[English] 日本語
Yorodumi
- PDB-5aew: Crystal structure of II9 variant of Biphenyl dioxygenase from Bur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aew
TitleCrystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl
Components(BIPHENYL DIOXYGENASE SUBUNIT ...) x 2
KeywordsOXIDOREDUCTASE / BIPHENYL DIOXYGENASE / BPHAE-II9 / BIPHENYL / POLYCHLORINATED BIPHENYLS
Function / homology
Function and homology information


biphenyl 2,3-dioxygenase / biphenyl 2,3-dioxygenase activity / : / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 ...Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Nuclear Transport Factor 2; Chain: A, - #50 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BIPHENYL / : / FE2/S2 (INORGANIC) CLUSTER / Biphenyl dioxygenase subunit alpha / Biphenyl dioxygenase subunit beta
Similarity search - Component
Biological speciesBURKHOLDERIA XENOVORANS LB400 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsDhindwal, S. / Gomez-Gil, L. / Sylvestre, M. / Eltis, L.D. / Bolin, J.T. / Kumar, P.
CitationJournal: J.Bacteriol. / Year: 2016
Title: Structural Basis of the Enhanced Pollutant-Degrading Capabilities of an Engineered Biphenyl Dioxygenase.
Authors: Dhindwal, S. / Gomez-Gil, L. / Neau, D.B. / Pham, T.T.M. / Sylvestre, M. / Eltis, L.D. / Bolin, J.T. / Kumar, P.
History
DepositionJan 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.3Jan 10, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
A: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
B: BIPHENYL DIOXYGENASE SUBUNIT BETA
C: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
D: BIPHENYL DIOXYGENASE SUBUNIT BETA
E: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
F: BIPHENYL DIOXYGENASE SUBUNIT BETA
G: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
H: BIPHENYL DIOXYGENASE SUBUNIT BETA
I: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
J: BIPHENYL DIOXYGENASE SUBUNIT BETA
K: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
L: BIPHENYL DIOXYGENASE SUBUNIT BETA
M: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
N: BIPHENYL DIOXYGENASE SUBUNIT BETA
O: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
P: BIPHENYL DIOXYGENASE SUBUNIT BETA
Q: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
R: BIPHENYL DIOXYGENASE SUBUNIT BETA
S: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
T: BIPHENYL DIOXYGENASE SUBUNIT BETA
U: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
V: BIPHENYL DIOXYGENASE SUBUNIT BETA
W: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
X: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)887,18957
Polymers883,02124
Non-polymers4,16833
Water72,3664017
1
S: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
T: BIPHENYL DIOXYGENASE SUBUNIT BETA
U: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
V: BIPHENYL DIOXYGENASE SUBUNIT BETA
W: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
X: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,75914
Polymers220,7556
Non-polymers1,0038
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
D: BIPHENYL DIOXYGENASE SUBUNIT BETA
E: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
F: BIPHENYL DIOXYGENASE SUBUNIT BETA
I: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
J: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,91315
Polymers220,7556
Non-polymers1,1589
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
B: BIPHENYL DIOXYGENASE SUBUNIT BETA
K: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
L: BIPHENYL DIOXYGENASE SUBUNIT BETA
O: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
P: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,75914
Polymers220,7556
Non-polymers1,0038
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
Q: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
R: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules

G: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
H: BIPHENYL DIOXYGENASE SUBUNIT BETA
M: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
N: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,75914
Polymers220,7556
Non-polymers1,0038
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_556x,y,z+11
identity operation1_555x,y,z1
MethodPISA
5
Q: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
R: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules

G: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
H: BIPHENYL DIOXYGENASE SUBUNIT BETA
M: BIPHENYL DIOXYGENASE SUBUNIT ALPHA
N: BIPHENYL DIOXYGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,75914
Polymers220,7556
Non-polymers1,0038
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
MethodPISA
Unit cell
Length a, b, c (Å)132.767, 133.191, 133.965
Angle α, β, γ (deg.)102.31, 102.54, 104.54
Int Tables number1
Space group name H-MP1

-
Components

-
BIPHENYL DIOXYGENASE SUBUNIT ... , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX

#1: Protein
BIPHENYL DIOXYGENASE SUBUNIT ALPHA / BIPHENYL 2 / 3-DIOXYGENASE / BIPHENYL DIOXYGEASE


Mass: 51471.262 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA XENOVORANS LB400 (bacteria)
Variant: II9 / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P37333, biphenyl 2,3-dioxygenase
#2: Protein
BIPHENYL DIOXYGENASE SUBUNIT BETA / BIPHENYL 2 / 3-DIOXYGENASE / BIPHENYL DIOXYGEASE


