[English] 日本語
Yorodumi
- PDB-3ro6: Crystal structure of Dipeptide Epimerase from Methylococcus capsu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ro6
TitleCrystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion
ComponentsPutative chloromuconate cycloisomerase
KeywordsISOMERASE / TIM barrel
Function / homology
Function and homology information


catechol-containing compound catabolic process / chloromuconate cycloisomerase activity / racemase and epimerase activity / racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / peptide metabolic process / amino acid catabolic process / magnesium ion binding
Similarity search - Function
Dipeptide epimerase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain ...Dipeptide epimerase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-Lys-D/L-Arg epimerase
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLukk, T. / Sakai, A. / Song, L. / Gerlt, J.A. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / ...Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / Nair, S.K. / Babbitt, P.C. / Almo, S.C. / Gerlt, J.A. / Jacobson, M.P.
History
DepositionApr 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Mar 14, 2012Group: Database references
Revision 1.4Mar 21, 2012Group: Database references
Revision 1.5Mar 28, 2012Group: Database references
Revision 1.6Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.7Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr2_auth_asym_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Putative chloromuconate cycloisomerase
A: Putative chloromuconate cycloisomerase
C: Putative chloromuconate cycloisomerase
D: Putative chloromuconate cycloisomerase
E: Putative chloromuconate cycloisomerase
F: Putative chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,13227
Polymers234,5536
Non-polymers1,57921
Water9,620534
1
B: Putative chloromuconate cycloisomerase
C: Putative chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7099
Polymers78,1842
Non-polymers5257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-92 kcal/mol
Surface area26020 Å2
MethodPISA
2
A: Putative chloromuconate cycloisomerase
hetero molecules

F: Putative chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7139
Polymers78,1842
Non-polymers5297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3300 Å2
ΔGint-71 kcal/mol
Surface area25890 Å2
MethodPISA
3
D: Putative chloromuconate cycloisomerase
E: Putative chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7099
Polymers78,1842
Non-polymers5257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-58 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.190, 150.670, 106.020
Angle α, β, γ (deg.)90.000, 104.660, 90.000
Int Tables number4
Space group name H-MP1211
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

-
Components

#1: Protein
Putative chloromuconate cycloisomerase / isomerase / dipeptide epimerase


Mass: 39092.113 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Strain: Bath / Gene: MCA1834 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q607C7
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Precipitant contained 10% PEG 4000, 0.2M MgSO4 and 0.1M MES. Protein solution contained 0.1M KCl, 0.05M HEPES (pH 8.0), 0.005M L-Arg-L-Lys, and 0.005M MgCl2. Protein concentration was 10 ...Details: Precipitant contained 10% PEG 4000, 0.2M MgSO4 and 0.1M MES. Protein solution contained 0.1M KCl, 0.05M HEPES (pH 8.0), 0.005M L-Arg-L-Lys, and 0.005M MgCl2. Protein concentration was 10 mg/mL, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 31, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→19.9 Å / Num. all: 121739 / Num. obs: 121455 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.315 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.240.6083.45376406336100
