[English] 日本語
Yorodumi
- PDB-6c4c: Crystal structure of 3-nitropropionate modified isocitrate lyase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c4c
TitleCrystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with glyoxylate and pyruvate
ComponentsIsocitrate lyase 1
KeywordsLYASE
Function / homology
Function and homology information


methylisocitrate lyase / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-NITROPROPANOIC ACID / GLYOXYLIC ACID / PYRUVIC ACID / Isocitrate lyase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKreitler, D.F. / Ray, S. / Murkin, A.S. / Gulick, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1255136 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116957 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: The Nitro Group as a Masked Electrophile in Covalent Enzyme Inhibition.
Authors: Ray, S. / Kreitler, D.F. / Gulick, A.M. / Murkin, A.S.
History
DepositionJan 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Mar 16, 2022Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 2.1Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isocitrate lyase 1
B: Isocitrate lyase 1
C: Isocitrate lyase 1
D: Isocitrate lyase 1
E: Isocitrate lyase 1
F: Isocitrate lyase 1
G: Isocitrate lyase 1
H: Isocitrate lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,72633
Polymers391,5558
Non-polymers1,17025
Water28,7701597
1
A: Isocitrate lyase 1
B: Isocitrate lyase 1
C: Isocitrate lyase 1
D: Isocitrate lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,29616
Polymers195,7784
Non-polymers51912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33740 Å2
ΔGint-222 kcal/mol
Surface area49230 Å2
MethodPISA
2
E: Isocitrate lyase 1
F: Isocitrate lyase 1
G: Isocitrate lyase 1
H: Isocitrate lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,42917
Polymers195,7784
Non-polymers65213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34230 Å2
ΔGint-198 kcal/mol
Surface area49210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.760, 87.130, 152.990
Angle α, β, γ (deg.)90.000, 116.550, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Isocitrate lyase 1 / ICL1 / Isocitrase / Isocitratase / Methylisocitrate lyase / MICA


Mass: 48944.398 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) (bacteria)
Strain: ATCC 35801 / TMC 107 / Erdman / Gene: icl1, ERDMAN_0512, Q643_00485 / Production host: Escherichia coli (E. coli)
References: UniProt: H8EVV4, isocitrate lyase, methylisocitrate lyase

-
Non-polymers , 5 types, 1622 molecules

#2: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H2O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H4O3
#5: Chemical ChemComp-3NP / 3-NITROPROPANOIC ACID


Mass: 119.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1597 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM EPPS, 100 mM MgCl2, 17.5%(w/v) PEG4000 (well solution); 10 mg/mL MtICL in 50 mM Tris pH 8.0, 100 mM NaCl, 5 mM MgSO4, 3 mM 3-nitropropionate, and 1 mM DTT (protein solution); 2 uL ...Details: 50 mM EPPS, 100 mM MgCl2, 17.5%(w/v) PEG4000 (well solution); 10 mg/mL MtICL in 50 mM Tris pH 8.0, 100 mM NaCl, 5 mM MgSO4, 3 mM 3-nitropropionate, and 1 mM DTT (protein solution); 2 uL total drop volume, 1:1 well solution:protein solution

