[English] 日本語
Yorodumi
- PDB-5uqh: Crystal Structure of the Catalytic Domain of the Inosine Monophos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uqh
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor p182
ComponentsInosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IMPDH / TIM barrel / delta CBS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


IMP dehydrogenase / IMP dehydrogenase activity / purine nucleotide biosynthetic process
Similarity search - Function
IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I ...IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-8L1 / INOSINIC ACID / ISOPROPYL ALCOHOL / : / : / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
Campylobacter jejuni subsp. jejuni CG8486 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsKim, Y. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the presence of TBK6
Authors: Kim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Gu, M. / Sacchettini, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_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.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,64338
Polymers348,1998
Non-polymers7,44430
Water10,683593
1
A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,69817
Polymers174,0994
Non-polymers3,59913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23880 Å2
ΔGint-127 kcal/mol
Surface area49910 Å2
MethodPISA
2
E: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,94521
Polymers174,0994
Non-polymers3,84517
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24350 Å2
ΔGint-114 kcal/mol
Surface area48670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.441, 141.281, 121.061
Angle α, β, γ (deg.)90.00, 94.36, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase / IMPDH


Mass: 43524.820 Da / Num. of mol.: 8
Mutation: CBS domain (residues 92-195) is replaced with a glycine
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter), (gene. exp.) Campylobacter jejuni subsp. jejuni CG8486 (Campylobacter)
Gene: guaB, CJ14980A_1064, guaB, Cj8486_1016 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic
References: UniProt: A0A1B3XFT6, UniProt: A5KFK9, IMP dehydrogenase

-
Non-polymers , 6 types, 623 molecules

#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-8L1 / N-{4-chloro-3-[4-(trifluoromethyl)-1,3-thiazol-2-yl]phenyl}-N'-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea


Mass: 496.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C22H20ClF3N4O2S
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 10 % (v/v) 2-propanol, 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 163771 / % possible obs: 99.3 % / Redundancy: 4 % / Rsym value: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 2.2→2.24 Å / Mean I/σ(I) obs: 1.32 / Num. unique obs: 7421 / CC1/2: 0.704 / Rsym value: 0.538 / % possible all: 89.3

