[English] 日本語
Yorodumi
- PDB-6qcl: Citryl-CoA lyase core module of Chlorobium limicola ATP citrate l... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qcl
TitleCitryl-CoA lyase core module of Chlorobium limicola ATP citrate lyase in complex with acetyl-CoA and L-malate
ComponentsATP-citrate lyase alpha-subunit
KeywordsLYASE / ATP citrate lyase / central metabolism / acetyl-Coa / citrate shuttle / rTCA cycle / citryl-CoA / lipogenesis
Function / homology
Function and homology information


acyltransferase activity, acyl groups converted into alkyl on transfer / citrate synthase (unknown stereospecificity) / tricarboxylic acid cycle / lipid metabolic process / lyase activity / ATP binding / cytoplasm
Similarity search - Function
ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / Citrate synthase-like, large alpha subdomain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily ...ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / Citrate synthase-like, large alpha subdomain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / (2S)-2-hydroxybutanedioic acid / TRIETHYLENE GLYCOL / citrate synthase (unknown stereospecificity)
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVerstraete, K. / Verschueren, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders1524918N Belgium
CitationJournal: Nature / Year: 2019
Title: Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.
Authors: Verschueren, K.H.G. / Blanchet, C. / Felix, J. / Dansercoer, A. / De Vos, D. / Bloch, Y. / Van Beeumen, J. / Svergun, D. / Gutsche, I. / Savvides, S.N. / Verstraete, K.
History
DepositionDec 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-citrate lyase alpha-subunit
B: ATP-citrate lyase alpha-subunit
C: ATP-citrate lyase alpha-subunit
D: ATP-citrate lyase alpha-subunit
E: ATP-citrate lyase alpha-subunit
F: ATP-citrate lyase alpha-subunit
G: ATP-citrate lyase alpha-subunit
H: ATP-citrate lyase alpha-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,47422
Polymers230,9308
Non-polymers4,54414
Water19,2041066
1
A: ATP-citrate lyase alpha-subunit
C: ATP-citrate lyase alpha-subunit
E: ATP-citrate lyase alpha-subunit
G: ATP-citrate lyase alpha-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,73711
Polymers115,4654
Non-polymers2,2727
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31350 Å2
ΔGint-191 kcal/mol
Surface area35390 Å2
MethodPISA
2
B: ATP-citrate lyase alpha-subunit
D: ATP-citrate lyase alpha-subunit
F: ATP-citrate lyase alpha-subunit
H: ATP-citrate lyase alpha-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,73711
Polymers115,4654
Non-polymers2,2727
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31350 Å2
ΔGint-191 kcal/mol
Surface area36010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.730, 100.817, 105.012
Angle α, β, γ (deg.)90.00, 102.99, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
ATP-citrate lyase alpha-subunit


Mass: 28866.275 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Prior the crystallization, the N-terminal sequence MGSSHHHHHHSSGLVPR was removed by thrombin cleavage.
Source: (gene. exp.) Chlorobium limicola (bacteria) / Gene: aclA / Plasmid: pET15b / Details (production host): N-terminal cleavable His-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9AJC4

-
Non-polymers , 6 types, 1080 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1066 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.1
Details: 0.2 M Calcium chloride 20% PEG 3350 pH 5.1 Protein buffer: 20 mM HEPES, pH 7.4 150 mM NaCl 10 mM acetyl-CoA 50 mM L-Malate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.6→45.62 Å / Num. obs: 270869 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 20.51 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.126 / Net I/σ(I): 11.86
