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- PDB-3opk: Crystal structure of divalent-cation tolerance protein CutA from ... -

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Basic information

Entry
Database: PDB / ID: 3opk
TitleCrystal structure of divalent-cation tolerance protein CutA from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
ComponentsDivalent-cation tolerance protein cutA
KeywordsMETAL BINDING PROTEIN / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CutA / divalent ions binding
Function / homology
Function and homology information


response to metal ion / copper ion binding / cytoplasm
Similarity search - Function
Divalent cation tolerance protein CutA, Enterobacteria / Divalent ion tolerance protein, CutA / CutA1 divalent ion tolerance protein / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Divalent-cation tolerance protein CutA
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNocek, B. / Mulligan, R. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of divalent-cation tolerance protein CutA from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Authors: Nocek, B. / Mulligan, R. / Papazisi, L. / Anderson, W. / Joachimiak, A.
History
DepositionSep 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_ref_seq_dif / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _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: Divalent-cation tolerance protein cutA
B: Divalent-cation tolerance protein cutA
C: Divalent-cation tolerance protein cutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0577
Polymers38,8913
Non-polymers1654
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-71 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.333, 107.925, 52.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Divalent-cation tolerance protein cutA


Mass: 12963.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: cutA, STM4324 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q7CPA2
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8 M sodium Acetate, 10mM ADP, 1mM Magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 28230 / Num. obs: 28212 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2 / % possible all: 95.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
CCP4model building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GSD
Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.975 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21867 1413 5 %RANDOM
Rwork0.17523 ---
all0.18 27030 --
obs0.17744 26615 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.591 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--0.01 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 10 148 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222638
X-RAY DIFFRACTIONr_bond_other_d0.0070.021632
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9873621
X-RAY DIFFRACTIONr_angle_other_deg1.34134085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6495344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.46826.28997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02115434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.734153
X-RAY DIFFRACTIONr_chiral_restr0.1150.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212908
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02435
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_it1.1461.51716
X-RAY DIFFRACTIONr_mcbond_other0.3091.5669
X-RAY DIFFRACTIONr_mcangle_it1.97722769
X-RAY DIFFRACTIONr_scbond_it3.2353922
X-RAY DIFFRACTIONr_scangle_it5.0614.5848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 89 -
Rwork0.252 1837 -
obs--94.09 %
