[English] 日本語
Yorodumi
- PDB-4apb: Crystal structure of Mycobacterium tuberculosis fumarase (Rv1098c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4apb
TitleCrystal structure of Mycobacterium tuberculosis fumarase (Rv1098c) S318C in complex with fumarate
ComponentsFUMARATE HYDRATASE CLASS II
KeywordsHYDROLASE / METABOLISM
Function / homology
Function and homology information


tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytosol
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FUMARIC ACID / Fumarate hydratase class II / Fumarate hydratase class II
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsBellinzoni, M. / Haouz, A. / Mechaly, A.E. / Alzari, P.M.
CitationJournal: FEBS Lett. / Year: 2012
Title: Conformational Changes Upon Ligand Binding in the Essential Class II Fumarase Rv1098C from Mycobacterium Tuberculosis.
Authors: Mechaly, A.E. / Haouz, A. / Miras, I. / Barilone, N. / Weber, P. / Shepard, W. / Alzari, P.M. / Bellinzoni, M.
History
DepositionMar 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2Jul 18, 2012Group: Atomic model / Derived calculations / Non-polymer description
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.pdbx_dist_value / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FUMARATE HYDRATASE CLASS II
B: FUMARATE HYDRATASE CLASS II
C: FUMARATE HYDRATASE CLASS II
D: FUMARATE HYDRATASE CLASS II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,11911
Polymers200,5354
Non-polymers5857
Water29,9231661
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33500 Å2
ΔGint-204.7 kcal/mol
Surface area51430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.997, 98.736, 188.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1987, 0.044, -0.9791), (0.0431, -0.9976, -0.0536), (-0.9791, -0.0528, 0.1963)15.5138, -5.992, 12.5082
2given(-0.5515, 0.7327, 0.3988), (0.7314, 0.1948, 0.6536), (0.4011, 0.6521, -0.6433)55.8111, -9.8194, -44.7595
3given(-0.2518, -0.7748, 0.5799), (-0.7767, -0.1957, -0.5987), (0.5774, -0.6012, -0.5525)47.92, 8.6731, -50.4362

-
Components

#1: Protein
FUMARATE HYDRATASE CLASS II / FUMARASE C


Mass: 50133.723 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: O53446, UniProt: P9WN93*PLUS, fumarate hydratase
#2: Chemical
ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1661 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 318 TO CYS ENGINEERED RESIDUE IN CHAIN B, SER 318 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, SER 318 TO CYS ENGINEERED RESIDUE IN CHAIN B, SER 318 TO CYS ENGINEERED RESIDUE IN CHAIN C, SER 318 TO CYS ENGINEERED RESIDUE IN CHAIN D, SER 318 TO CYS
Sequence detailsN-TER GLY IS A PURIFICATION TAG LEFTOVER

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.9 % / Description: NONE
Crystal growpH: 8 / Details: 20% PEG 3350, 0.2 M CACL2, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97895
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.94→49.37 Å / Num. obs: 134846 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 22.59 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.2 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ADM