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R7J

4r7j


Resolution: 2.201→46.721 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 7426 4.93 %random
Rwork0.1715 ---
obs0.1736 150699 90.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.5 Å2
Refinement stepCycle: LAST / Resolution: 2.201→46.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21304 0 480 593 22377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322077
X-RAY DIFFRACTIONf_angle_d0.85529807
X-RAY DIFFRACTIONf_dihedral_angle_d19.1398172
X-RAY DIFFRACTIONf_chiral_restr0.0453455
X-RAY DIFFRACTIONf_plane_restr0.0033772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2014-2.22650.3152770.23471590X-RAY DIFFRACTION30
2.2265-2.25260.27591360.22742427X-RAY DIFFRACTION46
2.2526-2.28010.26561590.21812836X-RAY DIFFRACTION54
2.2801-2.3090.27321950.22893311X-RAY DIFFRACTION64
2.309-2.33940.27831900.21993793X-RAY DIFFRACTION72
2.3394-2.37140.28031840.21744085X-RAY DIFFRACTION77
2.3714-2.40530.26692350.21344460X-RAY DIFFRACTION85
2.4053-2.44120.27162660.21964806X-RAY DIFFRACTION92
2.4412-2.47930.26542610.21055048X-RAY DIFFRACTION95
2.4793-2.520.26332630.20975211X-RAY DIFFRACTION98
2.52-2.56340.30412450.20785229X-RAY DIFFRACTION100
2.5634-2.610.24712550.19635268X-RAY DIFFRACTION100
2.61-2.66020.24512720.19515294X-RAY DIFFRACTION100
2.6602-2.71450.24782730.20045230X-RAY DIFFRACTION100
2.7145-2.77350.25942910.20835283X-RAY DIFFRACTION100
2.7735-2.8380.24562650.20235246X-RAY DIFFRACTION100
2.838-2.9090.2693050.20075264X-RAY DIFFRACTION100
2.909-2.98770.22752860.2065276X-RAY DIFFRACTION100
2.9877-3.07560.26262680.20185316X-RAY DIFFRACTION100
3.0756-3.17480.24472760.19555247X-RAY DIFFRACTION100
3.1748-3.28820.22293140.18855230X-RAY DIFFRACTION100
3.2882-3.41990.24342600.18625282X-RAY DIFFRACTION100
3.4199-3.57550.21493000.17465283X-RAY DIFFRACTION100
3.5755-3.76390.1912470.16015306X-RAY DIFFRACTION100
3.7639-3.99960.18532850.14555276X-RAY DIFFRACTION100
3.9996-4.30820.1612710.135318X-RAY DIFFRACTION100
4.3082-4.74140.15712640.12415301X-RAY DIFFRACTION100
4.7414-5.42660.16922630.13215329X-RAY DIFFRACTION100
5.4266-6.83350.18282580.14955349X-RAY DIFFRACTION100
6.8335-46.73130.14392620.13885379X-RAY DIFFRACTION99
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)
12.20630.54710.13631.2210.08471.1903-0.03260.068-0.3353-0.03-0.0125-0.17140.07220.12020.06080.19130.01380.02320.2117-0.03860.221140.4348-53.679818.3632
22.14060.5368-0.10314.8076-1.54432.5325-0.0628-0.2717-0.22660.4085-0.0722-0.34140.06780.32030.14590.17310.0502-0.05040.38270.0330.349457.0581-52.722225.3826
31.30350.25310.07950.7516-0.39240.6669-0.04670.1755-0.2092-0.1027-0.0137-0.15460.05570.16250.05440.2014-0.00850.03210.2823-0.05250.238945.2993-46.751813.2026
41.6511-0.1796-0.22441.6804-0.20741.3473-0.00340.01150.07860.19820.0724-0.332-0.22160.29380.00680.1908-0.0402-0.0060.312-0.05960.203143.717-38.988421.7495
52.6742-0.1861-0.31161.1796-0.04792.3140.05640.0215-0.02270.0095-0.0141-0.13570.0487-0.1281-0.06570.2475-0.05130.01310.2365-0.0070.329523.7884-54.342120.0459
67.1319-0.5495-0.51841.34750.42130.616-0.16960.0035-0.076-0.10880.10520.06720.1844-0.07670.05710.3098-0.0744-0.02580.3242-0.03080.18553.3794-52.35778.8813
72.40560.28080.52211.8195-0.51342.4738-0.0164-0.2794-0.48650.1533-0.03510.17510.2684-0.19870.05480.2554-0.07440.06580.26280.0570.3501-1.1512-65.884235.4565
81.9383-0.1813-0.38820.7801-0.1410.8982-0.02880.0722-0.5302-0.07230.00010.00290.2409-0.04810.01940.2466-0.058-0.00210.2132-0.03460.35679.3854-65.685921.6461
94.51351.23380.20913.56852.50062.0676-0.0314-0.56930.10620.2061-0.06760.30630.1006-0.17150.0890.2512-0.0276-0.00070.3816-0.00850.21037.28-45.245240.7005
100.6091-0.5446-0.39291.3206-0.20212.2043-0.0745-0.209-0.09040.09980.0446-0.01940.0335-0.0140.03740.175-0.05010.01410.17670.00820.22545.7454-51.654830.1257
112.3725-0.6527-0.4163.09640.57221.55260.0023-0.11110.3590.14-0.0999-0.1803-0.34660.01110.10320.4043-0.0735-0.0740.4104-0.00130.3439-0.9931-44.855414.7369