Mass: 22113.846 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA XENOVORANS LB400 (bacteria)
Variant: II9 / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P37334, biphenyl 2,3-dioxygenase

-
Non-polymers , 4 types, 4050 molecules

#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-BNL / BIPHENYL / Biphenyl


Mass: 154.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C12H10
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4017 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsMUTATION AT RESIDUE T335G, F336I, N338T, I341T

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.58 % / Description: NONE
Crystal growpH: 6
Details: PEG8000, 50MM MES PH 6.0, GLYCEROL 6% AND 50MM NACL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→129.1 Å / Num. obs: 634861 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 21
Reflection shellResolution: 1.88→23.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 94

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XR8

2xr8


Resolution: 1.88→23.34 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.271 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 32697 5 %RANDOM
Rwork0.22485 ---
obs0.22675 618963 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.014 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.66 Å2-0.61 Å2
2--0.89 Å20.56 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.88→23.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59211 0 168 4017 63396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01961167
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.93682923
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82357370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30723.3033121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.878159881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.67715505
X-RAY DIFFRACTIONr_chiral_restr0.0770.28490
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02148013
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5061.15329495
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9261.72536824
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.361.16331672
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.879→1.927 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 2387 -
Rwork0.323 44331 -
obs--93.01 %
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)
10.25480.0368-0.04390.1329-0.10360.2106-0.01690.0554-0.05130.0005-0.0236-0.010.01170.10290.04050.24970.010.04060.2986-0.03080.3035.6652-20.1866-19.6124
20.23050.0298-0.04940.1475-0.090.2741-0.01170.0365-0.0180.05080.02020.0269-0.05190.0019-0.00850.29110.02110.03990.2361-0.03690.3241-22.0886-10.7251-7.2342
30.1112-0.01550.00080.0591-0.07690.34170.01150.03770.0447-0.04690.0407-0.03870.0699-0.107-0.05220.2933-0.01850.00490.28270.00330.268-45.5371-45.6193-25.0342
40.25490.0224-0.14660.0876-0.14190.30280.0292-0.02550.0127-0.0170.0011-0.0209-0.0206-0.0414-0.03030.28540.01180.03170.2532-0.02320.3093-34.9284-38.06694.3643
50.12420.13940.0110.17220.01040.35370.02410.02040.0292-0.00020.021-0.01930.1625-0.2024-0.0450.2986-0.12960.00040.3240.00220.2356-67.6389-71.09137.5498
60.2326-0.0931-0.06610.1847-0.04840.28090.0014-0.03640.01090.00780.0357-0.03050.0671-0.0632-0.03710.2892-0.00650.03070.2731-0.01730.2827-44.5413-54.54122.5922
70.1545-0.06010.15870.0564-0.11980.36110.00360.02310.0124-0.02780.0161-0.0251-0.0683-0.1548-0.01970.23230.08270.03190.36570.02580.2676-80.2288-20.621832.3185
80.253-0.1225-0.04510.1426-0.14940.41760.01990.0068-0.0122-0.0210.0168-0.02720.0535-0.0979-0.03660.2754-0.01460.02960.31260.01530.2679-65.7619-45.855545.4329