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2017
RadiationMonochromator: 0.97946 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→47.393 Å / Num. obs: 169258 / % possible obs: 98 % / Redundancy: 3.7 % / Biso Wilson estimate: 33.86 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.198 / Rrim(I) all: 0.2316 / Net I/σ(I): 5.86
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.63 / Mean I/σ(I) obs: 0.77 / Num. unique obs: 16914 / CC1/2: 0.377 / Rrim(I) all: 1.903 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C4A
Resolution: 2.2→47.393 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1999 1.18 %
Rwork0.192 167118 -
obs0.1926 169117 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.68 Å2 / Biso mean: 47.5217 Å2 / Biso min: 17.7 Å2
Refinement stepCycle: final / Resolution: 2.2→47.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26436 0 103 1597 28136
Biso mean--39.61 35.68 -
Num. residues----3421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327118
X-RAY DIFFRACTIONf_angle_d0.49636892
X-RAY DIFFRACTIONf_chiral_restr0.0384051
X-RAY DIFFRACTIONf_plane_restr0.0034893
X-RAY DIFFRACTIONf_dihedral_angle_d12.25816010
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2550.40121380.3424119161205499
2.255-2.3160.33371480.3146119501209899
2.316-2.38410.33581410.2924119421208399
2.3841-2.46110.30791420.2792118921203499
2.4611-2.5490.32881460.2618120281217499
2.549-2.65110.30061410.2406118461198798
2.6511-2.77170.31181390.2359117281186797
2.7717-2.91780.30641410.2233117601190197
2.9178-3.10060.29971450.21391206512210100
3.1006-3.340.2121460.1907120221216899
3.34-3.6760.25381390.1675119581209799
3.676-4.20760.18591400.1413117441188496
4.2076-5.30.16871460.1316121031224999
5.3-47.40370.20661470.1468121641231198
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)
10.73180.0168-0.07970.8079-0.05351.13150.03270.0121-0.13260.04280.0005-0.03380.14990.0346-0.03590.23630.0062-0.03160.22210.01140.270174.6535-31.5195196.1562
21.1862-0.0196-0.17541.0499-0.19291.96530.01730.1920.0197-0.21740.0630.0945-0.0054-0.0273-0.08450.30360.0135-0.0150.2498-0.01520.276775.7117-29.1304175.1861
30.46090.1046-0.21361.14390.1911.13530.0503-0.05590.0680.0844-0.05050.29990.0324-0.20770.00260.2536-0.01170.010.29420.01880.360653.5047-20.5764201.1131
41.4868-1.4037-1.92046.65832.43488.98780.0763-0.33761.32460.19980.4842-0.4937-0.22550.4691-0.57530.6845-0.06250.19040.3099-0.04660.63478.329221.7802208.5914
50.59950.2506-0.0820.95470.1860.94440.0897-0.11080.26880.2739-0.03270.2049-0.2871-0.1291-0.05580.42570.03370.08830.2784-0.03220.407461.62251.4514212.6612
60.8325-0.6149-0.32392.42271.14451.40480.01760.02480.08630.1802-0.09750.4398-0.0292-0.2490.07680.28790.05060.03890.33630.04970.435348.0924-12.1208197.3638
77.11781.5721-1.81742.9002-0.47292.5473-0.15980.6879-0.4902-0.40110.1455-0.0175-0.1527-0.12080.01650.43980.0156-0.01750.37240.01830.303869.03-8.1548176.0866
89.03723.8419-5.0212.3258-2.85326.04751.02710.18011.8030.2013-0.05910.675-0.90390.0254-0.92880.79010.02140.11330.3490.08020.681377.968516.5052183.5197
90.9687-0.18850.67720.8932-0.20590.9764-0.0307-0.02760.26420.05980.0249-0.0639-0.28330.17780.02030.3466-0.08020.050.3385-0.00230.293192.49521.4224193.882
100.4598-0.5680.01391.27321.49775.5723-0.0773-0.0690.1795-0.23730.1266-0.0373-0.60420.3911-0.06360.3309-0.06990.02160.28060.00790.331589.50171.3227200.53
110.6623-0.4841-0.11951.610.5421.54510.05030.08810.1463-0.14590.022-0.1889-0.24450.364-0.06810.3452-0.07770.03880.36910.02220.294499.8292-7.0001178.7376