4adm


Resolution: 1.94→49.37 Å / Cor.coef. Fo:Fc: 0.9468 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.139 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.114
Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=15226. NUMBER WITH APPROX DEFAULT ...Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=15226. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=3. NUMBER OF LSSR (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.1745 6769 5.02 %RANDOM
Rwork0.1474 ---
obs0.1488 134762 99.55 %-
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.8744 Å20 Å20 Å2
2--8.509 Å20 Å2
3----7.6346 Å2
Refine analyzeLuzzati coordinate error obs: 0.207 Å
Refinement stepCycle: LAST / Resolution: 1.94→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13486 0 35 1661 15182
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113764HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9618754HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6411SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes355HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2084HARMONIC5
X-RAY DIFFRACTIONt_it13764HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion2.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1932SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18683SEMIHARMONIC4
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2292 518 5.28 %
Rwork0.1938 9294 -
all0.1957 9812 -
obs--99.55 %
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)
12.9229-1.35071.76741.81811.42073.42820.1537-0.05770.12040.128-0.035-0.3424-0.05920.3296-0.11880.0061-0.0575-0.2503-0.07130.04860.21762.50499.2665.444
21.17570.5936-0.60070.24840.74050.92350.0676-0.1256-0.00090.31050.0002-0.3463-0.22750.2187-0.0678-0.0115-0.0431-0.1891-0.14930.05440.056553.44199.6736-1.3432
31.3929-0.12170.23122.3544-2.05393.18670.1012-0.1937-0.00350.5019-0.1466-0.0913-0.2107-0.05380.04540.099-0.098-0.1847-0.10590.021-0.066440.2410.559513.7139
40.39770.35580.256500.18630.44690.1398-0.0663-0.12540.2572-0.1236-0.18570.0639-0.0017-0.01620.0634-0.0745-0.2094-0.08470.06220.001145.2656.37587.2768
50.63580.07540.30070.4708-0.02530.40250.07-0.145-0.01120.2089-0.0567-0.0665-0.0029-0.086-0.01340.0243-0.0477-0.0403-0.0166-0.0002-0.077517.13537.8183-4.5296
60.33520.05290.09620.6654-0.15470.43830.0635-0.036-0.00270.1183-0.051-0.0861-0.0002-0.0126-0.0125-0.0205-0.0311-0.058-0.04560.0093-0.04825.57659.2207-15.9582
71.3292-1.01330.60340.1949-0.60631.02220.003-0.2240.16470.1522-0.004-0.1426-0.0693-0.05960.00090.0306-0.0341-0.0638-0.0223-0.0183-0.003621.789318.21-11.1838
81.31151.60030.63292.5466-0.01830.5927-0.0087-0.09250.0119-0.3396-0.07020.0214-0.0459-0.16630.07880.00320.0395-0.01680.05420.01140.0143-0.749523.4271-30.8003
90-2.4322-0.110.22290.90542.37130.1186-0.08920.0488-0.8746-0.1737-0.0884-0.241-0.15950.0552-0.01230.0252-0.0393-0.0056-0.0079-0.0518-9.53075.8163-39.0414
102.5364-0.27110.45767.64842.10822.81590.20630.03750.2657-1.0862-0.27040.8215-0.4455-0.32090.0641-0.06390.0726-0.0827-0.09780.00690.0187-15.01212.5299-35.6479
113.37320.5761.29911.8102-2.12212.6186-0.0820.15390.0658-0.3159-0.09910.27180.3295-0.01820.1810.0743-0.0283-0.0340.07010.0115-0.0628-2.7057-11.3303-48.225
