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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5urq
TitleCrystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor p176
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-8L7 / 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: 2.7 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 p176
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 12, 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
H: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,10532
Polymers348,1998
Non-polymers6,90624
Water30617
1
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,55216
Polymers174,0994
Non-polymers3,45312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23350 Å2
ΔGint-126 kcal/mol
Surface area48410 Å2
MethodPISA
2
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,55216
Polymers174,0994
Non-polymers3,45312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23320 Å2
ΔGint-127 kcal/mol
Surface area48660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.487, 141.793, 121.640
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 43524.820 Da / Num. of mol.: 8
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
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-8L7 / N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-alpha-D-ribofuranosylamine


Mass: 475.965 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H30ClN3O5
#4: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
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: 2.7→50 Å / Num. obs: 91374 / % possible obs: 98.9 % / Redundancy: 3.3 % / Rsym value: 0.115 / Net I/σ(I): 10.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4135 / Rsym value: 0.736 / % possible all: 89.7

-
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
Resolution: 2.7→40.795 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 4505 4.94 %random
Rwork0.1801 ---
obs0.1827 91192 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21152 0 456 17 21625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821904
X-RAY DIFFRACTIONf_angle_d1.10129584
X-RAY DIFFRACTIONf_dihedral_angle_d17.33113224
X-RAY DIFFRACTIONf_chiral_restr0.1083462
X-RAY DIFFRACTIONf_plane_restr0.0063738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6816-2.71210.37311030.3071820X-RAY DIFFRACTION62
2.7121-2.7440.32631250.3022720X-RAY DIFFRACTION92
2.744-2.77740.34151310.28722774X-RAY DIFFRACTION94
2.7774-2.81260.37161750.2712853X-RAY DIFFRACTION98
2.8126-2.84960.32621660.26362894X-RAY DIFFRACTION99
2.8496-2.88860.35711560.26292946X-RAY DIFFRACTION100
2.8886-2.92990.3171540.24872920X-RAY DIFFRACTION100
2.9299-2.97360.31731480.26682966X-RAY DIFFRACTION100
2.9736-3.020.3031440.25952915X-RAY DIFFRACTION100
3.02-3.06950.36941510.26242976X-RAY DIFFRACTION100
3.0695-3.12240.31751530.25842940X-RAY DIFFRACTION100
3.1224-3.17920.31961850.24182893X-RAY DIFFRACTION100
3.1792-3.24030.32021530.23942933X-RAY DIFFRACTION100
3.2403-3.30640.28521480.22272968X-RAY DIFFRACTION100
3.3064-3.37830.2581500.20942964X-RAY DIFFRACTION100
3.3783-3.45680.2521570.19892917X-RAY DIFFRACTION100
3.4568-3.54320.25121300.19592951X-RAY DIFFRACTION100
3.5432-3.6390.21211210.18312987X-RAY DIFFRACTION100
3.639-3.7460.23791340.18582963X-RAY DIFFRACTION100
3.746-3.86680.2341300.17492963X-RAY DIFFRACTION100
3.8668-4.00490.21391760.16212915X-RAY DIFFRACTION100
4.0049-4.16510.22051740.14762940X-RAY DIFFRACTION100
4.1651-4.35440.1881460.1452939X-RAY DIFFRACTION100
4.3544-4.58370.19621410.13832964X-RAY DIFFRACTION100
