol 3350, 0.2M ammonium nitrate, 0.02%(w/v) sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.35→52.567 Å / Num. all: 104678 / Num. obs: 104678 / % possible obs: 97.4 % / Redundancy: 3 % / Biso Wilson estimate: 36.09 Å2 / Rsym value: 0.102
Reflection shell

Diffraction-ID: 1 / Redundancy: 3 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.35-2.480.5281.4154760.52898.6
2.48-2.630.3861.9145650.38698.4
2.63-2.810.2872.5136690.28798.2
2.81-3.030.1933.7127010.19397.9
3.03-3.320.1245.6116490.12497.6
3.32-3.720.0857.2105020.08597.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VR6
Resolution: 2.35→52.567 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8761 / SU ML: 0.36 / σ(F): 0 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2100 2.01 %Random, Thin shells
Rwork0.1712 ---
obs0.1723 104678 97.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.456 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 242.64 Å2 / Biso mean: 36.1 Å2 / Biso min: 9.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.0875 Å20 Å20.2392 Å2
2--0.3073 Å20 Å2
3----0.2198 Å2
Refinement stepCycle: LAST / Resolution: 2.35→52.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20437 0 127 565 21129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320915
X-RAY DIFFRACTIONf_angle_d0.65428307
X-RAY DIFFRACTIONf_chiral_restr0.0443299
X-RAY DIFFRACTIONf_plane_restr0.0023663
X-RAY DIFFRACTIONf_dihedral_angle_d12.2197722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Num. reflection Rfree: 210 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.4340.25450.2016103771058799
2.434-2.53140.26170.1861103151052598
2.5314-2.64660.25730.1843103391054998
2.6466-2.78610.23970.1862103191052998
2.7861-2.96070.24860.1872102971050798
2.9607-3.18930.24840.1842102541046497
3.1893-3.51010.21470.1748102651047597
3.5101-4.01790.23230.1577102101042097
4.0179-5.06150.1860.1385101631037396
5.0615-52.57970.17720.1495100391024994
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.2094-0.43290.32830.12070.09793.8644-0.03940.16240.5215-0.37950.02680.151-0.9018-0.29580.00560.29680.01140.00750.10040.03830.1946-13.93947.941329.7771
22.1086-0.12060.32241.20490.06320.10730.0143-0.4316-0.05990.2850.0273-0.14070.0606-0.0572-0.01310.3191-0.0198-0.01550.31080.00060.2195-10.732542.875236.1542
31.21830.25080.13621.45840.40631.3547-0.0875-0.0849-0.07410.25120.0434-0.265-0.14120.10030.05140.0261-0.0077-0.08190.08490.0080.151914.108126.367662.6002
41.49-1.725-3.16244.21221.98458.0032-1.04820.50191.04850.3642-0.34920.7543-0.7575-0.62591.2870.7314-0.1258-0.32090.73480.09491.1551-6.549223.977276.6342
51.8021-0.64561.1582.465-0.11353.1809-0.169-0.17550.40630.4718-0.2452-0.0033-0.7498-0.07390.40670.22640.005-0.09610.1754-0.07150.1957.910933.703869.9063