120.24990.065-0.12420.5882-0.02010.37750.02490.0097-0.02950.0151-0.05580.07370.0908-0.0920.031-0.0294-0.0393-0.02170.0026-0.0028-0.0592-0.8136-12.906-30.9072
132.6499-0.95211.12064.5151-1.153800.0684-0.0901-0.19530.1479-0.03820.30960.0462-0.2404-0.03020.0517-0.1092-0.05960.00540.060.00215.0774-18.8424-8.0487
142.38850.35721.2690.9729-0.52551.68870.2122-0.3232-0.21550.1683-0.1018-0.16630.2674-0.1111-0.11050.1543-0.0876-0.2215-0.08350.07240.013637.3666-20.55514.6827
151.4625-0.64121.03921.2457-0.20260.95860.051-0.1411-0.04590.2532-0.0314-0.07910.0309-0.1388-0.01960.0303-0.0966-0.0788-0.04610.0524-0.07720.7972-11.5122-2.7914
161.53130.34890.25771.6492-0.62770.0464-0.062-0.19820.05750.1681-0.01040.0397-0.1353-0.19110.0724-0.0214-0.03090.01960.0374-0.0255-0.0986-3.8207-4.5082-16.308
170.5335-0.09940.02710.8585-0.03390.23220.0641-0.0054-0.08250.1348-0.0778-0.130.0577-0.01850.0136-0.0023-0.0497-0.0785-0.04920.0267-0.025225.4175-14.0619-15.9233
181.74390.21281.47831.27080.02411.468-0.00720.07740.01160.0602-0.0544-0.25070.04320.06990.06160.0643-0.0684-0.2095-0.06740.11290.071549.208-19.19397.6635
190.39043.1766-0.95433.3122-2.42823.1093-0.2263-0.12350.27560.4762-0.1958-0.3004-0.36080.42380.42210.0412-0.0091-0.2284-0.10830.07990.004158.8142-16.325821.8451
200-4.52235.66630.25550.9324.1165-0.1124-0.1948-0.02680.0240.20070.17720.3378-0.1397-0.08830.0666-0.0833-0.1977-0.10690.0863-0.059843.2837-18.549517.7963
212.5667-0.4950.6172.8921-0.86921.1951-0.0306-0.17110.32670.3168-0.05370.0254-0.23370.00520.08440.0566-0.0025-0.0742-0.0377-0.02990.001731.500135.3954-16.5477
220.3381-0.35820.27261.0655-0.59251.58430.00030.0350.01290.00790.0061-0.363-0.10510.0963-0.0064-0.0595-0.0311-0.0343-0.07170.02080.098147.023830.3607-30.0622
230.0699-0.3032-0.18140.49-0.04760.05510.0019-0.00350.06280.1024-0.022-0.1956-0.07660.00010.0201-0.0258-0.0216-0.0532-0.06460.0190.041938.646929.0713-27.3013
240.5425-0.07540.15831.5052-0.46790.30830.0525-0.0074-0.08290.1131-0.059-0.40280.05240.05570.0065-0.0419-0.0046-0.0836-0.0850.02630.145754.1361-9.3006-24.1676
252.9633-0.5959-0.02540.53220.135600.05770.05460.0188-0.0344-0.0313-0.13370.0191-0.0487-0.0265-0.0857-0.00190.0107-0.10640.02310.026142.934122.2553-41.0968
260.33990.11990.05460.5267-0.08380.33470.0394-0.0284-0.07320.1529-0.0521-0.25540.00230.02880.0127-0.0339-0.0306-0.0915-0.08990.02650.04544.8861-0.0973-17.7534
270.92171.63561.63632.42880.84572.39710.0701-0.0888-0.03160.1501-0.1121-0.35730.17780.03830.042-0.06750.017-0.1382-0.17630.05970.24352.7172-37.2514-17.955
2800.4674-2.60431.6234-0.27020.3440.0436-0.1558-0.02950.2936-0.0442-0.2540.0027-0.16560.0006-0.0859-0.0577-0.2672-0.0520.12870.104552.2982-42.5851-10.2351
297.3761-1.97311.80613.7532-2.25540.27970.0008-0.2655-0.31650.1010.1777-0.38420.35050.067-0.1785-0.1057-0.0138-0.1877-0.28820.08740.363158.4715-47.9327-19.943
300.46340.39720.51691.34810.93130.6737-0.06330.1635-0.22980.00070.0708-0.0574-0.11530.4514-0.0075-0.1470.0101-0.1045-0.21620.02410.237361.8535-31.9582-23.8095
311.2181-0.85560.8654.907-0.21081.12870.02150.0968-0.31070.2846-0.001-0.18580.3-0.1377-0.02050.0271-0.0596-0.0625-0.08840.0190.063627.4602-39.1958-23.6003
321.8414-1.1749-0.12590.01032.36110.0617-0.02010.1473-0.013-0.09250.06480.1095-0.1958-0.0938-0.0447-0.0015-0.003-0.0318-0.0955-0.0070.021527.6819-23.4759-35.6448
