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- PDB-4il2: Crystal structure of D-mannonate dehydratase (rspA) from E. coli ... -

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Basic information

Entry
Database: PDB / ID: 4il2
TitleCrystal structure of D-mannonate dehydratase (rspA) from E. coli CFT073 (EFI TARGET EFI-501585)
ComponentsStarvation sensing protein rspA
KeywordsLYASE / TIM-barrel / Structural Genomics
Function / homology
Function and homology information


mannonate dehydratase / mannonate dehydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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 ...D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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
D-galactonate dehydratase family member RspA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLukk, T. / Wichelecki, D. / Imker, H.J. / Gerlt, J.A. / Nair, S.K.
CitationJournal: To be Published
Title: Mannonate degradation pathway in E. coli CFT073
Authors: Wichelecki, S. / Lukk, T. / Imker, H.J. / Nair, S.K. / Gerlt, J.A.
History
DepositionDec 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 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_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_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_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: Starvation sensing protein rspA
B: Starvation sensing protein rspA
C: Starvation sensing protein rspA
D: Starvation sensing protein rspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7848
Polymers195,6864
Non-polymers974
Water8,503472
1
A: Starvation sensing protein rspA
B: Starvation sensing protein rspA
hetero molecules

A: Starvation sensing protein rspA
B: Starvation sensing protein rspA
hetero molecules

A: Starvation sensing protein rspA
B: Starvation sensing protein rspA
hetero molecules

A: Starvation sensing protein rspA
B: Starvation sensing protein rspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,56716
Polymers391,3738
Non-polymers1948
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area48030 Å2
ΔGint-183 kcal/mol
Surface area84410 Å2
MethodPISA
2
C: Starvation sensing protein rspA
D: Starvation sensing protein rspA
hetero molecules

C: Starvation sensing protein rspA
D: Starvation sensing protein rspA
hetero molecules

C: Starvation sensing protein rspA
D: Starvation sensing protein rspA
hetero molecules

C: Starvation sensing protein rspA
D: Starvation sensing protein rspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,56716
Polymers391,3738
Non-polymers1948
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area47130 Å2
ΔGint-193 kcal/mol
Surface area82360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.780, 123.780, 112.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11B-631-

HOH

21B-725-

HOH

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Components

#1: Protein
Starvation sensing protein rspA


Mass: 48921.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: c1971, rspA / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8FHC7
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein solution was at 10 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl and 50 mM imidazole. Mother liqueur contained 25% PEG 1,500 and 20% v/v glycerol, vapor diffusion, sitting drop, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 23, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionNumber: 627522 / Rmerge(I) obs: 0.116 / D res high: 1.95 Å / Num. obs: 122958 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
8.723014019710.031
6.178.72256310010.038
5.036.17329810010.045
4.365.03390810010.042
3.94.36438010010.045
3.563.9484910010.051
3.33.56527710010.061
3.083.3565710010.076
2.913.08605310010.095
2.762.91631210010.118
2.632.76669099.910.148
2.522.63697610010.168
2.422.52724710010.199
2.332.42758610010.227
2.252.33783399.910.254
2.182.25808399.910.303
2.122.18832399.910.352
2.062.12860399.910.441
22.06885010010.537
ReflectionResolution: 1.95→30 Å / Num. all: 123046 / Num. obs: 122978 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.116 / Net I/σ(I): 12.82
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.95-20.6632.561100
2-2.060.5373.161100
2.06-2.120.4413.85199.9
2.12-2.180.3524.84199.9
2.18-2.250.3035.62199.9
2.25-2.330.2546.72199.9
2.33-2.420.2277.441100
2.42-2.520.1998.481100
2.52-2.630.1689.931100
2.63-2.760.14811.18199.9
2.76-2.910.11813.661100
2.91-3.080.09516.611100
3.08-3.30.07620.091100
3.3-3.560.06124.61100
3.56-3.90.05128.961100
3.9-4.360.04532.051100
4.36-5.030.04234.071100
5.03-6.170.04531.431100
6.17-8.720.03834.261100
8.72-300.03139.74197