62.34260.3493-0.41480.40790.21560.8992-0.1210.02010.03270.10530.0363-0.0208-0.1336-0.02090.10960.1638-0.0117-0.03680.10790.00260.12111.902127.387152.6944
71.7561.1723-0.14470.6826-0.55442.85130.04080.067-0.22760.1286-0.109-0.36450.3652-0.13450.02460.14410.0199-0.05380.07680.02350.201210.600713.108961.9885
81.6333-0.79390.23933.6351-1.01441.26190.1588-0.1783-0.3806-0.0883-0.03920.74880.1446-0.1901-0.15630.29490.0140.00650.29430.1070.4176-26.2202-3.603468.7566
90.7870.02050.20920.8701-0.80061.0337-0.0665-0.1063-0.2587-0.20290.21540.14660.0978-0.0474-0.06210.2130.01080.00050.10080.070.2309-16.8049-2.856659.4517
102.67930.7074-0.92780.8840.77021.4959-0.05150.1988-0.1386-0.203-0.0879-0.27080.31970.36150.160.19480.08250.05870.136-0.02280.17298.0571-0.176130.7694
115.0101-2.42330.25663.2769-1.21082.19460.19340.48940.41620.4795-0.17380.2223-1.314-0.4763-0.15180.51220.16750.05510.33240.00860.2902-9.02359.814322.1459
121.28461.32410.53741.8158-0.14261.5616-0.0522-0.0063-0.0341-0.3375-0.03670.33620.3521-0.21080.07850.28820.0273-0.01610.1459-0.06130.1882-5.8218-3.747828.6783
130.6530.38010.39071.50580.95651.56040.0204-0.1134-0.0695-0.0591-0.00260.16940.0731-0.0017-0.01450.1769-0.00650.01650.08140.00250.1766-5.68714.375446.0572
140.48170.2455-0.65550.28610.33172.60260.0796-0.09490.0186-0.00980.0376-0.1685-0.16030.0872-0.12020.1490.02540.05310.12360.00020.15968.96811.351135.875
151.7559-0.5587-0.22091.38290.57130.5132-0.1319-0.07240.02840.27650.0720.10220.0577-0.0520.06090.20610.0417-0.03370.1401-0.03140.1677-28.72738.66096.159
161.8794-2.2313-0.55254.38990.6360.223-0.3841-0.31880.09060.86510.2055-0.14970.0220.19840.10130.21280.1136-0.04290.1885-0.02840.0675-14.978123.34445.2666
171.1962-0.8637-0.13890.64950.31891.6958-0.0394-0.0014-0.27180.39270.2361-0.24420.47770.1096-0.2020.33690.0852-0.11080.1987-0.0310.2339-7.9929-5.9656-1.8999
180.2239-1.18440.34818.035-1.08190.8507-0.2412-1.0450.158-0.62610.9142-0.03230.0739-0.0442-0.56490.49410.0878-0.10220.6983-0.27310.7714-30.8203-10.187-5.3135
191.0352-0.5082-0.49283.2018-0.02562.1192-0.2148-0.5635-0.05021.1280.48860.07120.3077-0.2613-0.16070.420.04810.05080.26320.09040.2334-18.9212-5.32495.5919
201.735-0.37780.61581.8206-0.51440.5938-0.10940.125-0.0349-0.00660.0746-0.02670.11280.06420.02180.17430.0373-0.00630.1155-0.02290.0627-17.286111.2995-4.2757
210.60930.01580.84621.4881-0.01491.15560.12480.1623-0.1041-0.07810.135-0.04670.24910.1656-0.21440.21880.0785-0.01480.2001-0.05420.2185-9.2092-2.7176-13.8132
220.46390.54590.38620.8114-0.11861.40130.15580.0020.020.2031-0.028-0.15540.0548-0.0289-0.08150.29170.0001-0.01110.2010.10310.262140.494-60.812639.2146
230.95860.06420.17011.7348-0.6191.5431-0.3526-0.4082-0.04780.70610.55470.5887-0.1825-0.4067-0.24560.17610.05130.20610.31870.05910.18942.0426-40.811732.6247