332.7153-1.6537-0.40591.19440.22230-0.07780.2616-0.2827-0.1332-0.0863-0.15890.1373-0.02640.16410.0487-0.02770.0187-0.0381-0.02270.127440.5173-35.6401-42.102
340.2576-0.0696-0.020.8117-0.00980.09470.0060.0551-0.0652-0.0286-0.0047-0.16140.0413-0.0243-0.0014-0.0502-0.0134-0.0052-0.0663-0.0071-0.018231.6473-11.154-38.9383
350.0506-0.40240.20071.3505-1.02871.1926-0.06970.0171-0.07020.1427-0.103-0.3681-0.02570.09920.1728-0.0193-0.0003-0.0021-0.05590.00180.187348.3716-24.2277-38.6327
360.55070.04730.00660.6480.04450.26360.01890.0088-0.03710.036-0.0177-0.09610.0348-0.0377-0.0012-0.0276-0.0231-0.0168-0.04680.0059-0.024625.2729-3.3482-32.522
371.1165-0.77590.4930.8175-0.80230.0815-0.0034-0.0206-0.13290.02260.0604-0.03360.0735-0.0521-0.05690.0067-0.01420.0048-0.0302-0.01650.028123.9115-8.4448-39.314
381.0450.47430.67262.44290.63990.8673-0.1245-0.11890.1592-0.1857-0.03780.1282-0.1356-0.1840.1623-0.020.0389-0.01490.01390.0136-0.042417.986330.1889-42.0068
394.621-2.22621.44834.21921.95597.2247-0.2429-0.15950.6036-0.4677-0.0735-0.4403-0.9707-0.690.31640.03510.1144-0.159-0.1057-0.061-0.014220.813744.4547-45.8164
402.23994.30930.40551.8172-0.24951.9574-0.10170.23260.101-0.4314-0.01220.0426-0.11860.03420.11390.0194-0.010.0274-0.05990.0409-0.05326.122128.2812-52.4063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 9-24
2X-RAY DIFFRACTION2CHAIN A AND RESID 25-44
3X-RAY DIFFRACTION3CHAIN A AND RESID 45-91
4X-RAY DIFFRACTION4CHAIN A AND RESID 92-152
5X-RAY DIFFRACTION5CHAIN A AND RESID 153-260
6X-RAY DIFFRACTION6CHAIN A AND RESID 261-368
7X-RAY DIFFRACTION7CHAIN A AND RESID 369-392
8X-RAY DIFFRACTION8CHAIN A AND RESID 393-404
9X-RAY DIFFRACTION9CHAIN A AND RESID 405-429
10X-RAY DIFFRACTION10CHAIN A AND RESID 430-468
11X-RAY DIFFRACTION11CHAIN B AND RESID 9-19
12X-RAY DIFFRACTION12CHAIN B AND RESID 20-152
13X-RAY DIFFRACTION13CHAIN B AND RESID 153-166
14X-RAY DIFFRACTION14CHAIN B AND RESID 167-198
15X-RAY DIFFRACTION15CHAIN B AND RESID 199-222
16X-RAY DIFFRACTION16CHAIN B AND RESID 223-259
17X-RAY DIFFRACTION17CHAIN B AND RESID 260-384
18X-RAY DIFFRACTION18CHAIN B AND RESID 385-433
19X-RAY DIFFRACTION19CHAIN B AND RESID 434-455
20X-RAY DIFFRACTION20CHAIN B AND RESID 456-468
21X-RAY DIFFRACTION21CHAIN C AND RESID 9-44
22X-RAY DIFFRACTION22CHAIN C AND RESID 45-92
23X-RAY DIFFRACTION23CHAIN C AND RESID 93-153
24X-RAY DIFFRACTION24CHAIN C AND RESID 154-222
25X-RAY DIFFRACTION25CHAIN C AND RESID 223-259
26X-RAY DIFFRACTION26CHAIN C AND RESID 260-397
27X-RAY DIFFRACTION27CHAIN C AND RESID 398-425
28X-RAY DIFFRACTION28CHAIN C AND RESID 426-436
29X-RAY DIFFRACTION29CHAIN C AND RESID 437-455
30X-RAY DIFFRACTION30CHAIN C AND RESID 456-468
31X-RAY DIFFRACTION31CHAIN D AND RESID 9-43
32X-RAY DIFFRACTION32CHAIN D AND RESID 44-52
33X-RAY DIFFRACTION33CHAIN D AND RESID 53-90
34X-RAY DIFFRACTION34CHAIN D AND RESID 91-222
35X-RAY DIFFRACTION35CHAIN D AND RESID 223-259
36X-RAY DIFFRACTION36CHAIN D AND RESID 260-366
37X-RAY DIFFRACTION37CHAIN D AND RESID 367-386
38X-RAY DIFFRACTION38CHAIN D AND RESID 387-433
39X-RAY DIFFRACTION39CHAIN D AND RESID 434-455
40X-RAY DIFFRACTION40CHAIN D AND RESID 456-470

+
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