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.831 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 0 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 6075 4.94 %
Rwork0.1778 --
obs0.1794 122978 99.99 %
all-122977 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.985 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0674 Å2-0 Å20 Å2
2---0.0674 Å2-0 Å2
3---0.1349 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12364 0 4 472 12840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112720
X-RAY DIFFRACTIONf_angle_d1.47517266
X-RAY DIFFRACTIONf_dihedral_angle_d16.9664593
X-RAY DIFFRACTIONf_chiral_restr0.0931807
X-RAY DIFFRACTIONf_plane_restr0.0072237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.2642250.19723867X-RAY DIFFRACTION100
1.9722-1.99540.22762090.17523850X-RAY DIFFRACTION100
1.9954-2.01970.23061980.16893914X-RAY DIFFRACTION100
2.0197-2.04530.21112090.15853870X-RAY DIFFRACTION100
2.0453-2.07220.21992340.16583840X-RAY DIFFRACTION100
2.0722-2.10060.18531880.15313904X-RAY DIFFRACTION100
2.1006-2.13060.18352020.15433884X-RAY DIFFRACTION100
2.1306-2.16240.22611960.1653883X-RAY DIFFRACTION100
2.1624-2.19610.211880.15863877X-RAY DIFFRACTION100
2.1961-2.23210.18861980.16373913X-RAY DIFFRACTION100
2.2321-2.27060.20762060.1673874X-RAY DIFFRACTION100
2.2706-2.31190.22892020.16983903X-RAY DIFFRACTION100
2.3119-2.35630.21372020.17833867X-RAY DIFFRACTION100
2.3563-2.40440.22311980.17773863X-RAY DIFFRACTION100
2.4044-2.45670.21422000.1763923X-RAY DIFFRACTION100
2.4567-2.51380.22171940.18393888X-RAY DIFFRACTION100
2.5138-2.57660.22772200.18863891X-RAY DIFFRACTION100
2.5766-2.64630.22172010.18973885X-RAY DIFFRACTION100
2.6463-2.72410.22072060.19193854X-RAY DIFFRACTION100
2.7241-2.81190.20872080.18543932X-RAY DIFFRACTION100
2.8119-2.91230.20851830.18093897X-RAY DIFFRACTION100
2.9123-3.02880.21851970.18353913X-RAY DIFFRACTION100
3.0288-3.16660.22761850.18973901X-RAY DIFFRACTION100
3.1666-3.33330.24932050.20093910X-RAY DIFFRACTION100
3.3333-3.54180.19842210.1863900X-RAY DIFFRACTION100
3.5418-3.81480.20032020.17263885X-RAY DIFFRACTION100
3.8148-4.19770.18942190.16463922X-RAY DIFFRACTION100
4.1977-4.8030.17121890.15813926X-RAY DIFFRACTION100
4.803-6.0430.20341990.19463949X-RAY DIFFRACTION100
6.043-29.83490.19231910.18884018X-RAY DIFFRACTION100
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)
10.33830.13640.12210.4883-0.14980.37390.013-0.1276-0.02020.098-0.0098-0.1333-0.01620.0670.01270.11150.0157-0.03430.14680.02960.137-25.959145.2978-24.5235
20.07630.07650.1395-0.00870.0269-0.0173-0.0001-0.0702-0.13140.3040.0046-0.18960.18630.14940.0180.3131-0.0052-0.01150.2570.03070.1678-41.448241.5663-2.9622
30.1411-0.1622-0.02270.0943-0.00440.13210.0851-0.07880.16140.1272-0.13180.05370.00750.0277-0.02190.23550.03010.01810.26770.0340.1126-49.36947.82662.8804
40.1927-0.0374-0.12710.1661-0.19280.4491-0.0031-0.08710.00230.15030.102-0.08960.02210.1764-0.02390.22760.0216-0.00270.23970.00360.135-48.417451.6439-4.4327
50.4854-0.2405-0.31290.9966-0.11660.3069-0.0407-0.1614-0.00420.11550.0277-0.13480.00950.09070.01450.12350.0007-0.02630.13030.01760.0963-36.3652.5177-17.099
60.2558-0.27390.11810.4460.09340.2585-0.0155-0.1134-0.180.0843-0.0246-0.14070.06310.11740.01460.19350.033-0.04530.19650.03710.152-30.065336.1817-15.7474
70.58960.0740.15010.33380.09710.4153-0.0186-0.1435-0.1520.1502-0.0171-0.01610.1060.00080.02160.12090.0207-0.00070.0990.03370.1145-43.882323.7808-29.3501
80.2909-0.0739-0.21920.06960.04030.0436-0.04650.0264-0.1514-0.09170.0083-0.03740.2889-0.19010.01580.0971-0.01250.01250.0820.00960.1305-62.801621.6728-41.7497