90.2354-0.0602-0.07250.04970.01010.3455-0.0307-0.00190.0115-0.08540.01270.00290.28130.04850.0180.48120.06210.02810.1451-0.03610.2627-25.3335-84.0992-7.8581
100.16350.1105-0.09970.1173-0.19450.545-0.0023-0.0439-0.0028-0.0632-0.026-0.02780.07950.09070.02830.28640.06020.02360.2741-0.02880.2995-20.2205-58.688810.4638
110.2271-0.03050.04480.18750.00240.2725-0.0013-0.0728-0.03920.1073-0.0636-0.0208-0.04360.14750.0650.3038-0.0722-0.02970.32550.00270.239410.5205-6.878424.9761
120.28560.05310.06290.22820.00410.3501-0.0154-0.0533-0.00360.09420.01260.0463-0.10720.00710.00280.35980.00210.05470.2163-0.04970.2758-19.01491.783816.3708
130.17090.0205-0.00090.1914-0.00780.52980.01860.01560.0320.04550.0071-0.0396-0.20380.0865-0.02570.324-0.01670.02040.24120.00220.297-43.1849-7.838957.9416
140.14970.07380.02340.2572-0.04720.47660.0076-0.0303-0.00750.0379-0.0129-0.07960.00670.02070.00530.27220.03070.01210.29820.00870.2751-47.8653-38.892264.1643
150.31980.0354-0.090.07380.02620.310.03610.0550.13710.0203-0.0453-0.0292-0.12390.14640.00920.326-0.1463-0.00130.22070.01560.353211.138925.1143-9.1745
160.16060.00690.03510.0358-0.12050.4757-0.01790.05510.06150.04060.0110.0288-0.13750.02890.00690.35950.01850.04480.1715-0.02560.3427-19.38415.9144-6.425
170.1453-0.04760.030.1476-0.02010.5466-0.0477-0.08170.02240.09730.03670.0087-0.1811-0.27170.0110.28310.16170.08690.4148-0.00540.1968-55.356821.7712-46.7056
180.0960.0146-0.01650.1272-0.06770.4504-0.0019-0.0602-0.0240.05370.0758-0.00410.0271-0.177-0.07390.26610.00660.05410.36380.05990.2355-44.1493-7.1614-54.3626
190.67410.42260.74070.36990.58351.86430.1755-0.82380.52790.1403-0.65310.22610.2176-0.78160.47770.1298-0.29560.16321.1216-0.54340.5321-3.458-49.196365.0783
201.92730.85741.18460.45540.56010.902-0.11310.35240.38940.0685-0.00420.15930.08660.31710.11740.1957-0.0648-0.03660.46420.11870.288412.8892-52.226738.0966
211.0698-0.1154-0.0210.24930.01580.58090.5984-0.5367-0.3065-0.1734-0.13810.06020.4634-0.2774-0.46030.8454-0.4999-0.54210.48780.33680.3842-13.8565-91.655447.7902
222.34360.71431.53740.32220.2611.44610.48870.5115-0.25070.17670.00910.05140.32990.4961-0.49780.30250.2061-0.10370.449-0.13520.25812.409-74.114927.3452
230.92610.16620.23960.3667-0.0970.33210.4036-0.2846-0.19360.1398-0.3245-0.10990.25810.2818-0.0790.5192-0.048-0.32750.6150.13810.262228.5831-83.261667.6591
240.63640.28020.6821.1448-0.50551.82760.43890.6774-0.32260.4030.0262-0.37010.50980.908-0.46510.44550.4732-0.35940.8418-0.22920.417727.2802-74.481937.1807
250.01440.009-0.02270.0123-0.03990.17090.0013-0.00170.0062-0.00790.0179-0.01250.012-0.0242-0.01920.27880.02140.03310.2587-0.02170.2957-32.3485-32.72452.9343
260.0908-0.11030.01630.2703-0.04480.06070.0248-0.0061-0.028-0.0132-0.0994-0.0492-0.064-0.04270.07460.3249-0.01250.03560.2872-0.0890.2102-19.2299-25.922312.519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 1461
2X-RAY DIFFRACTION2B8 - 188
3X-RAY DIFFRACTION3C18 - 1462
4X-RAY DIFFRACTION4D7 - 188
5X-RAY DIFFRACTION5E18 - 1462
6X-RAY DIFFRACTION6F5 - 188
7X-RAY DIFFRACTION7G18 - 1461
8X-RAY DIFFRACTION8H8 - 188
9X-RAY DIFFRACTION9I18 - 1462
10X-RAY DIFFRACTION10J14 - 188
11X-RAY DIFFRACTION11K18 - 1462
12X-RAY DIFFRACTION12L8 - 188
13X-RAY DIFFRACTION13M18 - 1462
14X-RAY DIFFRACTION14N8 - 188
15X-RAY DIFFRACTION15O18 - 1462
16X-RAY DIFFRACTION16P8 - 188
17X-RAY DIFFRACTION17Q18 - 1462
18X-RAY DIFFRACTION18R9 - 188
19X-RAY DIFFRACTION19S18 - 1461
20X-RAY DIFFRACTION20T8 - 188
21X-RAY DIFFRACTION21U18 - 1461
22X-RAY DIFFRACTION22V8 - 188
23X-RAY DIFFRACTION23W18 - 1462
24X-RAY DIFFRACTION24X9 - 188
25X-RAY DIFFRACTION25Z1 - 719
26X-RAY DIFFRACTION26Y1 - 10

+
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