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- PDB-1ocx: E. coli maltose-O-acetyltransferase -

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Open data


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Basic information

Entry
Database: PDB / ID: 1ocx
TitleE. coli maltose-O-acetyltransferase
ComponentsMALTOSE O-ACETYLTRANSFERASE
KeywordsTRANSFERASE / ACETYL TRANSFERASE / LEFT-HANDED PARALLEL BETA-HELIX
Function / homology
Function and homology information


maltose O-acetyltransferase / maltose O-acetyltransferase activity / O-acyltransferase activity / protein-containing complex / identical protein binding
Similarity search - Function
: / Maltose/galactoside acetyltransferase / Maltose acetyltransferase hexapeptide capping motif / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...: / Maltose/galactoside acetyltransferase / Maltose acetyltransferase hexapeptide capping motif / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
TRIMETHYL LEAD ION / Maltose O-acetyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.15 Å
AuthorsLo Leggio, L. / Dal Degan, F. / Poulsen, P. / Larsen, S.
Citation
Journal: Biochemistry / Year: 2003
Title: The Structure and Specificity of Escherichia Coli Maltose Acetyltransferase Give New Insight Into the Laca Family of Acyltransferases.
Authors: Lo Leggio, L. / Degan, F.D. / Poulsen, P. / Andersen, S.M. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-Ray Analysis of Maltose O-Acetyltransferase.
Authors: Lo Leggio, L. / Dal Degan, F. / Poulsen, P. / Sorensen, S.O. / Harlow, K. / Harris, P. / Larsen, S.
History
DepositionFeb 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALTOSE O-ACETYLTRANSFERASE
B: MALTOSE O-ACETYLTRANSFERASE
C: MALTOSE O-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2258
Polymers59,9633
Non-polymers1,2625
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.623, 106.238, 175.433
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHR6AA2 - 31 - 2
21SERSERTHRTHR6BB2 - 31 - 2
31SERSERTHRTHR6CC2 - 31 - 2
12GLUGLULYSLYS2AA4 - 53 - 4
22GLUGLULYSLYS2BB4 - 53 - 4
32GLUGLULYSLYS2CC4 - 53 - 4
13GLUGLUGLUGLU3AA65
23GLUGLUGLUGLU3BB65
33GLUGLUGLUGLU3CC65
14LYSLYSGLYGLY2AA7 - 116 - 10
24LYSLYSGLYGLY2BB7 - 116 - 10
34LYSLYSGLYGLY2CC7 - 116 - 10
15GLUGLUGLUGLU3AA1211
25GLUGLUGLUGLU3BB1211
35GLUGLUGLUGLU3CC1211
16LEULEUARGARG2AA13 - 1512 - 14
26LEULEUARGARG2BB13 - 1512 - 14
36LEULEUARGARG2CC13 - 1512 - 14
17SERSERARGARG6AA16 - 2315 - 22
27SERSERARGARG6BB16 - 2315 - 22
37SERSERARGARG6CC16 - 2315 - 22
18ASPASPARGARG3AA24 - 2523 - 24
28ASPASPARGARG3BB24 - 2523 - 24
38ASPASPARGARG3CC24 - 2523 - 24
19LEULEULEULEU6AA2625
29LEULEULEULEU6BB2625
39LEULEULEULEU6CC2625
110ARGARGARGARG3AA2726
210ARGARGARGARG3BB2726
310ARGARGARGARG3CC2726
111ALAALAARGARG2AA28 - 2927 - 28
211ALAALAARGARG2BB28 - 2927 - 28
311ALAALAARGARG2CC28 - 2927 - 28
112GLNGLNGLNGLN3AA3029
212GLNGLNGLNGLN3BB3029
312GLNGLNGLNGLN3CC3029
113LEULEUILEILE2AA31 - 3230 - 31
213LEULEUILEILE2BB31 - 3230 - 31
313LEULEUILEILE2CC31 - 3230 - 31
114HISHISARGARG3AA33 - 3432 - 33
214HISHISARGARG3BB33 - 3432 - 33
314HISHISARGARG3CC33 - 3432 - 33
115TYRTYRSERSER2AA35 - 3834 - 37
215TYRTYRSERSER2BB35 - 3834 - 37
315TYRTYRSERSER2CC35 - 3834 - 37
116LEULEUTHRTHR6AA39 - 4438 - 43
216LEULEUTHRTHR6BB39 - 4438 - 43
316LEULEUTHRTHR6CC39 - 4438 - 43
117LEULEUARGARG2AA45 - 4644 - 45
217LEULEUARGARG2BB45 - 4644 - 45
317LEULEUARGARG2CC45 - 4644 - 45
118GLNGLNGLNGLN3AA47 - 4846 - 47
218GLNGLNGLNGLN3BB47 - 4846 - 47
318GLNGLNGLNGLN3CC47 - 4846 - 47
119ILEILEILEILE2AA4948
219ILEILEILEILE2BB4948
319ILEILEILEILE2CC4948
120LEULEULEULEU5AA5049
220LEULEULEULEU5BB5049
320LEULEULEULEU5CC5049
121ALAALAALAALA2AA5150
221ALAALAALAALA2BB5150
321ALAALAALAALA2CC5150
122ASPASPLEULEU3AA52 - 5351 - 52
222ASPASPLEULEU3BB52 - 5351 - 52
322ASPASPLEULEU3CC52 - 5351 - 52
123PHEPHEALAALA2AA54 - 6053 - 59
223PHEPHEALAALA2BB54 - 6053 - 59
323PHEPHEALAALA2CC54 - 6053 - 59
124TYRTYRTYRTYR3AA6160
224TYRTYRTYRTYR3BB6160
324TYRTYRTYRTYR3CC6160
125ILEILEPROPRO2AA62 - 6461 - 63
225ILEILEPROPRO2BB62 - 6461 - 63
325ILEILEPROPRO2CC62 - 6461 - 63
126THRTHRTHRTHR3AA6564
226THRTHRTHRTHR3BB6564
326THRTHRTHRTHR3CC6564
127PHEPHEALAALA2AA66 - 11965 - 118
227PHEPHEALAALA2BB66 - 11965 - 118
327PHEPHEALAALA2CC66 - 11965 - 118
128ARGARGARGARG3AA120119
228ARGARGARGARG3BB120119
328ARGARGARGARG3CC120119
129ASNASNALAALA2AA121 - 124120 - 123
229ASNASNALAALA2BB121 - 124120 - 123
329ASNASNALAALA2CC121 - 124120 - 123
130GLUGLUGLUGLU3AA125124
230GLUGLUGLUGLU3BB125124
330GLUGLUGLUGLU3CC125124
131LEULEUILEILE2AA126 - 179125 - 178
231LEULEUILEILE2BB126 - 179125 - 178
331LEULEUILEILE2CC126 - 179125 - 178
132ILEILELEULEU6AA180 - 183179 - 182
232ILEILELEULEU6BB180 - 183179 - 182
332ILEILELEULEU6CC180 - 183179 - 182