4.5837-4.87050.17551500.12882952X-RAY DIFFRACTION99
4.8705-5.24580.2031810.13512922X-RAY DIFFRACTION99
5.2458-5.77240.21441670.15092947X-RAY DIFFRACTION99
5.7724-6.60470.18431640.15622916X-RAY DIFFRACTION99
6.6047-8.30960.20091420.14062973X-RAY DIFFRACTION99
8.3096-40.79990.18531500.15572956X-RAY DIFFRACTION97
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)
11.933-0.24460.15362.1734-0.01631.3497-0.0042-0.0747-0.01860.15490.08430.06620.1835-0.0374-0.08610.39290.0429-0.03050.2816-0.01770.38437.95021.29061.8864
27.1108-0.92821.32825.9334-0.17732.03670.18880.0196-0.57240.30230.04190.09840.6464-0.1297-0.1730.6189-0.0263-0.03470.33160.07590.528228.0227-14.30656.5409
31.5493-0.1396-0.70451.46490.27561.34490.0302-0.02860.00980.17040.02040.07450.0704-0.0413-0.04790.40950.0141-0.03540.3029-0.01290.425330.33973.61631.844
41.9001-0.8748-0.54411.8909-0.5023.0862-0.00890.3084-0.11110.14140.0383-0.0397-0.1244-0.0941-0.05960.4164-0.0559-0.07870.3238-0.06390.560346.96811.0444-8.1672
52.17592.8768-1.48717.2442-5.42185.3880.00870.02960.07770.25620.32140.217-0.1547-0.1478-0.33030.45440.0217-0.05230.3498-0.03670.488552.61632.1656-9.5515
60.8448-0.7227-0.00873.64660.11890.79450.0280.202-0.1121-0.17850.0613-0.6450.00350.4252-0.07310.3693-0.02860.07370.5973-0.15480.762572.061914.779-26.4367
73.7049-0.2794-3.23791.13960.68893.0673-0.17930.0761-0.20490.14180.1443-0.6020.25890.35110.05470.350.0322-0.12250.507-0.07770.700771.78028.287-10.1548
80.7914-0.1760.03862.3159-0.41811.3929-0.0457-0.063-0.11930.13060.0753-0.2892-0.10160.2578-0.03070.3363-0.0289-0.05280.4116-0.10080.545262.442619.5516-11.2066
90.6098-0.69250.16383.12540.12490.9523-0.04650.1531-0.0337-0.39760.17360.01360.07640.0686-0.09980.4317-0.0565-0.00830.4513-0.0650.373254.442414.7215-29.2267
102.5815-0.40371.09491.798-1.57482.07990.00480.2558-0.2819-0.29060.14280.2948-0.0582-0.0368-0.2250.6789-0.0013-0.00720.573-0.14030.700950.675634.1243-21.8082
119.4421-2.18120.14253.43991.19012.995-0.0145-0.1021-0.29760.3861-0.03170.25740.12820.2170.03250.5664-0.0165-0.03070.40020.01170.335235.408144.1785-8.6588
121.83580.1374-0.26632.0530.62331.0521-0.06050.36050.0696-0.64440.07530.1289-0.25110.0579-0.03340.77060.0064-0.10270.53350.08580.444636.555557.0223-34.0197
132.83211.8695-2.44653.8957-0.50022.5656-0.10540.33231.5003-0.4890.23060.6246-0.5099-0.3192-0.10880.87170.0464-0.17820.55110.12840.763330.34166.6207-36.3936
141.87530.5591-0.08011.6816-0.32210.8061-0.08150.02880.2515-0.07530.1791-0.0014-0.23430.0211-0.09780.5349-0.0181-0.03150.3496-0.03080.385348.036653.4403-24.1271
151.2823-0.3742-0.18042.6481.04631.8428-0.08030.3122-0.0644-0.39560.07650.2719-0.0771-0.07130.00780.5291-0.0346-0.09220.45230.04670.469833.709242.8193-33.4925
165.91491.8641.21635.90992.77732.59380.01630.1429-0.3354-0.6067-0.27890.82730.2629-0.54260.27190.68520.0311-0.02560.52220.00330.498925.653642.2898-14.6151
177.66685.6999-5.2578.0988-5.08256.3457-0.25160.2144-0.0278-0.05760.30070.08290.2245-0.0946-0.07630.41930.0454-0.02790.349-0.03550.331925.205927.63593.6417
181.7852-1.04680.07812.0419-0.73782.56420.00890.2163-0.0137-0.0369-0.09180.837-0.0297-0.6120.04140.43580.0527-0.00890.6668-0.07751.0916-3.38834.3045-4.0132
195.52221.1497-2.05992.2662-0.9162.4171-0.16040.157-0.75550.1897-0.10250.3517-0.3783-0.57780.25680.47140.15720.00220.4492-0.01720.91225.329150.0363-2.9106
201.29350.0072-0.79432.4535-0.76212.4496-0.1277-0.109-0.17610.21860.08340.47190.0337-0.25270.06730.32560.0481-0.00840.3581-0.02050.561815.411439.9168-0.8928