2.24-2.280.5623.7235335595299.9
2.28-2.320.5253.93330125546100
2.32-2.370.4754.3737992638599.9
2.37-2.420.4055.03352235919100
2.42-2.480.385.27384196445100
2.48-2.540.3345.8934984585499.9
2.54-2.610.2916.63368556183100
2.61-2.680.2587.3833118555899.9
2.68-2.770.2278.29376776313100
2.77-2.870.1859.85367756173100
2.87-2.980.15611.5334608579699.8
2.98-3.120.12713.41376586328100
3.12-3.490.09617.04721841218799.9
3.49-3.760.06822.4236161611699.9
3.76-4.130.05725.6534993598399.8
4.13-4.720.0528.835677608199.8
4.72-5.920.04828.8436043612999.9
5.920.04231.3835628617196.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXdev_721refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.895 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8545 / SU ML: 0.69 / σ(F): 2 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 6073 5 %random
Rwork0.1744 ---
all0.207 121430 --
obs0.1771 121424 99.96 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.944 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 201.31 Å2 / Biso mean: 29.0025 Å2 / Biso min: 3.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.3527 Å20 Å2-0.5126 Å2
2--0.7574 Å20 Å2
3----0.4047 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15827 0 83 534 16444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816272
X-RAY DIFFRACTIONf_angle_d1.26422066
X-RAY DIFFRACTIONf_chiral_restr0.0952536
X-RAY DIFFRACTIONf_plane_restr0.0072904
X-RAY DIFFRACTIONf_dihedral_angle_d13.7086152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.2250.31542000.225538104010
2.225-2.25110.2892020.206638394041
2.2511-2.27850.29252010.211338234024
2.2785-2.30730.28342020.215938404042
2.3073-2.33760.25522020.197938254027
2.3376-2.36960.30482010.209838184019
2.3696-2.40340.25922050.194238974102
2.4034-2.43920.25721990.19337743973
2.4392-2.47730.29032030.195338654068
2.4773-2.51780.2552010.194138124013
2.5178-2.56110.26962040.196238774081
2.5611-2.60760.26392000.187938124012
2.6076-2.65760.24412030.193738524055
2.6576-2.71180.2622020.19538374039
2.7118-2.77060.25722010.190238114012
2.7706-2.83490.26442050.184339054110
2.8349-2.90550.23032010.179638034004
2.9055-2.98380.23842010.189338194020
2.9838-3.07130.27452030.186438564059
3.0713-3.17010.22962040.182538814085
3.1701-3.28290.24492020.180538454047
3.2829-3.41370.20912030.167738434046
3.4137-3.56830.22142010.165238174018
3.5683-3.75520.1972030.166138574060
3.7552-3.98870.18822040.157238754079
3.9887-4.29380.18972010.139638294030
4.2938-4.72070.18172040.136838684072
4.7207-5.39190.21042030.14838624065
5.3919-6.74880.23282050.184738844089
6.7488-19.8960.16912070.155339154122
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)
10.0617-0.02880.0040.054-0.03990.0361-0.0184-0.05090.06290.08080.0004-0.04150.0058-0.0162-0.02090.148-0.0317-0.00990.1171-0.07160.14210.656511.207149.7366
20.0025-0.0012-0.00060.0019-0.00170.0029-0.0384-0.03220.00990.0315-0.0034-0.00380.0438-0.0075-00.19360.0264-0.00980.2326-0.05430.134812.8055-3.929952.7761
30.00790.00350.00050.00560.00350.0027-0.003-0.03060.023-0.0008-0.0161-0.0219-0.01220.034600.1666-0.00210.00380.1473-0.02870.188523.57055.86541.0828
40.27850.09970.05750.03790.01920.1532-0.0373-0.01860.11890.01970.02090.0735-0.07480.037-0.04790.11530.00820.02580.07420.00150.09024.37945.304536.8315
50.02890.0143-0.00280.01570.00610.0099-0.0201-0.0848-0.04250.0234-0.0130.0451-0.0493-0.035-0.0140.1960.05030.07990.18710.00470.1918-15.4843-7.340846.4794
60.0107-0.0189-0.01430.04030.03130.021-0.0192-0.0216-0.10180.0330.02340.12220.0217-0.02140.06420.06120.02510.04370.04720.00960.1955-10.6684-18.738741.0477
70.00380.00220.00160.0078-0.00480.00350.01890.01730.0068-0.0069-0.0213-0.0124-0.0728-0.0385-00.090.02030.00440.1137-0.00650.1314.7107-19.058433.226
