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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uqg
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor p200
ComponentsInosine-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 activity / IMP dehydrogenase / purine nucleotide biosynthetic process
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / 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 ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / 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-8L4 / INOSINIC ACID / : / : / 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: 2.03 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 Campylobacter jejuni in the complex with inhibitor p200
Authors: Kim, 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)
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
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,19634
Polymers348,1998
Non-polymers5,99726
Water13,854769
1
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,09817
Polymers174,0994
Non-polymers2,99913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23290 Å2
ΔGint-133 kcal/mol
Surface area49200 Å2
MethodPISA
2
C: Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,09817
Polymers174,0994
Non-polymers2,99913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23560 Å2
ΔGint-126 kcal/mol
Surface area48140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.887, 137.963, 116.548
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 43524.820 Da / Num. of mol.: 8
Mutation: the CBS domain (residues 92-195) is replaced with 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 , 5 types, 795 molecules

#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-8L4 / 3-(2-{[(4-chlorophenyl)carbamoyl]amino}propan-2-yl)-N-hydroxybenzene-1-carboximidamide


Mass: 346.811 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H19ClN4O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 44.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5 % (w/v) 2-propanol, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 194228 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rsym value: 0.119 / Net I/σ(I): 11.6
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.62 / Num. unique obs: 9561 / CC1/2: 0.558 / Rsym value: 0.772 / % possible all: 98.9

-
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: 2.03→35.905 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.94
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 9631 4.96 %random
Rwork0.1659 ---
obs0.1678 194122 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.6 Å2
Refinement stepCycle: LAST / Resolution: 2.03→35.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21174 0 392 769 22335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821917
X-RAY DIFFRACTIONf_angle_d1.15229577
X-RAY DIFFRACTIONf_dihedral_angle_d17.3718134
X-RAY DIFFRACTIONf_chiral_restr0.1073444
X-RAY DIFFRACTIONf_plane_restr0.0083751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0242-2.04720.29232860.24335321X-RAY DIFFRACTION86
2.0472-2.07130.28772970.2356139X-RAY DIFFRACTION99
2.0713-2.09660.27052880.21586121X-RAY DIFFRACTION99
2.0966-2.12310.25653270.20456165X-RAY DIFFRACTION99
2.1231-2.1510.25633540.20216078X-RAY DIFFRACTION99
2.151-2.18050.26083130.19336175X-RAY DIFFRACTION99
2.1805-2.21160.23723360.19016106X-RAY DIFFRACTION99
2.2116-2.24470.24683020.18716127X-RAY DIFFRACTION100