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 43070 / CC1/2: 0.552 / Rrim(I) all: 0.1462 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6hxj
Resolution: 1.6→45.62 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.177 13820 5.1 %RANDOM
Rwork0.157 ---
obs0.158 270868 98.8 %-
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.1731 Å20 Å2-0.5593 Å2
2--2.1299 Å20 Å2
3---1.0432 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: 1 / Resolution: 1.6→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15543 0 288 1066 16897
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132410HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0158788HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7204SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes374HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4754HARMONIC5
X-RAY DIFFRACTIONt_it32410HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion14.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2140SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies33HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact36965SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 984 5.05 %
Rwork0.2117 18497 -
all0.2121 19481 -
obs--96.38 %
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)
11.38350.1276-0.05690.359-0.70972.37680.0601-0.004-0.10370.0204-0.10260.0610.0482-0.16970.0424-0.0706-0.0179-0.0124-0.0036-0.0266-0.0065-28.281748.0354-59.7111
21.34580.55150.42711.57610.07820.8456-0.08270.19760.0505-0.2225-0.02630.237-0.1126-0.1350.109-0.02210.0168-0.04810.0462-0.02180.0004-26.333356.9211-72.0758
31.03830.46930.10390.92550.23060.2981-0.03560.10850.1043-0.1179-0.0040.1536-0.0647-0.01420.0397-0.05910.0078-0.0187-0.04810.005-0.0764-11.445968.6508-64.0303
45.8161-2.18772.27710.68120.26262.24610.0913-0.18-0.0874-0.3831-0.4770.5407-0.5311-0.59920.3856-0.00010.184-0.13190.0558-0.15350.1131-27.352879.4325-59.0061
53.1175-1.9252-2.02832.93152.92786.0727-0.14630.17221.3985-0.18290.1196-0.0995-0.4482-0.23990.0267-0.13140.066-0.2457-0.23730.05540.2676-28.110381.2117-74.416
63.480.02191.62181.29620.31891.099-0.143-0.29550.22-0.12380.00120.2649-0.1854-0.15340.1419-0.07020.0337-0.0328-0.0663-0.0036-0.0561-17.866769.7188-64.6343
70.10120.16350.42531.72111.86251.6285-0.03470.05790.04360.11780.1386-0.0967-0.08220.2282-0.1040.0176-0.0280.00650.02510.0043-0.01097.626175.5185-53.9732
81.46730.58271.86632.05610.74821.12030.0871-0.2120.09050.1475-0.09520.03540.1126-0.26740.0081-0.019-0.03040.0208-0.0133-0.0189-0.03674.357783.9406-29.9007
90.5337-0.0885-0.12360.85290.36620.9078-0.06040.0036-0.11970.1395-0.10730.26160.2234-0.23350.1677-0.0625-0.05850.0684-0.0523-0.0555-0.0351-38.04977.2717-2.4092
101.61180.3132-0.04260.88810.1830.4097-0.10220.1291-0.02990.09640.02120.19140.0918-0.0660.081-0.0285-0.02510.0404-0.0197-0.0225-0.0216-32.72188.8599-1.2326
111.1953-1.002-0.95910.62060.77060.73260.0175-0.02320.03390.03690.0507-0.07890.03970.0522-0.06820.00590.0160.0164-0.01540.0039-0.0148-0.899-1.0317-11.0066
120.4420.29650.06480.8768-0.0070.27380.0574-0.03660.06560.1368-0.04830.0021-0.02430.0172-0.0091-0.0237-0.01320.009-0.0499-0.0082-0.0599-4.112270.9695-34.2728
130.9472-2.3326-2.08117.41313.67364.0774-0.1245-0.32560.27720.18140.15760.0271-0.5315-0.5187-0.03310.02860.1739-0.00130.1082-0.0967-0.0264-25.642874.0972-32.7647
144.6496-2.7965-0.34243.294-0.25513.86290.44640.221-0.6014-0.0479-0.44110.9198-0.2446-0.7337-0.0053-0.180.06470.0196-0.0652-0.1744-0.0574-28.388670.3564-22.5272