120.62050.4763-0.47811.0164-1.20373.20.0717-0.1590.05570.1006-0.0799-0.2501-0.3120.49130.00860.327-0.09040.00150.487-0.02770.4173109.7523-5.813203.8595
136.4432-2.187-1.59681.63780.84281.4913-0.2808-0.89930.05550.50150.17670.0626-0.01220.17180.10020.6703-0.15430.02240.6119-0.08680.411588.61033.4323225.5549
140.83650.2657-0.29210.62940.10581.29040.0278-0.2328-0.17710.1555-0.0378-0.03560.0980.25730.01430.29460.0043-0.02840.34520.05370.279285.6393-26.429217.1266
151.51360.3430.05750.77030.41991.19480.1081-0.42560.15420.3336-0.0809-0.0592-0.19340.1626-0.02790.5425-0.08690.00360.55220.01940.316585.6403-16.3161235.1151
160.46940.3315-0.06850.82910.0770.50760.0088-0.069-0.05360.0451-0.0121-0.2138-0.10720.4005-0.00430.2938-0.0148-0.04830.49340.00230.347105.8854-16.303203.0892
173.07490.85030.9331.855-1.10012.51480.1735-0.3336-0.07730.16450.0424-0.36240.02510.5284-0.250.3710.0688-0.05120.4832-0.06520.386866.971812.2825157.7334
180.7611-0.3238-0.30630.80120.21211.63020.02170.05840.07510.08010.0554-0.0648-0.29490.1221-0.07140.3359-0.01250.03630.2078-0.00170.265147.793223.0477146.9673
190.98780.0147-0.83240.9103-0.04840.8912-0.0071-0.22320.07570.3010.06250.1358-0.09630.1824-0.06170.53520.00910.03170.3181-0.02390.318744.036819.9088169.9429
205.6686-2.2327-0.55143.31981.15711.30450.152-0.54410.53160.33390.1699-0.093-0.44380.1577-0.3110.6695-0.06240.11570.3282-0.01650.318947.543635.2757168.0944
211.33190.34270.38042.37810.01731.9380.15-0.02230.2666-0.00250.09560.0514-0.6930.1583-0.22970.6556-0.03390.12060.2837-0.03590.362244.107938.7142159.7668
220.6593-0.2713-0.15592.05-1.26254.48570.11770.20760.3452-0.04140.09320.1065-0.7409-0.5054-0.23750.58710.12930.09280.35470.09380.436429.377136.4995134.051
231.5639-0.2268-0.67830.27530.82082.2818-0.03230.26630.1787-0.14040.1147-0.0686-0.13480.0906-0.09360.50080.00030.06490.34060.02270.311947.280125.2132120.0931
242.203-0.4310.95660.72440.90152.6121-0.05280.4756-0.3094-0.25770.13450.42710.5742-0.7529-0.13240.5165-0.263-0.06170.7098-0.01580.570112.6086-2.8009126.3764
250.9276-0.04-0.46570.63560.39172.57820.0660.31530.0887-0.05630.01160.241-0.1951-0.4582-0.07240.29490.0251-0.00530.32440.05610.30726.484916.4909131.5325
261.80910.641-0.74331.2815-0.19041.5327-0.04080.56460.052-0.37910.11310.15680.0218-0.4399-0.07710.5001-0.0346-0.06290.55830.03590.310727.660314.1346110.466
271.09780.33320.45010.8070.43152.5510.03050.27590.2616-0.02090.05810.2345-0.5004-0.3207-0.07530.51990.14450.07910.40970.14070.397527.907233.7032130.0406
281.55811.1458-1.25650.7996-0.96635.18660.13620.06370.20220.351-0.04920.2811-0.413-0.2581-0.08960.41950.11110.09990.27530.01460.349623.706224.3446160.2725
294.00890.0405-1.15973.0770.5844.1083-0.02210.0665-0.01860.23380.05410.59080.0912-0.8005-0.07250.3311-0.00080.05960.47040.02160.47839.80564.3948155.2404
301.19930.1343-0.21540.99340.06141.5275-0.15780.1205-0.21390.05670.0650.23380.4247-0.21130.09380.4314-0.03920.08280.2454-0.01250.325229.9331-7.8109148.4773
310.80790.24960.11630.8560.07911.5055-0.0964-0.0804-0.11060.33330.06380.02530.1320.03270.03370.58390.0420.12530.2850.01270.391731.3074-1.1653170.9669
321.3017-0.7101-0.11852.23570.40770.908-0.1187-0.1748-0.29930.35660.01980.23740.4321-0.04580.10940.7668-0.01840.16010.30440.01970.444330.4296-19.536166.4281
331.05320.4584-0.591.35481.03592.9926-0.2573-0.0031-0.5291-0.08640.09290.01090.72080.15640.15630.78210.07570.16120.2790.00740.486449.3281-22.8789140.0659
341.2658-0.54160.38082.7383-2.01052.67210.0160.3073-0.2266-0.5299-0.0780.10190.895-0.18080.06970.705-0.11930.05520.437-0.12320.396733.8965-14.2271122.6378