2.2447-2.27970.22123070.18216199X-RAY DIFFRACTION99
2.2797-2.31710.24073120.17996170X-RAY DIFFRACTION100
2.3171-2.3570.2333410.17616127X-RAY DIFFRACTION100
2.357-2.39990.22493160.1796203X-RAY DIFFRACTION100
2.3999-2.4460.23633050.17816159X-RAY DIFFRACTION100
2.446-2.4960.21823700.1676085X-RAY DIFFRACTION100
2.496-2.55020.21853170.17156205X-RAY DIFFRACTION100
2.5502-2.60950.21143000.16886204X-RAY DIFFRACTION100
2.6095-2.67480.20473350.17146137X-RAY DIFFRACTION100
2.6748-2.74710.24393170.1786200X-RAY DIFFRACTION100
2.7471-2.82790.21253260.17236201X-RAY DIFFRACTION100
2.8279-2.91910.21083190.17496205X-RAY DIFFRACTION100
2.9191-3.02340.22743450.18296117X-RAY DIFFRACTION100
3.0234-3.14440.21523250.17866216X-RAY DIFFRACTION100
3.1444-3.28740.20892990.17166228X-RAY DIFFRACTION100
3.2874-3.46060.20243240.17216196X-RAY DIFFRACTION100
3.4606-3.67720.20793600.16216195X-RAY DIFFRACTION100
3.6772-3.96080.16483070.14246212X-RAY DIFFRACTION100
3.9608-4.35870.16073180.13496232X-RAY DIFFRACTION100
4.3587-4.9880.14753260.12856222X-RAY DIFFRACTION100
4.988-6.27890.1733270.1516237X-RAY DIFFRACTION100
6.2789-35.91050.16683320.14776309X-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)
11.61832.3746-1.78736.4412-4.75164.58610.1333-0.21310.01270.3090.01230.109-0.2650.0722-0.20350.15390.0227-0.00540.1845-0.02450.2065-50.472225.241148.4424
21.314-0.0778-0.42973.587-0.01721.27440.0540.0193-0.0533-0.1789-0.1032-0.35490.04410.14690.04920.15180.0110.01890.20680.00570.2457-34.562211.273733.1594
34.1225-0.0281-0.2178.1713-2.05584.31880.00210.98510.1469-0.85290.0682-0.6996-0.1236-0.0621-0.02530.32760.07910.12830.38580.00140.3442-27.78363.14626.5162
40.5847-0.0227-0.21350.8472-0.15590.99750.0123-0.064-0.06460.0027-0.0289-0.16670.04740.19780.02160.1611-0.0032-0.0160.20730.01160.2567-36.35778.586945.2068
50.46770.0608-0.0882.22780.55331.1073-0.07140.0846-0.0762-0.2950.0622-0.08480.1262-0.0370.01280.1541-0.008-0.01370.16020.00450.1432-48.28977.886429.185
63.1947-0.29361.00310.74910.17132.5709-0.0070.0318-0.0564-0.0884-0.01770.12320.0046-0.0519-0.01780.24930.0103-0.00170.12640.01140.2619-52.174627.013236.2568
71.51270.2076-0.17291.2807-0.2980.68310.0172-0.1015-0.00690.05380.0009-0.00060.0692-0.0249-0.03370.1931-0.0056-0.01850.18740.02880.1468-65.8843-4.644560.5032
85.5098-2.6258-0.13434.250.18632.57010.01760.308-0.7732-0.21150.07820.07870.85870.0469-0.11190.4446-0.0494-0.06410.23610.00180.2832-74.093-24.66660.4485
94.1774-1.67150.55862.4447-0.44731.35950.0419-0.4403-0.27080.23910.07660.10590.2442-0.1625-0.06840.3048-0.0664-0.02970.21680.03720.1933-75.7701-17.530768.3165
100.928-1.20340.18554.6444-0.13180.3551-0.1106-0.1819-0.03790.40390.11430.0480.0852-0.1360.00180.23380.00810.03280.31020.05530.2218-81.1712-4.757273.7193
111.2158-0.2736-0.20840.7473-0.02170.7552-0.0234-0.09650.06460.06310.032-0.02310.0001-0.0735-0.0140.17540.0003-0.00670.19670.01740.1697-71.37080.652963.9442
121.86450.0193-0.17341.52090.20820.5090.06180.1426-0.1989-0.1538-0.07560.15570.0714-0.12090.04360.2234-0.0194-0.02190.18910.01390.1664-74.4326-5.826748.5418
130.68940.0432-0.38721.880.25582.3710.06060.0134-0.0163-0.0259-0.0009-0.0852-0.0317-0.0196-0.03240.1274-0.0288-0.010.2008-0.00530.2593-56.19754.532250.6698
141.4130.9412-0.42615.8597-2.16152.96340.06710.0071-0.148-0.0404-0.11350.21580.36220.04510.10420.25670.0015-0.00280.2493-0.03760.2001-90.4593-16.4686-5.2152
152.54630.5645-1.41391.3875-0.91312.537-0.010.04990.16160.0621-0.00930.1173-0.1515-0.13830.03830.24030.014-0.03050.1977-0.01510.2047-110.66-1.96611.9772