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)
14.53673.2449-0.95965.055-0.10930.87320.0883-0.2013-0.08290.1396-0.08020.01180.01860.0103-0.00810.24720.0084-0.02310.27020.00070.260439.377721.150765.2566
25.64271.8304-1.1990.9443-1.61544.86750.1809-0.1587-0.20960.1436-0.2491-0.0878-0.33810.29250.06820.2613-0.0465-0.01710.30010.02470.312152.077329.143667.5063
33.15121.9632-2.78515.1946-5.140910.52870.1202-0.20520.28340.4061-0.12690.3052-0.61450.0930.00670.3155-0.0325-0.00160.29650.00230.25846.175827.919174.6502
41.5239-0.6421-0.66662.282-2.29663.1591-0.1316-0.0737-0.17340.25020.04820.0659-0.13750.01840.08340.3164-0.02470.01230.2939-0.00570.208141.448822.371878.3913
51.42281.1677-1.50610.9248-1.19442.4001-0.0115-0.0842-0.0467-0.0025-0.0656-0.07960.03030.04620.07710.26740.0118-0.01060.26420.00340.276448.285421.604763.8528
68.8412-2.67942.44646.1906-4.20092.703-0.46550.24320.3430.590.37-0.0023-0.4916-0.08590.09550.34380.0366-0.06160.25530.03530.295940.72636.353149.3999
724.1667-8.310412.5183.6408-4.32396.3775-0.4625-0.02420.56060.39930.21010.0688-0.3377-0.02570.25240.31550.0570.030.20270.08310.32145.038437.595149.1279
82.78013.0458-2.60833.3836-2.47353.18460.1044-0.0175-0.03110.0963-0.0704-0.0299-0.0622-0.0497-0.03390.25070.0017-0.00630.26970.00730.272344.391223.27463.7519
91.7611.561-0.68953.5144-0.86531.70640.0846-0.04960.02020.1882-0.08630.0842-0.0961-0.14710.00170.26910.00110.01010.2887-0.01730.256933.698423.933372.2522
106.25781.97971.78834.3492-1.5231.18810.0327-0.21380.06620.1489-0.1706-0.0935-0.1007-0.01210.13790.2829-0.0077-0.00850.2612-0.03810.254141.272334.564768.8117
117.92363.38543.58894.00340.37091.5086-0.0312-0.13850.1722-0.009-0.0816-0.16110.0038-0.0690.11280.2436-0.00230.00140.2747-0.01140.276337.363932.750663.3693
120.6988-0.97510.6611.4266-0.35570.75570.0568-0.02090.01130.0065-0.0821-0.05640.1044-0.09260.02530.2681-0.00620.02130.24570.03080.319735.442411.032964.2069
130.3763-0.331-1.69988.06253.12324.63840.1387-0.04060.03590.3391-0.10710.4291-0.09740.121-0.03150.3563-0.020.05050.26220.02280.242339.475110.670675.8888
145.1813-3.8789-2.82732.63422.36497.9278-0.30.1143-0.80550.2102-0.10210.35290.0847-0.68310.40210.25230.0170.02250.22330.00720.457118.51414.192955.6684
151.47620.29630.93253.16810.10810.2282-0.05670.1778-0.02720.21790.11410.04960.02460.0733-0.05740.2709-0.02250.00960.26290.01630.289226.951710.169454.5812
161.75290.56691.31351.17810.53760.88250.00220.0213-0.12820.05520.0638-0.22550.0094-0.0048-0.0660.2592-0.00950.00640.23630.0150.318950.93734.764457.5977
171.36710.74280.90742.29540.9062.2503-0.07170.1453-0.0546-0.1960.16910.178-0.04730.1379-0.09740.259-0.00120.01190.2554-0.00610.278246.12463.21450.8977
180.2642-0.8294-1.98781.45553.43098.30650.0092-0.0407-0.0102-0.04450.0799-0.1213-0.14130.021-0.08910.27620.0067-0.0010.3020.01030.252753.645616.227661.1722
19-0.16910.37190.1124-0.28323.192915.3549-0.1467-0.17530.0640.0725-0.02330.01740.76620.31030.170.40.1267-0.04460.50860.02220.178250.477215.762478.4746
2015.8136-9.1668-3.29987.560410.872222.5583-0.4002-0.89520.08680.18180.7195-0.1610.62061.0487-0.31940.3540.0266-0.0320.27360.04340.250655.493216.313471.2006
216.35123.15793.99161.78921.6782.62290.07490.0285-0.1361-0.0008-0.0476-0.09380.05420.0303-0.02740.25310.00410.00210.2666-0.01020.28745.44938.720356.0083
222.88810.52830.68130.3921-1.30216.44360.0163-0.16140.01070.0055-0.01350.09150.2039-0.0708-0.00280.2745-0.0067-0.00070.22470.00430.309637.9961-0.577257.2059
233.87350.43771.00850.17590.88165.77320.0697-0.0497-0.16290.0509-0.0321-0.18880.1-0.072-0.03760.27580.0059-0.03370.19620.02480.334548.72280.138364.732