243.81843.1794-0.69572.6667-0.42792.161-0.283-0.0120.2476-0.4492-0.3919-0.0717-0.39290.52320.50160.4844-0.083-0.08360.43260.16160.411512.9951-22.563727.5363
251.0342-0.17740.23931.2031-0.78130.4654-0.2225-0.4343-0.05991.01840.16920.1659-0.1432-0.0773-0.0060.48250.18020.12590.3678-0.09170.25484.0681-27.712937.4271
261.8745-0.82390.88241.76550.33360.7221-0.291-0.63340.1490.90390.4332-0.0798-0.1918-0.2447-0.03750.50940.1116-0.01080.3489-0.01790.157617.762-40.696636.9408
270.8226-0.61650.3691.21620.37810.6618-0.0643-0.00290.0780.06780.01960.1364-0.1453-0.07920.00810.1786-0.01410.03320.1633-0.02320.122313.81-45.050423.2688
281.4226-0.522-1.22454.3481-0.84961.706-0.01350.130.0582-0.33360.23180.57120.0311-0.2546-0.19060.06950.01440.03140.26840.03530.19540.3648-39.146518.8913
292.97110.11980.14243.07160.46670.96340.0923-0.01050.15450.0876-0.01090.2290.1778-0.3183-0.09710.0793-0.0119-0.02110.12070.0360.044113.0178-19.14684.9205
305.8123-2.61883.23911.3682-2.05673.5803-0.094-0.10441.08130.2675-0.4485-0.6994-1.10850.47450.68680.4829-0.0981-0.15730.1836-0.03310.360736.9065-15.285218.0884
311.5657-0.5310.27970.9092-0.25180.9275-0.1268-0.3205-0.07090.1104-0.01650.0121-0.08710.09340.12190.277-0.0602-0.17030.2561-0.0240.249847.7125-30.524639.3035
320.8606-0.3404-0.34830.32050.05791.176-0.2998-0.2660.09690.27820.05790.2212-0.2774-0.1280.15730.40630.0285-0.11710.3143-0.07590.252639.8842-27.529445.3304
330.0977-0.6727-0.2644.60712.44382.0125-0.2048-0.40080.26080.4668-0.30750.6515-0.0968-0.57210.34420.32230.066-0.07870.3786-0.10580.41830.6135-24.873433.1309
340.3659-0.37930.711.38410.31162.5204-0.1703-0.02690.0520.26990.01950.1069-0.12550.04550.15360.1847-0.0005-0.03720.1187-0.00320.128235.2266-29.419222.1872
350.87930.74820.76471.6411-0.79713.28110.0074-0.0191-0.0339-0.0089-0.1291-0.36430.26530.39810.07720.0903-0.008-0.07390.14920.04060.18950.8763-38.028129.9084
361.3069-0.6460.64520.4272-0.17992.68450.01240.0472-0.1059-0.0284-0.0679-0.00880.0360.10070.03780.1585-0.0263-0.01550.12530.00390.158-2.933532.019723.6332
372.52790.20670.71720.75990.41941.4051-0.0670.1889-0.3673-0.28160.14420.3823-0.0448-0.23-0.11350.138-0.0255-0.11330.247-0.00410.3768-40.333512.89436.6199
380.1231-0.30720.13081.0729-0.16962.3280.2498-0.03460.42610.26130.0846-0.05540.2450.5972-0.25380.1521-0.0292-0.02360.4135-0.06210.3946-29.0055-5.026243.99
390.5717-0.39780.00590.39710.12410.91310.00470.327-0.4008-0.31360.1494-0.04340.11230.0846-0.17240.1752-0.0746-0.06670.182-0.06810.3048-30.68656.923732.6398
402.55052.99471.1844.16473.127.68080.33440.1383-0.01450.4669-0.60710.83141.105-0.74970.18160.3087-0.03050.02860.2015-0.07730.3276-20.862915.545852.0485
412.8409-0.34441.80250.80560.31881.827-0.3438-0.30470.0185-0.04310.1070.1151-0.2216-0.22160.2170.1208-0.0122-0.02440.129-0.0110.1853-30.305823.551338.8179