121.48160.2132-0.17685.5844-2.80982.5076-0.07610.4879-0.044-0.0850.04370.03550.05190.03790.050.253-0.0621-0.030.4597-0.02430.1666.6994-33.3064-4.2702
132.16260.199-0.27951.3656-0.27172.38180.07160.24540.3950.03760.02890.3423-0.3436-0.3841-0.09050.22830.0479-0.04270.40710.07550.3703-19.1259-21.29025.3145
140.72380.2169-0.65790.9084-0.31460.71470.01490.3380.0018-0.11110.0350.13610.0661-0.1819-0.04610.2284-0.0431-0.06270.40250.01010.2372-11.3052-36.18222.1334
151.8137-0.0669-0.20852.54460.02592.2661-0.0249-0.19190.27260.5233-0.09160.127-0.36870.02910.06710.2153-0.0241-0.09410.2908-0.02950.2845-4.8142-22.647516.1597
162.56080.30690.57492.6140.6371.85640.04260.11020.02670.06740.04540.0293-0.12260.0033-0.07160.2504-0.06110.02580.39590.04660.22619.9227-24.52620.3296
171.2687-0.3166-0.14261.0970.15321.1942-0.02550.430.1904-0.2197-0.0178-0.1358-0.05840.07050.0320.2536-0.0671-0.00230.44870.04580.21634.0911-23.0458-3.9784
181.1754-0.3603-1.04462.6941-0.38261.77930.03410.50120.9284-0.0494-0.1022-0.3078-0.49760.15850.0350.4614-0.1109-0.03420.48850.23630.546533.979-2.9468-8.0453
191.1179-0.08870.39280.17210.1040.5959-0.05340.58140.2866-0.23460.02090.0132-0.12370.01480.02690.3391-0.0658-0.00940.53810.10820.245624.0323-19.6135-10.5353
202.0156-0.25210.16542.47270.64421.495-0.15040.08070.56980.06880.0969-0.0687-0.1686-0.0320.04550.2158-0.0597-0.03340.23970.05130.182428.4432-14.05348.811
212.26121.03510.23011.5036-0.40042.616-0.1280.2835-0.0535-0.13430.0182-0.06550.2227-0.00510.09650.16170.00980.00140.2386-0.02720.175634.7053-34.07775.7386
221.34840.1519-0.13961.31690.02481.0825-0.0438-0.0882-0.12690.12550.0370.04050.14920.00820.01150.2540.0233-0.00320.1497-0.01530.170531.1029-27.421862.5454
233.49590.51760.94472.7649-1.53961.66910.0653-0.1702-0.70070.1318-0.03660.06990.37970.07170.05430.39890.02780.02030.14670.01430.285125.8267-40.299667.8751
241.3868-0.0417-0.34881.1535-0.04281.0042-0.0394-0.1451-0.05770.26160.02270.0634-0.006-0.05060.01650.25550.02380.01210.161-0.00370.162425.7064-21.203668.0923
251.95960.1337-0.28022.02530.83261.5564-0.03760.3393-0.193-0.0748-0.05490.26240.0089-0.16430.09160.21690.0046-0.00560.12740.00320.14824.9463-25.769150.0907
261.20440.0337-0.46542.2901-0.15712.7945-0.00310.0385-0.0340.02580.117-0.0459-0.10570.0451-0.12240.1218-0.0024-0.0070.1609-0.02010.212242.4218-15.216352.2668
272.6161.8558-1.58344.5806-1.6712.7676-0.18580.05870.0368-0.07930.0870.01610.05470.02020.08760.28660.0362-0.00010.18-0.02340.215920.61011.296264.0168
281.6669-0.64210.03231.4362-0.26042.2822-0.00370.1007-0.0237-0.01320.01560.9995-0.0505-0.5134-0.0270.24910.062-0.03740.3974-0.05180.7482-8.39867.60156.65
293.95180.3176-0.98790.0421-0.1590.73340.0530.2190.07710.1967-0.03040.4779-0.2535-0.2976-0.01040.34270.13180.02080.2767-0.04590.56340.641123.634457.6
300.62540.57390.13061.1643-0.43531.4188-0.045-0.01040.04360.0316-0.00430.3758-0.1686-0.09870.05470.23930.0560.0160.1752-0.03640.321610.72713.51659.5546
312.57930.88811.20552.9253-0.0614.3963-0.17040.443-0.2714-0.83590.08270.41570.1606-0.45650.02080.4384-0.0069-0.08930.2851-0.08350.46732.2872-0.292243.0719
321.89840.27730.4052.2062-0.70182.2009-0.04790.31180.0383-0.28990.03710.58040.0121-0.1854-0.05330.21660.0588-0.05120.2361-0.0950.35815.70491.705248.6302
332.03820.0299-0.52772.74831.03121.70660.01880.16610.0389-0.20440.03020.0507-0.0507-0.0012-0.03060.25860.0686-0.01450.21160.02090.267717.4805-7.345759.2939
347.1161-2.51930.14822.42680.43531.4931-0.0405-0.0841-0.10780.22360.0612-0.01410.04760.111-0.02770.3336-0.0175-0.00170.1932-0.01460.222930.73917.751651.7174
351.7020.2364-0.62131.6404-0.04572.0581-0.03670.41660.2844-0.61220.07080.1631-0.3255-0.0943-0.05670.6163-0.0032-0.06170.2930.08110.271232.977333.010825.266
361.504-2.0981.14094.051-2.42242.2662-0.01810.15360.2235-0.39940.0514-0.2984-0.0990.0034-0.03050.4806-0.09110.09230.2151-0.0010.233249.50531.226531.933
371.4228-0.2228-0.24530.94710.56560.5473-0.03160.09940.0785-0.26570.0724-0.0267-0.11590.0013-0.03830.3634-0.02680.00890.17210.00910.160838.655223.963938.7989
385.71950.98873.02463.28850.46261.59590.25620.5357-0.3714-0.325-0.0320.04420.0170.2122-0.19660.5191-0.0382-0.02330.358-0.0870.223333.09110.283519.375