164.10451.1886-0.58177.3282-0.60650.98890.2032-0.10180.7320.13420.0750.3305-0.7752-0.1262-0.20740.40920.08320.02490.3293-0.06840.3329-121.09254.32096.7678
172.25942.5922-0.57165.4007-1.96732.8432-0.11540.12790.2049-0.29670.19470.41480.0573-0.3411-0.06590.25110.06840.01610.254-0.02940.2119-121.774-4.01162.1189
182.6196-3.0090.42114.3825-0.9720.6005-0.06710.0973-0.00330.02030.0295-0.0155-0.0493-0.15930.05730.2334-0.0085-0.02950.27550.00220.1899-120.1083-18.89612.422
190.7565-0.0326-0.31651.2846-0.53840.5869-0.00290.1765-0.0725-0.0946-0.0436-0.0170.0507-0.07330.04880.2632-0.0043-0.010.2427-0.01940.1765-105.7548-16.29280.0907
200.91470.0576-0.62822.1796-0.33150.94290.1029-0.16860.13240.5267-0.08020.0197-0.28980.0123-0.02190.2958-0.0224-0.06160.2153-0.04710.1987-101.8217-3.081514.0046
213.08120.03481.66072.30170.34852.0043-0.0080.0222-0.04180.01610.033-0.0880.00240.0827-0.00660.2186-0.03380.0630.1740.01970.176-87.6195-5.6768-1.1417
227.0079-3.2575-0.33153.37330.61231.4881-0.0911-0.02760.02290.31660.0459-0.0724-0.01680.08830.03640.199-0.01360.01180.20560.01960.1737-67.471737.609948.6555
233.62751.2827-1.7542.2847-0.02973.28110.08510.06660.48960.09990.02660.0796-0.3673-0.176-0.18670.26030.05260.02850.20020.05640.2907-70.747753.736133.9318
242.94060.1418-1.09432.882-0.53472.8920.11870.40490.2632-0.24740.06520.255-0.2596-0.3346-0.16020.19340.0192-0.02510.20470.04110.1632-65.095649.692217.598
258.1509-2.7144-0.28955.1775-0.86063.3968-0.0370.09060.41470.10830.0998-0.1776-0.71030.19830.00970.3128-0.02990.01130.2010.0260.152-55.09554.238619.1482
262.4245-2.68822.06285.3224-4.0133.62630.05440.04480.224-0.0691-0.0438-0.0454-0.1930.094-0.03980.1982-0.01880.02440.1296-0.01590.1666-48.380150.243928.3073
271.2858-0.1085-0.27930.79710.2280.5825-0.013-0.06950.07010.07830.06110.0634-0.073-0.0035-0.04360.19970.0098-0.00240.17570.00060.1886-58.493743.402136.5954
283.30230.57031.52385.07583.2622.9777-0.04540.4025-0.2048-0.24470.02150.296-0.0148-0.07050.05310.2205-0.0048-0.04530.2584-0.01030.2506-71.348630.305316.1349
296.3191-0.93160.97462.2259-0.33512.0983-0.00860.1416-0.253-0.13750.0929-0.12270.03350.1197-0.09620.2361-0.0049-0.00830.2205-0.00880.1756-58.627930.059221.0155
301.22080.1117-2.26621.57732.57349.6231-0.00370.02130.1255-0.07620.04870.1914-0.4384-0.33030.04230.14690.0362-0.00280.18040.02870.3059-79.14844.398534.1268
312.01781.22550.58643.47310.19011.52460.0411-0.0357-0.0389-0.1443-0.0596-0.03520.043-0.12140.02270.17430.03270.07080.2758-0.00790.2417-77.219135.586542.2354
327.0548-1.57291.36250.90420.4091.7393-0.031-0.3797-0.1305-0.13950.06770.1453-0.0189-0.1263-0.05270.3086-0.03890.02040.20920.04860.2468-69.7567-18.7518-4.1102
332.1924-0.9950.44033.0172-0.59231.156-0.03940.14870.3644-0.1671-0.0738-0.3087-0.18070.17090.11360.2913-0.0463-0.00780.21630.03610.2456-62.121710.4631-8.0493
340.93190.13140.56760.52180.16090.1507-0.01570.1901-0.0252-0.19840.01510.0128-0.02820.0751-0.00570.3112-0.0110.00970.29470.02120.1939-73.9166-1.5466-12.8336
351.3336-0.48280.01051.44330.20130.3813-0.0484-0.06970.23550.03150.0089-0.1054-0.0792-0.0210.03160.2563-0.0111-0.03330.20390.00650.1987-68.84393.92536.1397
361.63780.7007-0.11161.9133-0.08313.3258-0.0112-0.00210.05410.01-0.0297-0.00290.16120.03420.0290.18710.0322-0.02320.14910.00980.2399-63.3201-15.48625.3171
371.31070.9103-1.27675.5951-3.26184.47-0.06240.2343-0.0513-0.22030.11530.04640.0033-0.1703-0.10670.2056-0.038-0.01280.2531-0.0270.2595-72.0093-35.83228.1339