NCS oper: (Code: given
Matrix: (-0.36843, 0.82206, 0.43414), (-0.83462, -0.49818, 0.23503), (0.40948, -0.27575, 0.86965)
Vector: 42.247, 13.796, -12.817)

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Components

#1: Protein MALTOSE O-ACETYLTRANSFERASE / MALTOSE ACETYLTRANSFERASE


Mass: 19987.771 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH TRIMETHYL LEAD / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: NF1830 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P77791, maltose O-acetyltransferase
#2: Chemical
ChemComp-PBM / TRIMETHYL LEAD ION


Mass: 252.304 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H9Pb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.01 %
Description: INITIAL PHASES WERE OBTAINED FROM DATA COLLECTED AT ELETTRA, WHILE FINAL REFINEMENT WAS CARRIED OUT AGAINST THE DATA COLLECTED AT ESRF
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: HANGING DROP CRYSTALLIZATION CRYSTALS FORM IN A 3 UL (RESERVOIR) + 1 UL (PROTEIN AT 15 MG/ML) DROP WITH RESERVOIR 0.1 M NA CITRATE PH 5.6, 3% ETHANOL, 15 % PEG 4000). ADDITION OF 6 UL OF ...Details: HANGING DROP CRYSTALLIZATION CRYSTALS FORM IN A 3 UL (RESERVOIR) + 1 UL (PROTEIN AT 15 MG/ML) DROP WITH RESERVOIR 0.1 M NA CITRATE PH 5.6, 3% ETHANOL, 15 % PEG 4000). ADDITION OF 6 UL OF RESERVOIR AND 1 UL OF 50 MM TRIMETHYL LEAD ACETATE CAUSES CRYSTAL DISSOLUTION AND GROWTH OF CRYSTALS WITH DIFFERENT HABIT FROM WHICH THE STRUCTURE WAS SOLVED.
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium citrate1reservoirpH5.6
23 %ethanol1reservoir
315 %PEG40001reservoir
415 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.15→15 Å / Num. obs: 33084 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.396 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 15 Å / Num. measured all: 120930 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.396