390.8757-0.17160.26431.10390.28261.67430.06250.2679-0.0196-0.367-0.10620.1199-0.2306-0.15490.04710.3712-0.0244-0.06990.26080.02090.243225.383218.853331.9267
402.83340.62620.33734.25550.46720.8883-0.09210.1462-0.1977-0.628-0.08320.24450.0749-0.1970.17920.43080.04670.00810.2865-0.00170.243620.974215.760645.529
411.65961.8543-1.45613.9379-2.464.0414-0.10540.02850.078-0.18140.1568-0.1538-0.03520.0232-0.04950.2001-0.018-0.01680.1653-0.05980.207949.34246.896648.4262
421.8856-0.1229-0.00062.66450.17911.3717-0.02280.1948-0.0643-0.36170.0832-0.58080.04120.3378-0.01430.2418-0.02440.11980.3231-0.09590.403967.711-11.748833.5916
430.6810.0948-0.16041.2508-0.22311.1923-0.0458-0.10490.04020.07510.0522-0.3383-0.02760.1923-0.00880.2208-0.0208-0.01780.2477-0.06360.302359.7742-9.394948.9028
443.48511.98751.94931.93150.02823.9781-0.03880.14240.056-0.36910.2148-0.0601-0.25190.1747-0.16960.3671-0.02460.0380.2187-0.05220.217246.8748-15.605524.8094
450.6294-0.1509-0.06582.24550.53752.0049-0.07020.1125-0.0617-0.28680.1253-0.16910.06020.0745-0.04640.1722-0.01650.01490.2359-0.05910.205751.108-9.047434.3156
462.4876-0.6530.22881.0818-0.58241.957-0.08430.1693-0.012-0.29340.080.1387-0.0344-0.0938-0.02260.4012-0.03710.0020.2298-0.03420.320546.03217.841738.6092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 226 )
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 386 )
4X-RAY DIFFRACTION4chain 'A' and (resid 387 through 441 )
5X-RAY DIFFRACTION5chain 'A' and (resid 442 through 481 )
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 25 )
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 235 )
8X-RAY DIFFRACTION8chain 'B' and (resid 236 through 361 )
9X-RAY DIFFRACTION9chain 'B' and (resid 362 through 382 )
10X-RAY DIFFRACTION10chain 'B' and (resid 383 through 441 )
11X-RAY DIFFRACTION11chain 'B' and (resid 442 through 481 )
12X-RAY DIFFRACTION12chain 'C' and (resid 0 through 25 )
13X-RAY DIFFRACTION13chain 'C' and (resid 26 through 236 )
14X-RAY DIFFRACTION14chain 'C' and (resid 237 through 360 )
15X-RAY DIFFRACTION15chain 'C' and (resid 361 through 441 )
16X-RAY DIFFRACTION16chain 'C' and (resid 442 through 481 )
17X-RAY DIFFRACTION17chain 'D' and (resid 0 through 63 )
18X-RAY DIFFRACTION18chain 'D' and (resid 64 through 235 )
19X-RAY DIFFRACTION19chain 'D' and (resid 236 through 361 )
20X-RAY DIFFRACTION20chain 'D' and (resid 362 through 441 )
21X-RAY DIFFRACTION21chain 'D' and (resid 442 through 481 )
22X-RAY DIFFRACTION22chain 'E' and (resid 0 through 86 )
23X-RAY DIFFRACTION23chain 'E' and (resid 87 through 235 )
24X-RAY DIFFRACTION24chain 'E' and (resid 236 through 369 )
25X-RAY DIFFRACTION25chain 'E' and (resid 370 through 441 )
26X-RAY DIFFRACTION26chain 'E' and (resid 442 through 482 )
27X-RAY DIFFRACTION27chain 'F' and (resid 0 through 25 )
28X-RAY DIFFRACTION28chain 'F' and (resid 26 through 235 )
29X-RAY DIFFRACTION29chain 'F' and (resid 236 through 263 )
30X-RAY DIFFRACTION30chain 'F' and (resid 264 through 349 )
31X-RAY DIFFRACTION31chain 'F' and (resid 350 through 382 )
32X-RAY DIFFRACTION32chain 'F' and (resid 383 through 441 )
33X-RAY DIFFRACTION33chain 'F' and (resid 442 through 481 )
34X-RAY DIFFRACTION34chain 'G' and (resid 0 through 23 )
35X-RAY DIFFRACTION35chain 'G' and (resid 24 through 236 )
36X-RAY DIFFRACTION36chain 'G' and (resid 237 through 263 )
37X-RAY DIFFRACTION37chain 'G' and (resid 264 through 366 )
38X-RAY DIFFRACTION38chain 'G' and (resid 367 through 407 )
39X-RAY DIFFRACTION39chain 'G' and (resid 408 through 441 )
40X-RAY DIFFRACTION40chain 'G' and (resid 442 through 481 )
41X-RAY DIFFRACTION41chain 'H' and (resid 0 through 25 )
42X-RAY DIFFRACTION42chain 'H' and (resid 26 through 235 )
43X-RAY DIFFRACTION43chain 'H' and (resid 236 through 360 )
44X-RAY DIFFRACTION44chain 'H' and (resid 361 through 382 )
45X-RAY DIFFRACTION45chain 'H' and (resid 383 through 441 )
46X-RAY DIFFRACTION46chain 'H' and (resid 442 through 481 )

+
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