150.49850.05720.07180.56760.27530.69280.03080.0262-0.0130.0687-0.04290.08010.0364-0.1170.0121-0.0569-0.01060.0098-0.03460.0028-0.059-18.028853.5915-47.6566
160.3866-0.1053-0.04390.6594-0.03490.34350.01060.0098-0.0435-0.034-0.0188-0.0640.04180.04680.0083-0.02020.00990.0201-0.0241-0.0048-0.0216-6.35197.8864-22.0603
170.40850.34790.47944.77694.20154.8719-0.04080.1105-0.12780.12730.1379-0.03190.1426-0.0621-0.0972-0.0552-0.04380.00550.063-0.0358-0.0187-24.56564.7721-33.3526
186.21081.8272-0.62542.5357-0.51131.8494-0.07140.26130.4343-0.19810.11180.4381-0.0188-0.2653-0.0404-0.13420.0057-0.0268-0.0307-0.0116-0.1131-22.44329.4464-44.2566
190.2430.3480.01271.25830.73521.3058-0.04930.14280.0582-0.0105-0.00860.2030.0384-0.14580.0579-0.0882-0.0099-0.0014-0.0024-0.0127-0.0453-18.064911.5393-35.2249
201.4871-0.1175-0.52830.77880.10710.6321-0.0615-0.05420.1222-0.1256-0.01780.2578-0.1094-0.17760.0794-0.04980.0488-0.01760.0189-0.03790.0095-35.83532.1116-9.7418
211.51631.13931.25143.72341.56964.43450.0141-0.09070.08130.0596-0.03650.23880.0668-0.26130.0224-0.003-0.04860.0011-0.06220.0261-0.0836-15.658747.9037-30.2341
221.40860.7014-0.09051.536-0.10691.20640.1264-0.16290.02570.3657-0.1109-0.02430.12140.0107-0.01540.1024-0.0355-0.0236-0.01720.0167-0.0725-5.77756.027-22.6706
232.42210.48730.12274.4198-2.82664.18690.1731-0.1597-0.23610.3617-0.1828-0.12030.05580.14170.00970.0677-0.026-0.0338-0.03970.0163-0.06985.077362.9849-25.1365
240.64150.03290.13230.58560.09780.52520.01610.0180.07610.0047-0.03140.0253-0.0365-0.01990.0152-0.01240.00010.0027-0.02570.0012-0.0325-5.326372.9166-45.5751
252.3509-0.98691.25282.1657-0.79631.54980.08130.1656-0.2935-0.01970.0242-0.09060.14350.0899-0.1055-0.00210.011-0.0075-0.0117-0.02520.007810.607154.7462-42.6199
265.6144-1.2867-2.40537.5661-0.6883-0.8909-0.04110.2063-0.4678-0.21540.1209-0.72520.22830.4977-0.0797-0.07880.03420.04830.0469-0.10940.068322.661950.462-46.9
270.7325-1.2454-1.08821.0483-0.74882.2492-0.02350.09830.0164-0.0667-0.1041-0.0721-0.30050.22950.1276-0.0153-0.0683-0.0316-0.02240.0227-0.054816.687267.4993-44.5114
281.86490.90211.1794.49720.38125.45750.1024-0.1761-0.06750.5375-0.1378-0.3315-0.0123-0.07160.03540.0095-0.034-0.0768-0.03690.0298-0.071415.290663.3645-27.237
291.0646-0.00190.15370.90920.05810.4620.049-0.0044-0.06330.0852-0.0281-0.1002-0.02250.083-0.0209-0.0393-0.018-0.0142-0.03640.0023-0.07519.050762.7926-37.8832
300.69370.1027-0.15610.0178-0.3440.77540.04430.27460.3272-0.19330.1986-0.0514-0.24660.0005-0.24290.066-0.0452-0.00460.07060.0628-0.0296-3.69879.7662-66.2416
311.6084-1.4494-0.89082.47440.87831.49770.06130.1178-0.0327-0.1724-0.03230.059-0.2055-0.0221-0.02910.02550.00070.0502-0.05520.024-0.0479-12.006328.3513-33.0849
320.4254-0.0767-0.01120.36920.02810.58460.0057-0.00490.032-0.02110.0092-0.1071-0.0590.078-0.0149-0.0141-0.00670.0319-0.0253-0.0166-0.0124-3.053416.2764-17.179
335.0459-0.0941-2.18155.22620.60553.1239-0.2398-0.62830.00381.04580.2097-0.00170.14960.46140.03010.0180.1103-0.0087-0.02130.0416-0.150610.004519.4223-0.821
341.0720.47950.20161.18520.10110.5403-0.0305-0.0066-0.0101-0.00850.0088-0.1405-0.00630.10810.0217-0.0650.00830.0329-0.039-0.0068-0.05586.157915.965-14.2526
350.2813-0.01710.16990.7195-0.31151.9402-0.0574-0.1376-0.1070.36720.17510.07420.3857-0.174-0.11770.05050.00640.05240.01050.0373-0.057-20.6454-1.31866.5858
362.71831.6271.82661.79661.29942.0577-0.15730.36160.4865-0.26030.06420.2065-0.27380.12530.09310.0001-0.0363-0.0123-0.00220.0719-0.0337-2.892177.4513-71.0691
370.18920.98020.04371.86990.47031.6142-0.14210.1629-0.0017-0.31690.1448-0.0065-0.1180.1336-0.0028-0.01930.0085-0.01650.04160.002-0.0699-9.904959.8568-76.4108