80.03330.0121-0.0010.00430.00010.0041-0.0110.06190.001-0.06170.0063-0.0623-0.0066-0.00380.00030.14060.02440.01580.0705-0.01170.10668.9015-5.370333.6035
90.03320.0066-0.00110.0032-0.01090.0844-0.0205-0.02320.01730.04490.01630.0187-0.012-0.00720.00310.08020.01610.01410.0436-0.03210.0997-0.04570.68639.0282
100.05410.0394-0.00760.0299-0.00690.0197-0.0103-0.00040.04740.06470.05340.0513-0.107-0.0110.00530.17970.04350.01840.1163-0.05190.2223-2.568812.406939.2929
110.1029-0.0481-0.02950.04150.0440.06710.01150.0467-0.14170.02270.0017-0.01330.0186-0.00160.0610.10010.0065-0.0090.0457-0.03240.129-37.2810.341157.1977
120.0632-0.0166-0.06230.08870.11570.1554-0.00560.0075-0.08040.0150.1298-0.11920.06140.20350.5275-0.04140.10840.12020.0776-0.1306-0.0018-20.388724.924967.769
130.1252-0.04480.05780.0423-0.00940.0328-0.01420.11980.0621-0.07520.03860.01450.0293-0.05170.02050.1941-0.02270.03510.13750.06660.143820.19978.04853.0133
140.0066-0.00730.00050.0076-0.00030.0043-0.02350.04210.05960.00820.01460.0293-0.0347-0.0372-00.17250.00770.0360.13340.0570.15557.38548.460512.7646
150.1203-0.0068-0.01130.0122-0.04630.2043-0.041-0.02210.12860.01410.0506-0.0386-0.1010.0262-0.02940.1269-0.01470.01590.1020.00320.135526.29514.915516.857
160.02620.01680.010.02240.0110.0050.00290.0438-0.0277-0.04320.0375-0.0923-0.01260.03980.17780.0678-0.01680.14530.1189-0.06960.27239.9044-17.09388.9014
170.0091-0.0087-0.00780.01270.02560.07430.0268-0.047-0.0298-0.0136-0.0298-0.0178-0.0482-0.0055-0.00220.1024-0.02870.02070.08390.01280.134522.5287-19.337217.7934
180.0057-0.0006-0.00430.00330.00250.0042-0.0076-0.00810.02970.05020.0413-0.0272-0.0101-0.0099-00.1564-0.01080.02330.09710.01170.159220.2972-5.369119.041
190.0182-0.01450.00310.01280.00030.0028-0.00360.03460.0854-0.01790.0122-0.0734-0.001-0.008200.1385-0.03130.02090.110.02480.179230.0824-0.105514.2038
200.0288-0.00210.00260.00850.01850.04450.00580.02840.022-0.01220.0289-0.0173-0.06090.02140.01140.1445-0.05190.05620.10410.01830.263834.023911.43514.8529
210.0214-0.02730.00960.0399-0.01230.02630.02080.0066-0.033-0.0363-0.01130.01740.01080.00430.02370.17170.0081-0.07420.06310.08050.1652-14.07138.5373-2.6978
220.0278-0.02370.02380.07280.03640.0943-0.0058-0.0774-0.06650.08860.00450.02480.0503-0.0649-0.04670.11680.0020.01480.1270.06580.1029-13.717919.5511.1902
230.03020.022-0.03160.0223-0.02210.04950.0262-0.0234-0.03660.00010.03890.07180.0389-0.13090.25960.0292-0.0610.00040.2090.09520.0897-36.70422.6582-22.2774
240.0033-0.00330.00240.0032-0.00030.00850.0355-0.00360.03190.02870.00270.0857-0.03490.0131-00.09580.00320.01250.11490.03610.1113-20.87634.0299-20.0022
250.0379-0.00960.00560.0062-0.00360.00330.0155-0.031-0.03050.01790.01550.04480.0198-0.0620.14040.1023-0.02110.02880.11610.07830.0864-23.259723.5483-5.64
260.0510.05650.02780.12040.0970.09310.0318-0.0351-0.03630.0844-0.0341-0.03230.0662-0.05640.0880.2114-0.07170.01250.30330.13720.231-29.709415.04315.5046
270.05620.03560.03420.05020.01660.0273-0.0389-0.08480.0323-0.0076-0.01250.0216-0.0584-0.0231-0.1460.3109-0.00180.06850.2267-0.0590.0662-12.124851.392618.7141
280.01320.00480.00410.0069-0.00130.0034-0.0037-0.0212-0.00240.0229-0.00190.01980.0054-0.014-0.03810.0966-0.01160.07890.13660.02390.0496-23.136641.541913.7171
290.0278-0.0223-0.00230.0545-0.03110.0331-0.0529-0.15090.02650.16850.0155-0.04240.02490.0252-0.00290.17340.00990.03950.12560.0060.1217-3.544640.929911.0208
300.0270.026-0.03070.0256-0.02960.03560.0284-0.03010.04910.0318-0.01070.006-0.03320.05330.04580.145-0.0728-0.07360.173-0.02960.254914.174957.96154.7615
310.0379-0.01450.01460.0831-0.00820.0083-0.02610.02930.0997-0.0157-0.0329-0.2196-0.02190.08540.00250.09220.00180.00040.12490.04590.15749.206958.3674-7.8167