382.04960.80220.3223.0092-0.50641.25410.0795-0.2065-0.28350.1938-0.0955-0.28230.11340.12360.01640.23640.0315-0.02980.24540.03160.2948-52.5009-36.730923.218
392.29240.5656-0.74175.1712-2.11943.06090.017-0.33530.07880.2932-0.1997-0.7511-0.02590.53580.13910.23540.0201-0.07430.3005-0.00230.2935-41.4058-26.720224.1175
403.03280.8472-1.48575.6852-2.32023.7241-0.0608-0.3016-0.2180.3381-0.0688-0.37460.12030.46080.16760.28110.0448-0.06120.31230.01960.3979-40.6686-34.727922.4391
412.4096-1.44062.06972.3132-2.34993.8941-0.07980.0422-0.16350.03710.015-0.2860.08420.09850.08350.2117-0.0030.02810.2336-0.01380.3232-42.2595-28.79316.7351
421.66870.21730.15561.0322-0.67841.4076-0.00410.1449-0.2878-0.101-0.1049-0.23740.17930.20950.10070.15510.01050.02870.19650.00510.2589-50.1791-30.90696.7641
431.813-0.39760.14012.1535-1.03521.0772-0.10620.2563-0.2529-0.19710.17990.05810.1932-0.0567-0.06250.2536-0.0310.02790.2096-0.01830.2358-60.5014-29.98363.7832
442.51770.531-1.19821.0648-0.48792.2970.0243-0.0305-0.0923-0.0992-0.00360.0141-0.122-0.1213-0.02670.199-0.0104-0.00940.16620.01680.2443-62.4723-34.240714.8317
451.2216-0.0121-0.50191.43090.53791.85440.0397-0.13140.04040.20280.0024-0.095-0.15020.1608-0.04910.253-0.0236-0.02920.2162-0.00280.2176-57.0517-18.147124.7429
463.47793.17981.63035.39072.63213.13480.1484-0.11940.10220.3435-0.12690.07250.2195-0.0287-0.07870.25730.00010.00690.18460.02210.239-65.0483-39.539926.3359
472.7475-0.5136-0.13641.75240.19912.7458-0.0549-0.03640.07640.0577-0.0534-0.08840.0154-0.14860.03950.1809-0.0740.00560.17450.0210.2431-74.4614-35.446819.6061
480.8127-0.17790.07931.1412-0.14961.1976-0.0462-0.0931-0.0870.01040.04170.03990.0726-0.1084-0.00440.2129-0.0216-0.0020.2153-0.01550.208-98.6831-38.601320.4325
492.96130.41430.92832.5498-1.59362.8437-0.0931-0.2954-0.08680.24630.21660.208-0.0251-0.3029-0.0860.33360.03360.07520.3066-0.00880.1999-101.9923-47.216637.4578
501.082-0.0463-0.19280.94710.02190.7694-0.0812-0.054-0.07150.04130.0572-0.01370.127-0.0260.01850.2309-0.01340.00040.2215-0.00090.2201-89.3672-44.388425.2576
512.0241-0.50750.49920.72680.12321.6657-0.0355-0.2690.02420.12240.0485-0.0438-0.0052-0.0193-0.00080.1961-0.0303-0.0070.15670.01390.1977-93.8267-32.205628.9479
522.04910.3295-1.07054.1225-0.03052.44060.0278-0.16230.15290.1734-0.037-0.1895-0.18740.06650.01270.20450.0306-0.05890.23030.03070.188-98.8941-25.676513.2761
530.8212-0.10090.09310.9713-0.16991.0263-0.0342-0.08470.0771-0.05930.02250.09910.0145-0.1392-0.00750.17480.01270.00510.2495-0.01440.2241-91.550423.401757.6756
542.86370.8666-1.07162.5391-1.44552.9050.05560.20840.0302-0.13560.03410.39830.0419-0.4016-0.09760.15660.0297-0.02220.337-0.02150.3064-110.293529.840251.375
553.92550.9374-0.70730.5434-0.41070.67690.12810.20640.41310.0436-0.02440.2307-0.1826-0.3187-0.08090.20860.08420.05090.2696-0.01650.3309-97.553944.152753.5125
560.51750.1998-0.06360.9246-0.73860.7111-0.0009-0.0624-0.00060.0491-0.01180.0639-0.0788-0.06790.02690.14340.03940.01020.2105-0.01670.2177-88.984732.111654.8799
572.86281.75720.39057.56220.58232.9537-0.02210.4714-0.1123-0.6987-0.01070.05390.4297-0.17590.06020.3608-0.0209-0.02670.3821-0.02590.2271-95.065122.183833.2
581.08640.21560.18521.2416-1.03072.50470.01450.0103-0.033-0.11980.15250.21970.2197-0.3263-0.25870.15090.03940.01350.2068-0.0350.2477-92.936319.491147.5125