90.1963-0.1175-0.07690.6995-0.11950.49750.03990.1422-0.1518-0.0752-0.0282-0.13810.12880.1480.0160.08380.01280.00610.08890.0070.0936-44.971442.115-59.3621
100.9774-0.31240.0760.8574-0.75190.28160.04610.0105-0.1065-0.0116-0.0279-0.02660.11070.03020.00920.0528-0.00410.0070.0576-0.00330.0515-53.652335.8915-43.7774
110.8312-0.0112-0.02790.20330.24780.297-0.04230.0235-0.1611-0.05550.0315-0.03070.08970.00140.02030.06680.01210.00920.0815-0.00540.0852-37.625329.0285-45.0729
120.44440.02940.02420.4704-0.04090.6985-0.00830.06910.0873-0.05860.00340.0441-0.0689-0.0193-0.00030.09050.01540.01040.05880.01310.1145-16.500134.2456-76.0673
130.2647-0.141-0.05760.00650.062-0.00180.0645-0.37180.13190.0905-0.0585-0.0196-0.05820.18050.02560.0770.00280.01320.05730.00340.0804-2.175818.8707-51.3131
140.7906-0.1930.45621.0656-0.22140.7944-0.01860.04910.01470.01460.01320.0244-0.0641-0.00680.00890.0188-0.00290.01150.02080.00960.0309-7.589516.9835-70.2686
150.4951-0.31490.05290.2987-0.25220.41390.0311-0.0270.09920.09560.0080.0668-0.11-0.0276-0.01180.0650.0090.00460.07490.01380.1012-21.701730.5146-67.8635
160.4650.3192-0.01830.49040.15320.51330.018-0.05820.169-0.0134-0.00910.0326-0.101-0.0387-0.01110.1133-0.01490.01320.02460.02440.0922-9.466839.7225-70.2239
170.12270.10350.26760.4377-0.14410.3903-0.00620.01360.0028-0.03460.03770.1639-0.0228-0.1349-0.02390.0930.0056-0.02840.14870.02110.1316-41.15968.8303-83.9907
180.21970.0944-0.205-0.0220.0640.11120.05020.2027-0.0228-0.2626-0.09250.0849-0.008-0.1292-0.00870.28950.0371-0.06730.29230.02510.1658-30.670814.3819-108.9523
190.36240.0461-0.0280.24150.21090.3194-0.09960.10480.024-0.21460.18660.18480.0834-0.1059-0.00250.26260.0281-0.04360.3061-0.00340.1698-28.7839-2.4399-112.5524
200.0921-0.06260.0725-0.0189-0.07450.1390.00530.14820.0122-0.3416-0.0205-0.22110.07810.11870.01920.28160.0142-0.03680.36510.01320.1484-18.5585-2.7074-118.4444
210.7379-0.189-0.01940.48380.36850.17850.03010.1819-0.0133-0.1263-0.00750.03580.004-0.0275-0.01220.17130.0014-0.02860.15440.0190.0899-20.59955.7289-99.6581
220.0627-0.0418-0.04810.09260.02670.1216-0.0340.26360.1384-0.2327-0.00440.1273-0.1551-0.18140.00070.23660.0326-0.06260.27250.02240.2147-37.143415.5727-104.8931
230.70830.03760.30040.6928-0.21090.53850.01570.0248-0.0079-0.1438-0.02670.2054-0.0751-0.13820.02840.1246-0.0097-0.03850.18720.00520.0989-40.84170.8011-99.7005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 13:151)
2X-RAY DIFFRACTION2chain 'A' and (resseq 152:195)
3X-RAY DIFFRACTION3chain 'A' and (resseq 196:213)
4X-RAY DIFFRACTION4chain 'A' and (resseq 214:243)
5X-RAY DIFFRACTION5chain 'A' and (resseq 244:376)
6X-RAY DIFFRACTION6chain 'A' and (resseq 377:415)
7X-RAY DIFFRACTION7chain 'B' and (resseq 12:111)
8X-RAY DIFFRACTION8chain 'B' and (resseq 112:130)
9X-RAY DIFFRACTION9chain 'B' and (resseq 131:243)
10X-RAY DIFFRACTION10chain 'B' and (resseq 244:376)
11X-RAY DIFFRACTION11chain 'B' and (resseq 377:415)
12X-RAY DIFFRACTION12chain 'C' and (resseq 12:195)
13X-RAY DIFFRACTION13chain 'C' and (resseq 196:214)
14X-RAY DIFFRACTION14chain 'C' and (resseq 215:318)
15X-RAY DIFFRACTION15chain 'C' and (resseq 319:376)
16X-RAY DIFFRACTION16chain 'C' and (resseq 377:415)
17X-RAY DIFFRACTION17chain 'D' and (resseq 13:111)
18X-RAY DIFFRACTION18chain 'D' and (resseq 112:151)
19X-RAY DIFFRACTION19chain 'D' and (resseq 152:195)
20X-RAY DIFFRACTION20chain 'D' and (resseq 196:213)
21X-RAY DIFFRACTION21chain 'D' and (resseq 214:344)
22X-RAY DIFFRACTION22chain 'D' and (resseq 345:376)
23X-RAY DIFFRACTION23chain 'D' and (resseq 377:415)

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