320.0586-0.018-0.01060.026-0.00560.00610.0059-0.04470.00680.0513-0.0023-0.0055-0.00290.0204-0.02430.0789-0.00540.0180.0324-0.0005-0.0232-3.705946.2955-1.0841
330.0944-0.018-0.03530.08570.04130.0278-0.0369-0.05640.03530.0966-0.0394-0.0617-0.0306-0.0198-0.0240.266-0.0147-0.08020.31270.04850.13413.519840.557518.3279
34-0.0012-0.0003-0.00090.001-0.00440.0053-0.01690.0220.017-0.0199-0.0067-0.0034-0.01340.008-0.07480.2617-0.0893-0.00230.06030.05010.011137.937245.987533.8504
350.16480.00050.08580.00020.00030.045-0.03030.09930.03190-0.02-0.0125-0.06210.0694-0.01020.2641-0.08460.05680.2394-0.00290.112950.034638.883339.7456
360.00380.00590.0010.1094-0.10720.1123-0.1270.03820.0976-0.2017-0.07850.1803-0.101-0.0795-0.82920.1990.0341-0.14110.1251-0.0680.280319.855844.272947.2205
370.06150.03110.01510.0211-0.00690.062-0.0215-0.02460.0411-0.0659-0.02780.1919-0.1006-0.02350.02370.15520.0116-0.06720.1396-0.08880.282918.876751.973861.0708
380.02210.0014-0.01740.053-0.02210.0218-0.0103-0.0591-0.0261-0.06030.0245-0.03510.0178-0.0071-0.00390.0841-0.0141-0.0260.078-0.01670.092131.003846.903864.8148
390.1658-0.0334-0.10240.02370.00040.0876-0.0806-0.0552-0.0689-0.00760.0010.0460.02170.0493-0.00390.1629-0.0316-0.02310.1111-0.00150.122835.431639.353253.05
400.0698-0.0024-0.10270.0014-0.00170.2955-0.08340.01590.0451-0.0741-0.01330.0387-0.0222-0.023-0.26920.2237-0.034-0.07730.08450.00460.12526.531439.973945.6279
410.0062-0.0071-0.0040.01450.01810.0315-0.01880.02030.0153-0.0402-0.0020.0304-0.0226-0.0027-0.03070.2965-0.0442-0.11320.1478-0.02490.146423.931333.300835.7136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resseq 1:48)B0
2X-RAY DIFFRACTION2chain 'B' and (resseq 49:66)B0
3X-RAY DIFFRACTION3chain 'B' and (resseq 67:96)B0
4X-RAY DIFFRACTION4chain 'B' and (resseq 97:140)B0
5X-RAY DIFFRACTION5chain 'B' and (resseq 141:166)B0
6X-RAY DIFFRACTION6chain 'B' and (resseq 167:223)B0
7X-RAY DIFFRACTION7chain 'B' and (resseq 224:261)B0
8X-RAY DIFFRACTION8chain 'B' and (resseq 262:286)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 287:328)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 329:354)B0
11X-RAY DIFFRACTION11chain 'A' and (resseq 1:115)A0
12X-RAY DIFFRACTION12chain 'A' and (resseq 116:355)A0
13X-RAY DIFFRACTION13chain 'C' and (resseq 1:66)C0
14X-RAY DIFFRACTION14chain 'C' and (resseq 67:96)C0
15X-RAY DIFFRACTION15chain 'C' and (resseq 97:140)C0
16X-RAY DIFFRACTION16chain 'C' and (resseq 141:223)C0
17X-RAY DIFFRACTION17chain 'C' and (resseq 224:261)C0
18X-RAY DIFFRACTION18chain 'C' and (resseq 262:286)C0
19X-RAY DIFFRACTION19chain 'C' and (resseq 287:328)C0
20X-RAY DIFFRACTION20chain 'C' and (resseq 329:355)C0
21X-RAY DIFFRACTION21chain 'D' and (resseq 1:66)D0
22X-RAY DIFFRACTION22chain 'D' and (resseq 67:140)D0
23X-RAY DIFFRACTION23chain 'D' and (resseq 141:223)D0
24X-RAY DIFFRACTION24chain 'D' and (resseq 224:261)D0
25X-RAY DIFFRACTION25chain 'D' and (resseq 262:328)D0
26X-RAY DIFFRACTION26chain 'D' and (resseq 329:355)D0
27X-RAY DIFFRACTION27chain 'E' and (resseq 1:66)E0
28X-RAY DIFFRACTION28chain 'E' and (resseq 67:96)E0
29X-RAY DIFFRACTION29chain 'E' and (resseq 97:140)E0
30X-RAY DIFFRACTION30chain 'E' and (resseq 141:166)E0
31X-RAY DIFFRACTION31chain 'E' and (resseq 167:223)E0
32X-RAY DIFFRACTION32chain 'E' and (resseq 224:328)E0
33X-RAY DIFFRACTION33chain 'E' and (resseq 329:354)E0
34X-RAY DIFFRACTION34chain 'F' and (resseq 1:66)F0
35X-RAY DIFFRACTION35chain 'F' and (resseq 67:96)F0
36X-RAY DIFFRACTION36chain 'F' and (resseq 97:181)F0
37X-RAY DIFFRACTION37chain 'F' and (resseq 182:223)F0
38X-RAY DIFFRACTION38chain 'F' and (resseq 224:261)F0
39X-RAY DIFFRACTION39chain 'F' and (resseq 262:285)F0
40X-RAY DIFFRACTION40chain 'F' and (resseq 286:328)F0
41X-RAY DIFFRACTION41chain 'F' and (resseq 329:354)F0

+
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