211.46320.78630.00532.13940.79482.3958-0.16730.433-0.1314-0.40720.04040.36420.2396-0.35240.11830.46690.0074-0.13330.6198-0.03250.82778.429129.7115-18.9628
223.182-0.46083.10533.1155-2.93697.02120.3098-0.08260.1539-0.084-0.36980.31170.4519-0.21880.10240.35470.02770.05570.42-0.06250.66189.875718.6390.3621
234.06-0.5842-2.17073.03620.99454.3506-0.03350.49630.034-0.1772-0.06550.06430.4381-0.21980.08580.580.0352-0.00450.5027-0.01230.668722.20318.9782-1.4942
241.37130.01720.18391.46270.01311.7259-0.09520.1534-0.2714-0.04630.0785-0.44870.12240.25670.01670.3337-0.01590.07210.4535-0.08170.687845.1413-27.3968-42.0478
252.52760.91850.63675.9129-2.7223.17060.0053-0.3362-0.00690.1888-0.0703-0.64030.05850.41330.12910.39390.0727-0.00620.71330.05370.942562.0571-26.0714-35.3878
260.91820.5330.00511.6382-0.34311.2653-0.11780.2931-0.3649-0.22040.1306-0.38650.17240.2883-0.02260.3785-0.03710.07160.5959-0.14710.671651.258-22.8786-51.6128
271.0465-2.2418-0.31426.83161.13246.9278-0.1158-0.09670.1312-0.0412-0.1885-0.3308-0.05280.42390.34890.303-0.0621-0.11770.475-0.08660.528147.2107-8.9687-32.2409
281.073-0.3770.29823.24170.06773.16920.08460.089-0.25650.5985-0.21320.29980.04110.05990.13840.1912-0.02950.01410.4115-0.07330.437641.912-20.4245-35.5867
292.063-0.9957-1.22381.85320.07990.98280.0362-0.13980.45130.23410.0493-0.08620.0628-0.088-0.11760.5629-0.1015-0.07140.7373-0.12690.860928.5292-28.0244-40.3682
301.57630.32080.07290.61530.12251.0205-0.05930.0241-0.3622-0.08970.0810.29750.2043-0.3268-0.0460.401-0.0697-0.02260.5283-0.01950.75975.651-34.0006-33.8992
313.5762-0.0907-1.53991.29230.28652.0829-0.0995-0.1571-0.57160.03750.05570.27070.3002-0.26070.06320.4916-0.13690.02410.54670.0630.87588.3715-45.7628-27.0787
323.19090.208-0.07071.10310.1751.3014-0.09650.2995-0.5765-0.11290.08860.01480.2671-0.06950.00680.3914-0.1174-0.0040.4906-0.08390.672713.2809-36.7168-40.6227
331.46980.0462-0.7120.78191.15852.3761-0.1348-0.47990.11830.05020.04540.23130.0115-0.09040.08620.3714-0.07480.03030.44040.04570.596411.0029-23.2112-26.5739
341.93530.63870.99594.37461.03460.67870.3479-0.20740.17570.3603-0.64550.3395-0.3127-0.35480.30440.7716-0.13710.00620.8766-0.04070.6083.8113-18.6203-45.6629
356.8312-1.88342.18362.74560.6014.170.27560.1886-0.0585-0.297-0.115-0.03390.2728-0.2336-0.16110.4738-0.10810.01470.5590.0180.428132.878-10.9369-63.7792
361.35560.0293-0.26252.581-0.22931.3615-0.02280.37380.4617-0.13210.0545-0.1809-0.189-0.0344-0.02690.451-0.1019-0.00120.6960.15130.681240.427113.7803-64.5908
374.9488-2.5471-0.38217.6977-2.40543.7012-0.01910.78730.635-0.03920.0571-0.0306-0.63950.14910.00230.6547-0.1715-0.03590.74620.18510.806539.64223.8612-69.1599
388.07034.04541.84912.33961.77382.7099-0.30740.73380.8587-0.36620.15680.1644-0.426-0.23050.16440.6289-0.0816-0.16150.99840.32820.651326.247616.0932-76.5264
393.5080.2020.7621.7318-0.21560.6787-0.0370.69010.1265-0.38560.03880.0512-0.0382-0.16890.01480.4605-0.0503-0.01220.69880.07210.497329.59724.3408-69.5418
406.64390.93184.52486.4441.14088.3616-0.0913-0.07370.22440.0988-0.0008-0.1636-0.243-0.24260.10010.4083-0.04470.01640.44490.01170.459527.79916.5573-49.1988
413.382-2.445-0.52345.78292.60373.591-0.35740.39410.63440.03650.747-0.5484-0.23750.413-0.42190.3973-0.0429-0.03950.68090.06760.48446.68551.7356-57.3139
422.06620.4090.38821.13920.63415.3219-0.08090.241-0.2561-0.12260.1562-0.2550.09520.1609-0.0510.4893-0.06-0.0140.5484-0.0920.712439.2845-7.6256-54.432
431.69290.40870.1058.6903-3.53063.3871-0.02890.69420.0458-0.4226-0.11810.40440.14370.34330.16370.4468-0.047-0.02630.8013-0.00580.333111.4876-6.9355-64.6291