353.9027-0.4384-0.82461.5739-1.62783.13990.11190.16030.2421-0.0977-0.1534-0.2384-0.02120.3902-0.01480.3844-0.0290.07330.35510.01070.320867.473514.8424128.131
360.31080.48290.10790.6725-0.12911.8112-0.09340.0111-0.1351-0.10690.0088-0.12980.47240.25480.07960.42420.08450.07340.2673-0.02320.320754.0563-3.4897137.6562
370.59260.21420.21631.05010.22461.9236-0.13120.2356-0.2191-0.26320.0181-0.02410.48440.07110.1160.59890.01040.10530.381-0.05240.349453.7514-5.4685115.881
381.2551-0.0007-0.37370.8086-0.39640.6525-0.14710.1607-0.3192-0.1687-0.0343-0.08830.50710.04620.1790.81990.05360.14270.3019-0.07810.479549.418-22.7981139.3775
391.66440.1054-0.41192.05470.67392.3078-0.0947-0.2013-0.27530.481-0.0354-0.00510.72360.37250.08260.54670.10880.00140.3530.04990.328452.6156-6.5507164.2776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 174 )A0 - 174
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 325 )A175 - 325
3X-RAY DIFFRACTION3chain 'A' and (resid 326 through 427 )A326 - 427
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 19 )B1 - 19
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 319 )B20 - 319
6X-RAY DIFFRACTION6chain 'B' and (resid 320 through 386 )B320 - 386
7X-RAY DIFFRACTION7chain 'B' and (resid 387 through 427 )B387 - 427
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 19 )C1 - 19
9X-RAY DIFFRACTION9chain 'C' and (resid 20 through 115 )C20 - 115
10X-RAY DIFFRACTION10chain 'C' and (resid 116 through 173 )C116 - 173
11X-RAY DIFFRACTION11chain 'C' and (resid 174 through 304 )C174 - 304
12X-RAY DIFFRACTION12chain 'C' and (resid 305 through 386 )C305 - 386
13X-RAY DIFFRACTION13chain 'C' and (resid 387 through 427 )C387 - 427
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 173 )D1 - 173
15X-RAY DIFFRACTION15chain 'D' and (resid 174 through 340 )D174 - 340
16X-RAY DIFFRACTION16chain 'D' and (resid 341 through 428 )D341 - 428
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 46 )E1 - 46
18X-RAY DIFFRACTION18chain 'E' and (resid 47 through 174 )E47 - 174
19X-RAY DIFFRACTION19chain 'E' and (resid 175 through 278 )E175 - 278
20X-RAY DIFFRACTION20chain 'E' and (resid 279 through 304 )E279 - 304
21X-RAY DIFFRACTION21chain 'E' and (resid 305 through 348 )E305 - 348
22X-RAY DIFFRACTION22chain 'E' and (resid 349 through 386 )E349 - 386
23X-RAY DIFFRACTION23chain 'E' and (resid 387 through 428 )E387 - 428
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 46 )F1 - 46
25X-RAY DIFFRACTION25chain 'F' and (resid 47 through 201 )F47 - 201
26X-RAY DIFFRACTION26chain 'F' and (resid 202 through 302 )F202 - 302
27X-RAY DIFFRACTION27chain 'F' and (resid 303 through 386 )F303 - 386
28X-RAY DIFFRACTION28chain 'F' and (resid 387 through 428 )F387 - 428
29X-RAY DIFFRACTION29chain 'G' and (resid 1 through 46 )G1 - 46
30X-RAY DIFFRACTION30chain 'G' and (resid 47 through 174 )G47 - 174
31X-RAY DIFFRACTION31chain 'G' and (resid 175 through 278 )G175 - 278
32X-RAY DIFFRACTION32chain 'G' and (resid 279 through 348 )G279 - 348
33X-RAY DIFFRACTION33chain 'G' and (resid 349 through 386 )G349 - 386
34X-RAY DIFFRACTION34chain 'G' and (resid 387 through 427 )G387 - 427
35X-RAY DIFFRACTION35chain 'H' and (resid 1 through 46 )H1 - 46
36X-RAY DIFFRACTION36chain 'H' and (resid 47 through 173 )H47 - 173
37X-RAY DIFFRACTION37chain 'H' and (resid 174 through 319 )H174 - 319
38X-RAY DIFFRACTION38chain 'H' and (resid 320 through 386 )H320 - 386
39X-RAY DIFFRACTION39chain 'H' and (resid 387 through 428 )H387 - 428

+
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