2410.1345-2.52578.23440.7816-2.18438.07310.0244-0.163-0.011-0.0077-0.1073-0.12360.1493-0.13370.08290.26620.00020.01910.26030.01510.278842.49936.87165.3826
251.4564-1.0512-1.48072.66920.84381.06670.02490.15630.0321-0.14350.02450.03410.0037-0.1807-0.04930.2803-0.0252-0.02810.3212-0.02230.227334.254411.095844.8376
261.9625-1.33711.21596.6639-3.62341.8806-0.12880.0006-0.3215-0.07860.1541-0.03230.027-0.1314-0.02520.2891-0.02270.01820.2593-0.03410.290839.78741.537245.4082
274.09640.2598-3.39222.3835-1.87873.1636-0.0098-0.4232-0.14590.28480.00770.026-0.13630.24130.00210.2790.0293-0.02820.32680.02260.262616.628927.940570.9523
283.2587-0.1588-3.50640.858-0.033.595-0.194-0.03070.08780.02570.24570.09280.2158-0.0195-0.05170.24560.0275-0.00080.30210.00050.285823.506622.215861.3218
293.4075-0.1917-2.63771.5-0.8592.2945-0.12260.2034-0.1834-0.0140.01710.09460.1381-0.10180.10560.2717-0.0149-0.01090.2866-0.01630.253344.325117.855846.6822
301.7592-0.2046-0.16991.45340.43410.02380.05560.05380.0389-0.1040.0132-0.0017-0.0223-0.0226-0.06880.2579-0.0052-0.00660.28010.01560.263145.947827.279542.3969
314.5978-0.57410.81121.98721.10141.6056-0.07510.03070.12030.04490.00660.0275-0.1395-0.10490.06850.2516-0.00850.00820.22980.02250.276838.260728.880547.1134
320.39-0.1316-0.2075.35442.41722.3783-0.0380.0433-0.18350.0047-0.1989-0.0235-0.03250.04250.23680.2635-0.00380.01710.2494-0.0210.30352.374513.777449.9145
3313.261911.630513.367911.98053.196211.1671-2.0683-1.7399-1.2876-2.7030.5509-1.8034-1.178-1.96921.51730.4143-0.04540.25480.2108-0.11310.931753.04030.576743.7445
345.1807-4.3146-3.6211.40962.96721.596-0.09870.3657-0.1954-0.1784-0.0383-0.32780.0405-0.27220.13710.34760.0193-0.00540.2416-0.04220.28555.131713.948746.8653
358.5467-3.0477-0.37121.47310.67840.6205-0.1357-0.09560.12480.01790.1667-0.0978-0.05530.0389-0.0310.2652-0.00710.00880.26830.00070.278739.149822.914950.7422
362.43030.248-1.39510.39230.22291.0173-0.04360.0981-0.1031-0.04690.0002-0.007-0.0158-0.03060.04330.2673-0.00360.00960.27570.00380.259236.419920.066540.8577
3712.28180.1728-10.80334.74274.899113.5247-0.1869-0.0111-0.2396-0.1810.1334-0.07480.10250.05360.05350.3113-0.0037-0.03680.24060.01140.290741.838212.831440.8922
380.02870.21530.14511.51620.46650.5162-0.0273-0.01020.01270.09860.04960.07190.07550.0889-0.02220.27090.016-0.00960.273-0.01850.267831.744321.201358.8126
391.7835-0.45270.92430.9651-0.60621.51720.01880.0990.14740.014-0.03610.0030.09820.04990.01720.25470.00410.00430.25740.00670.289530.407432.636454.8363
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 22
2X-RAY DIFFRACTION2A23 - 28
3X-RAY DIFFRACTION3A29 - 33
4X-RAY DIFFRACTION4A34 - 39
5X-RAY DIFFRACTION5A40 - 50
6X-RAY DIFFRACTION6A51 - 56
7X-RAY DIFFRACTION7A57 - 62
8X-RAY DIFFRACTION8A63 - 72
9X-RAY DIFFRACTION9A73 - 83
10X-RAY DIFFRACTION10A84 - 89
11X-RAY DIFFRACTION11A90 - 94
12X-RAY DIFFRACTION12A95 - 104
13X-RAY DIFFRACTION13A105 - 115
14X-RAY DIFFRACTION14B1 - 6
15X-RAY DIFFRACTION15B7 - 13
16X-RAY DIFFRACTION16B14 - 37
17X-RAY DIFFRACTION17B38 - 44
18X-RAY DIFFRACTION18B45 - 51
19X-RAY DIFFRACTION19B52 - 59
20X-RAY DIFFRACTION20B60 - 64
21X-RAY DIFFRACTION21B65 - 72
22X-RAY DIFFRACTION22B73 - 79
23X-RAY DIFFRACTION23B80 - 89
24X-RAY DIFFRACTION24B90 - 98
25X-RAY DIFFRACTION25B99 - 106
26X-RAY DIFFRACTION26B107 - 115
27X-RAY DIFFRACTION27C-2 - 4
28X-RAY DIFFRACTION28C5 - 16
29X-RAY DIFFRACTION29C17 - 22
30X-RAY DIFFRACTION30C23 - 36
31X-RAY DIFFRACTION31C37 - 45
32X-RAY DIFFRACTION32C46 - 53
33X-RAY DIFFRACTION33C54 - 60
34X-RAY DIFFRACTION34C61 - 65
35X-RAY DIFFRACTION35C66 - 72
36X-RAY DIFFRACTION36C73 - 89
37X-RAY DIFFRACTION37C90 - 94
38X-RAY DIFFRACTION38C95 - 104
39X-RAY DIFFRACTION39C105 - 115

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