442.61030.0607-0.73421.5642-0.70672.38080.06550.35980.50860.0270.06340.3849-0.2857-0.3334-0.16280.40540.0509-0.06410.81130.09990.7835-13.18055.855-55.3376
451.3280.2444-0.8291.4132-0.45960.9950.03430.53270.1099-0.21770.04580.31780.0857-0.4211-0.07080.4061-0.1078-0.13410.81860.00320.5664-8.3721-9.6916-58.0388
461.09930.71570.17622.5213-0.38453.7896-0.1212-0.02560.30890.2351-0.10040.1395-0.3935-0.00130.19160.2886-0.0168-0.11760.55810.00140.64150.05353.6862-44.5968
470.1892-0.3231-0.25821.9732-0.70121.552-0.2146-0.25760.34690.01260.2568-0.3072-0.28790.0972-0.08130.5082-0.0869-0.00180.9318-0.07140.842314.74811.7881-60.0835
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 235 )
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 441 )
4X-RAY DIFFRACTION4chain 'A' and (resid 442 through 482 )
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 23 )
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 235 )
7X-RAY DIFFRACTION7chain 'B' and (resid 236 through 263 )
8X-RAY DIFFRACTION8chain 'B' and (resid 264 through 356 )
9X-RAY DIFFRACTION9chain 'B' and (resid 357 through 441 )
10X-RAY DIFFRACTION10chain 'B' and (resid 442 through 481 )
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 23 )
12X-RAY DIFFRACTION12chain 'C' and (resid 24 through 86 )
13X-RAY DIFFRACTION13chain 'C' and (resid 87 through 218 )
14X-RAY DIFFRACTION14chain 'C' and (resid 219 through 349 )
15X-RAY DIFFRACTION15chain 'C' and (resid 350 through 441 )
16X-RAY DIFFRACTION16chain 'C' and (resid 442 through 480 )
17X-RAY DIFFRACTION17chain 'D' and (resid 0 through 25 )
18X-RAY DIFFRACTION18chain 'D' and (resid 26 through 235 )
19X-RAY DIFFRACTION19chain 'D' and (resid 236 through 263 )
20X-RAY DIFFRACTION20chain 'D' and (resid 264 through 349 )
21X-RAY DIFFRACTION21chain 'D' and (resid 350 through 422 )
22X-RAY DIFFRACTION22chain 'D' and (resid 423 through 441 )
23X-RAY DIFFRACTION23chain 'D' and (resid 442 through 482 )
24X-RAY DIFFRACTION24chain 'E' and (resid 0 through 74 )
25X-RAY DIFFRACTION25chain 'E' and (resid 75 through 226 )
26X-RAY DIFFRACTION26chain 'E' and (resid 227 through 356 )
27X-RAY DIFFRACTION27chain 'E' and (resid 357 through 395 )
28X-RAY DIFFRACTION28chain 'E' and (resid 396 through 441 )
29X-RAY DIFFRACTION29chain 'E' and (resid 442 through 481 )
30X-RAY DIFFRACTION30chain 'F' and (resid 0 through 86 )
31X-RAY DIFFRACTION31chain 'F' and (resid 87 through 263 )
32X-RAY DIFFRACTION32chain 'F' and (resid 264 through 361 )
33X-RAY DIFFRACTION33chain 'F' and (resid 362 through 441 )
34X-RAY DIFFRACTION34chain 'F' and (resid 442 through 481 )
35X-RAY DIFFRACTION35chain 'H' and (resid 0 through 23 )
36X-RAY DIFFRACTION36chain 'H' and (resid 24 through 74 )
37X-RAY DIFFRACTION37chain 'H' and (resid 75 through 234 )
38X-RAY DIFFRACTION38chain 'H' and (resid 235 through 261 )
39X-RAY DIFFRACTION39chain 'H' and (resid 262 through 360 )
40X-RAY DIFFRACTION40chain 'H' and (resid 361 through 422 )
41X-RAY DIFFRACTION41chain 'H' and (resid 423 through 441 )
42X-RAY DIFFRACTION42chain 'H' and (resid 442 through 482 )
43X-RAY DIFFRACTION43chain 'G' and (resid 0 through 25 )
44X-RAY DIFFRACTION44chain 'G' and (resid 26 through 226 )
45X-RAY DIFFRACTION45chain 'G' and (resid 227 through 356 )
46X-RAY DIFFRACTION46chain 'G' and (resid 357 through 441 )
47X-RAY DIFFRACTION47chain 'G' 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://pdbjlvh1.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