421.36790.48560.31782.4659-0.80431.41540.1064-0.323-0.25820.26770.0980.6048-0.0741-0.2112-0.23720.0992-0.00140.01680.2210.08840.3463-39.944313.978350.6449
431.70880.4712-0.15890.93490.66432.18320.09340.17530.0065-0.21440.02590.0802-0.1397-0.2297-0.0860.2332-0.02830.11960.1704-0.07690.18994.4927-57.908857.4341
440.33430.5181-0.27582.6552-0.87180.8344-0.21950.2138-0.0548-1.1490.132-0.47840.02050.18130.01660.4404-0.15230.17610.3451-0.07360.299926.0886-33.439460.5885
451.26770.7771.05250.88641.24652.1585-0.397-0.16220.1626-0.64590.34380.0946-0.81320.01040.03630.2086-0.1051-0.00380.12560.00420.14424.8942-12.257975.4021
460.7969-0.74370.42632.21051.05892.8179-0.07980.5146-0.139-0.3384-0.30730.4973-0.4173-0.59450.30710.3772-0.074-0.05250.26270.0020.35414.8513-7.718672.5864
473.04280.2240.5822.02320.54280.56-0.26230.4855-0.0482-0.63380.3470.2739-0.1708-0.1542-0.07510.3777-0.1126-0.10820.30660.0790.251913.753-19.299363.8329
480.5376-0.4651-0.76412.4677-0.11781.2649-0.10650.116-0.0891-0.24230.2312-0.0623-0.0126-0.2266-0.10050.1645-0.07070.01620.1782-0.02890.135817.3007-33.479171.3711
491.041-0.0914-0.72042.51490.44830.6635-0.0051-0.19490.08740.05740.142-0.0802-0.09880.08-0.11570.1501-0.0595-0.01980.1845-0.02830.16327.0824-21.502983.2034
502.75690.69580.19541.62890.64760.74480.2363-0.1147-0.2279-0.01920.0341-0.12140.3261-0.0378-0.19270.35880.006-0.05930.3408-0.05720.288551.3894-11.9897-28.2103
510.74290.2323-0.43462.50250.25152.5120.1999-0.02240.16690.3518-0.21630.57350.047-0.46190.1160.1637-0.0860.13030.279-0.10530.300127.044212.9663-1.6697
524.54281.4733-2.81182.1378-0.87041.87010.164-0.8893-0.74311.0642-0.335-0.43230.72110.5186-0.00810.9904-0.1734-0.08630.4986-0.05430.328643.854515.96812.3846
530.45380.26880.10650.7584-0.29521.04760.21470.08610.06090.4167-0.22260.13310.43440.03860.03710.4956-0.15220.09770.3112-0.02220.249834.29357.06396.9097
541.59761.4659-0.23781.5085-0.5931.43760.03690.0048-0.06030.1836-0.0887-0.02160.1014-0.15610.09030.1706-0.01330.00220.1486-0.020.199839.26589.8408-10.9654
551.80980.0378-1.21040.332-0.01881.52330.0973-0.1094-0.07660.09790.01560.1009-0.27420.2292-0.12960.1737-0.00430.04340.1863-0.08350.198734.166323.6852-7.9387
560.3562-0.0119-0.89760.5946-0.22253.24850.258-0.15630.24640.227-0.05440.4676-0.7763-0.4156-0.19870.26580.01120.12110.2862-0.16090.43129.607927.1168-1.127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:34)A1 - 34
2X-RAY DIFFRACTION2(chain A and resid 35:67)A35 - 67
3X-RAY DIFFRACTION3(chain A and resid 68:130)A68 - 130
4X-RAY DIFFRACTION4(chain A and resid 131:141)A131 - 141
5X-RAY DIFFRACTION5(chain A and resid 142:205)A142 - 205
6X-RAY DIFFRACTION6(chain A and resid 206:267)A206 - 267
7X-RAY DIFFRACTION7(chain A and resid 268:338)A268 - 338
8X-RAY DIFFRACTION8(chain B and resid 1:51)B1 - 51
9X-RAY DIFFRACTION9(chain B and resid 52:78)B52 - 78