380.5738-0.2411-0.22150.65060.26280.4269-0.01010.0446-0.0337-0.0136-0.02140.01770.0285-0.01710.0315-0.04050.0073-0.0022-0.0127-0.0059-0.0414-8.694747.0187-64.3957
39-0.1317-0.22140.48160.8814-0.79292.41150.0784-0.2061-0.08210.25460.00690.09690.0751-0.2565-0.08530.0431-0.04840.0238-0.00130.0142-0.0287-19.343549.9047-32.2853
403.6786-1.4948-0.79821.14410.56030.7026-0.1189-0.3111-0.36040.32810.0740.13850.2773-0.00820.0450.08390.01690.0549-0.0410.0484-0.0487-22.24511.00311.1997
410.9654-0.7177-0.81381.48370.76531.6186-0.1514-0.1693-0.06530.34690.06950.16020.2078-0.030.082-0.0122-0.00790.0519-0.0039-0.0258-0.0841-30.789618.441913.1108
420.3724-0.036-0.05810.80770.41530.4642-0.01270.04860.0066-0.0915-0.06170.0903-0.0439-0.07810.0745-0.02320.00410.00070.0051-0.0189-0.0147-28.392120.8643-11.9906
430.5810.6981.01491.0511.13221.74860.0325-0.0029-0.07510.08210.0107-0.13520.060.0329-0.0433-0.0011-0.0019-0.0019-0.0031-0.0206-0.0076-16.500131.15226.3216
442.0231-0.0371.52013.2531.8037.8485-0.0340.1202-0.0095-0.11570.046-0.0868-0.10770.2271-0.0119-0.0361-0.0266-0.0065-0.026-0.0036-0.0309-10.444142.99449.6162
451.88260.593-0.89250.41160.19941.53310.0028-0.16980.02050.032-0.0860.1046-0.0397-0.07770.0832-0.01430.01980.0107-0.0239-0.0389-0.0255-29.238936.78156.9863
463.21461.10880.07451.6388-0.25593.7876-0.1005-0.12570.17750.0912-0.06960.047-0.3305-0.10670.17010.00520.0097-0.0262-0.0183-0.0415-0.0101-22.080342.914210.8445
470.46850.0160.1991.09410.71510.7448-0.0034-0.0131-0.01250.0484-0.03280.07880.0128-0.07010.0362-0.0315-0.00640.0147-0.011-0.016-0.0382-26.919826.09672.1986
480.50410.5861-1.30930.8742-0.45591.87810.03670.22060.1252-0.24460.017-0.0443-0.1387-0.0769-0.05370.06920.0321-0.004-0.02730.021-0.0204-19.201429.0563-30.3566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|351 - A|373 }
2X-RAY DIFFRACTION2{ A|374 - A|398 }
3X-RAY DIFFRACTION3{ A|399 - A|445 }
4X-RAY DIFFRACTION4{ A|446 - A|467 }
5X-RAY DIFFRACTION5{ A|468 - A|542 }
6X-RAY DIFFRACTION6{ A|543 - A|581 }
7X-RAY DIFFRACTION7{ A|582 - A|593 }
8X-RAY DIFFRACTION8{ A|594 - A|607 }
9X-RAY DIFFRACTION9{ B|352 - B|542 }
10X-RAY DIFFRACTION10{ B|543 - B|581 }
11X-RAY DIFFRACTION11{ B|582 - B|607 }
12X-RAY DIFFRACTION12{ C|347 - C|445 }
13X-RAY DIFFRACTION13{ C|446 - C|467 }
14X-RAY DIFFRACTION14{ C|468 - C|556 }
15X-RAY DIFFRACTION15{ C|557 - C|607 }
16X-RAY DIFFRACTION16{ D|347 - D|445 }
17X-RAY DIFFRACTION17{ D|446 - D|467 }
18X-RAY DIFFRACTION18{ D|468 - D|518 }
19X-RAY DIFFRACTION19{ D|519 - D|581 }
20X-RAY DIFFRACTION20{ D|582 - D|607 }
21X-RAY DIFFRACTION21{ E|352 - E|373 }
22X-RAY DIFFRACTION22{ E|374 - E|398 }
23X-RAY DIFFRACTION23{ E|399 - E|412 }
24X-RAY DIFFRACTION24{ E|413 - E|445 }
25X-RAY DIFFRACTION25{ E|446 - E|467 }
26X-RAY DIFFRACTION26{ E|468 - E|482 }
27X-RAY DIFFRACTION27{ E|483 - E|500 }
28X-RAY DIFFRACTION28{ E|501 - E|518 }
29X-RAY DIFFRACTION29{ E|519 - E|581 }
30X-RAY DIFFRACTION30{ E|582 - E|607 }
31X-RAY DIFFRACTION31{ F|352 - F|383 }
32X-RAY DIFFRACTION32{ F|384 - F|467 }
33X-RAY DIFFRACTION33{ F|468 - F|500 }
34X-RAY DIFFRACTION34{ F|501 - F|581 }
35X-RAY DIFFRACTION35{ F|582 - F|607 }
36X-RAY DIFFRACTION36{ G|347 - G|383 }
37X-RAY DIFFRACTION37{ G|384 - G|412 }
38X-RAY DIFFRACTION38{ G|413 - G|581 }
39X-RAY DIFFRACTION39{ G|582 - G|607 }
40X-RAY DIFFRACTION40{ H|347 - H|383 }
41X-RAY DIFFRACTION41{ H|384 - H|412 }
42X-RAY DIFFRACTION42{ H|413 - H|445 }
43X-RAY DIFFRACTION43{ H|446 - H|467 }
44X-RAY DIFFRACTION44{ H|468 - H|482 }
45X-RAY DIFFRACTION45{ H|483 - H|518 }
46X-RAY DIFFRACTION46{ H|519 - H|534 }
47X-RAY DIFFRACTION47{ H|535 - H|581 }
48X-RAY DIFFRACTION48{ H|582 - H|607 }

+
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