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.15→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.197 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INDIVIDUAL B-FACTOR REFINEMENT WAS PRECEEDED BY TLS REFINEMENT IN WHICH EACH MONOMER WAS DIVIDED INTO THREE TLS GROUPS. THE DEPOSITED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INDIVIDUAL B-FACTOR REFINEMENT WAS PRECEEDED BY TLS REFINEMENT IN WHICH EACH MONOMER WAS DIVIDED INTO THREE TLS GROUPS. THE DEPOSITED STRUCTURE SHOWS ANISOTROPIC B FACTORS THAT RESULT FROM THE COMBINATION OF THE TLS COMPONENTS WITH THE RESIDUAL INDIVIDUAL B FACTORS. THE CCP4 PROGRAM TLSANAL WAS USED TO COMBINE THE TWO.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3117 9.9 %RANDOM
Rwork0.194 ---
obs0.198 28344 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.3 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.15→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4212 0 20 304 4536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214326
X-RAY DIFFRACTIONr_bond_other_d0.0010.023972
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.9425877
X-RAY DIFFRACTIONr_angle_other_deg0.7642.9929195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6853543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7715750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024866
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02867
X-RAY DIFFRACTIONr_nbd_refined0.2390.31023
X-RAY DIFFRACTIONr_nbd_other0.2170.33969
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5388
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1090.511
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3550.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4180.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4921.52715
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.924401
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7531611
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7754.51476
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A935tight positional0.040.05
2B935tight positional0.050.05
3C935tight positional0.050.05
1A1269medium positional0.280.5
2B1269medium positional0.210.5
3C1269medium positional0.210.5
1A514loose positional0.565
2B514loose positional0.645
3C514loose positional0.835
1A935tight thermal0.120.5
2B935tight thermal0.140.5
3C935tight thermal0.130.5
1A1269medium thermal0.52
2B1269medium thermal0.472
3C1269medium thermal0.492
1A514loose thermal1.2610
2B514loose thermal1.2610
3C514loose thermal1.3410
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 195
Rwork0.214 1939
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)
14.1576-1.6303-2.59349.80444.14099.3703-0.3401-0.9032-0.80430.6017-0.0367-0.33070.23660.66940.37680.08290.144-0.04930.48390.21020.403559.606311.919771.1002
22.70191.5806-1.98965.2136-3.57936.79560.3443-0.6390.28670.5231-0.3131-0.176-0.23390.5507-0.03120.1555-0.0750.03690.2222-0.10090.168939.314637.115177.6871
39.3572-1.05743.43733.4516-0.68766.1882-0.1699-0.67320.04920.48290.0030.17590.03540.34080.1670.3244-0.07860.04760.2030.07410.098328.45546.206780.704
44.07590.26730.41172.0266-0.663.5973-0.0502-0.0398-0.0866-0.03920.0189-0.1646-0.02660.30280.03130.02380.04830.02260.1357-0.01070.125551.579121.812557.1836
52.64610.42560.08032.67340.63673.00780.1104-0.0510.11490.0195-0.05570.22780.0233-0.1544-0.05470.03970.02620.03040.01970.00670.117328.357729.3964.4865
62.5940.4661-1.1522.831-0.38253.7335-0.0504-0.082-0.2744-0.1303-0.0019-0.11930.58990.1310.05230.2224-0.0036-0.02580.0280.03740.139433.60544.60562.6393
711.329917.9869-2.141425.1501-3.9537-1.1796-0.41750.0275-1.3124-0.86690.1079-0.71850.76090.11240.30960.6020.19090.08150.3268-0.07070.617347.8842-1.434755.6953
820.5795-2.2088-12.54783.9080.09982.31520.00540.38680.3022-0.53050.0459-0.84370.05860.2744-0.05140.296-0.05770.10140.33220.00720.399248.449238.399456.0502
91.8662-5.4311-0.181513.1054-3.3115-0.4410.18870.09830.0428-0.1053-0.19691.11660.2182-0.57810.00820.179-0.0515-0.03360.3262-0.00670.403715.096418.832566.0617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 55
2X-RAY DIFFRACTION2B2 - 55
3X-RAY DIFFRACTION3C2 - 55
4X-RAY DIFFRACTION4A56 - 110
5X-RAY DIFFRACTION4A129 - 183
6X-RAY DIFFRACTION5B56 - 110
7X-RAY DIFFRACTION5B129 - 183
8X-RAY DIFFRACTION6C56 - 110
9X-RAY DIFFRACTION6C129 - 183
10X-RAY DIFFRACTION7A111 - 128
11X-RAY DIFFRACTION8B111 - 128
12X-RAY DIFFRACTION9C111 - 128
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.55

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Yorodumi

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  • 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

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