592.2297-0.232-0.67122.7321.68092.68820.0290.02410.0611-0.04360.0166-0.05820.0122-0.0202-0.02440.15350.0372-0.02790.14480.06420.1683-81.304413.113456.4478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 205 )
4X-RAY DIFFRACTION4chain 'A' and (resid 206 through 361 )
5X-RAY DIFFRACTION5chain 'A' and (resid 362 through 441 )
6X-RAY DIFFRACTION6chain 'A' and (resid 442 through 481 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 74 )
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 204 )
9X-RAY DIFFRACTION9chain 'B' and (resid 205 through 235 )
10X-RAY DIFFRACTION10chain 'B' and (resid 236 through 263 )
11X-RAY DIFFRACTION11chain 'B' and (resid 264 through 369 )
12X-RAY DIFFRACTION12chain 'B' and (resid 370 through 441 )
13X-RAY DIFFRACTION13chain 'B' and (resid 442 through 481 )
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 23 )
15X-RAY DIFFRACTION15chain 'C' and (resid 24 through 74 )
16X-RAY DIFFRACTION16chain 'C' and (resid 75 through 204 )
17X-RAY DIFFRACTION17chain 'C' and (resid 205 through 235 )
18X-RAY DIFFRACTION18chain 'C' and (resid 236 through 263 )
19X-RAY DIFFRACTION19chain 'C' and (resid 264 through 361 )
20X-RAY DIFFRACTION20chain 'C' and (resid 362 through 441 )
21X-RAY DIFFRACTION21chain 'C' and (resid 442 through 481 )
22X-RAY DIFFRACTION22chain 'D' and (resid 0 through 23 )
23X-RAY DIFFRACTION23chain 'D' and (resid 24 through 45 )
24X-RAY DIFFRACTION24chain 'D' and (resid 46 through 212 )
25X-RAY DIFFRACTION25chain 'D' and (resid 213 through 235 )
26X-RAY DIFFRACTION26chain 'D' and (resid 236 through 263 )
27X-RAY DIFFRACTION27chain 'D' and (resid 264 through 361 )
28X-RAY DIFFRACTION28chain 'D' and (resid 362 through 382 )
29X-RAY DIFFRACTION29chain 'D' and (resid 383 through 422 )
30X-RAY DIFFRACTION30chain 'D' and (resid 423 through 441 )
31X-RAY DIFFRACTION31chain 'D' and (resid 442 through 481 )
32X-RAY DIFFRACTION32chain 'E' and (resid 0 through 23 )
33X-RAY DIFFRACTION33chain 'E' and (resid 24 through 235 )
34X-RAY DIFFRACTION34chain 'E' and (resid 236 through 349 )
35X-RAY DIFFRACTION35chain 'E' and (resid 350 through 441 )
36X-RAY DIFFRACTION36chain 'E' and (resid 442 through 482 )
37X-RAY DIFFRACTION37chain 'F' and (resid 0 through 23 )
38X-RAY DIFFRACTION38chain 'F' and (resid 24 through 62 )
39X-RAY DIFFRACTION39chain 'F' and (resid 63 through 86 )
40X-RAY DIFFRACTION40chain 'F' and (resid 87 through 235 )
41X-RAY DIFFRACTION41chain 'F' and (resid 236 through 263 )
42X-RAY DIFFRACTION42chain 'F' and (resid 264 through 302 )
43X-RAY DIFFRACTION43chain 'F' and (resid 303 through 327 )
44X-RAY DIFFRACTION44chain 'F' and (resid 328 through 349 )
45X-RAY DIFFRACTION45chain 'F' and (resid 350 through 422 )
46X-RAY DIFFRACTION46chain 'F' and (resid 423 through 441 )
47X-RAY DIFFRACTION47chain 'F' and (resid 442 through 481 )
48X-RAY DIFFRACTION48chain 'G' and (resid 0 through 62 )
49X-RAY DIFFRACTION49chain 'G' and (resid 63 through 218 )
50X-RAY DIFFRACTION50chain 'G' and (resid 219 through 382 )
51X-RAY DIFFRACTION51chain 'G' and (resid 383 through 441 )
52X-RAY DIFFRACTION52chain 'G' and (resid 442 through 481 )
53X-RAY DIFFRACTION53chain 'H' and (resid 0 through 62 )
54X-RAY DIFFRACTION54chain 'H' and (resid 63 through 235 )
55X-RAY DIFFRACTION55chain 'H' and (resid 236 through 263 )
56X-RAY DIFFRACTION56chain 'H' and (resid 264 through 366 )
57X-RAY DIFFRACTION57chain 'H' and (resid 367 through 390 )
58X-RAY DIFFRACTION58chain 'H' and (resid 391 through 441 )
59X-RAY DIFFRACTION59chain '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