10X-RAY DIFFRACTION10(chain B and resid 79:125)B79 - 125
11X-RAY DIFFRACTION11(chain B and resid 126:143)B126 - 143
12X-RAY DIFFRACTION12(chain B and resid 144:205)B144 - 205
13X-RAY DIFFRACTION13(chain B and resid 206:267)B206 - 267
14X-RAY DIFFRACTION14(chain B and resid 268:338)B268 - 338
15X-RAY DIFFRACTION15(chain C and resid 1:62)C1 - 62
16X-RAY DIFFRACTION16(chain C and resid 63:76)C63 - 76
17X-RAY DIFFRACTION17(chain C and resid 77:129)C77 - 129
18X-RAY DIFFRACTION18(chain C and resid 130:142)C130 - 142
19X-RAY DIFFRACTION19(chain C and resid 143:205)C143 - 205
20X-RAY DIFFRACTION20(chain C and resid 206:267)C206 - 267
21X-RAY DIFFRACTION21(chain C and resid 268:338)C268 - 338
22X-RAY DIFFRACTION22(chain D and resid 1:66)D1 - 66
23X-RAY DIFFRACTION23(chain D and resid 67:125)D67 - 125
24X-RAY DIFFRACTION24(chain D and resid 126:140)D126 - 140
25X-RAY DIFFRACTION25(chain D and resid 141:182)D141 - 182
26X-RAY DIFFRACTION26(chain D and resid 183:232)D183 - 232
27X-RAY DIFFRACTION27(chain D and resid 233:274)D233 - 274
28X-RAY DIFFRACTION28(chain D and resid 275:338)D275 - 338
29X-RAY DIFFRACTION29(chain E and resid 1:67)E1 - 67
30X-RAY DIFFRACTION30(chain E and resid 68:82)E68 - 82
31X-RAY DIFFRACTION31(chain E and resid 83:136)E83 - 136
32X-RAY DIFFRACTION32(chain E and resid 137:182)E137 - 182
33X-RAY DIFFRACTION33(chain E and resid 183:208)E183 - 208
34X-RAY DIFFRACTION34(chain E and resid 209:267)E209 - 267
35X-RAY DIFFRACTION35(chain E and resid 268:338)E268 - 338
36X-RAY DIFFRACTION36(chain F and resid 1:67)F1 - 67
37X-RAY DIFFRACTION37(chain F and resid 68:125)F68 - 125
38X-RAY DIFFRACTION38(chain F and resid 126:143)F126 - 143
39X-RAY DIFFRACTION39(chain F and resid 144:236)F144 - 236
40X-RAY DIFFRACTION40(chain F and resid 237:249)F237 - 249
41X-RAY DIFFRACTION41(chain F and resid 250:269)F250 - 269
42X-RAY DIFFRACTION42(chain F and resid 270:338)F270 - 338
43X-RAY DIFFRACTION43(chain G and resid 1:65)G1 - 65
44X-RAY DIFFRACTION44(chain G and resid 66:91)G66 - 91
45X-RAY DIFFRACTION45(chain G and resid 92:131)G92 - 131
46X-RAY DIFFRACTION46(chain G and resid 132:158)G132 - 158
47X-RAY DIFFRACTION47(chain G and resid 159:205)G159 - 205
48X-RAY DIFFRACTION48(chain G and resid 206:267)G206 - 267
49X-RAY DIFFRACTION49(chain G and resid 268:338)G268 - 338
50X-RAY DIFFRACTION50(chain H and resid 1:66)H1 - 66
51X-RAY DIFFRACTION51(chain H and resid 67:125)H67 - 125
52X-RAY DIFFRACTION52(chain H and resid 126:144)H126 - 144
53X-RAY DIFFRACTION53(chain H and resid 145:206)H145 - 206
54X-RAY DIFFRACTION54(chain H and resid 207:267)H207 - 267
55X-RAY DIFFRACTION55(chain H and resid 268:297)H268 - 297
56X-RAY DIFFRACTION56(chain H and resid 298:338)H298 - 338

+
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