[English] 日本語
Yorodumi
- PDB-4gyp: Crystal structure of the heterotetrameric complex of GlucD and Gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gyp
TitleCrystal structure of the heterotetrameric complex of GlucD and GlucDRP from E. coli K-12 MG1655 (EFI TARGET EFI-506058)
Components
  • Glucarate dehydratase-related protein
  • Glucarate dehydratase
KeywordsLYASE/LYASE / TIM-BARREL / LYASE-LYASE complex / Structural genomics / Enzyme Function Initiative (EFI)
Function / homology
Function and homology information


cellular catabolic process / glucarate dehydratase activity / D-glucarate catabolic process / glucarate dehydratase / Lyases; Carbon-oxygen lyases; Hydro-lyases / amino acid catabolic process / lyase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Glucarate dehydratase / D-Glucarate dehydratase-like / 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 ...Glucarate dehydratase / D-Glucarate dehydratase-like / 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
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Glucarate dehydratase / Glucarate dehydratase-related protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLukk, T. / Ghasempur, S. / Imker, H.J. / Gerlt, J.A. / Nair, S.K. / Enzyme Function Initiative (EFI)
CitationJournal: to be published
Title: Glucarate dehydratase and its related protein from Escherichia coli form a heterotetrameric complex.
Authors: Lukk, T. / Ghasempur, S. / Imker, H.J. / Nair, S.K. / Gerlt, J.A.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Structure summary
Revision 1.2Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_label_asym_id / _struct_ref_seq_dif.details / _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: Glucarate dehydratase
B: Glucarate dehydratase
C: Glucarate dehydratase-related protein
D: Glucarate dehydratase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,78818
Polymers199,1944
Non-polymers1,59414
Water26,1221450
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.470, 113.020, 128.590
Angle α, β, γ (deg.)90.000, 105.890, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Glucarate dehydratase / / GDH / GlucD


Mass: 49196.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2787, gudD, JW2758, ygcX / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AES2, glucarate dehydratase
#2: Protein Glucarate dehydratase-related protein / GDH-RP / GlucDRP


Mass: 50399.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2788, gudX, JW2759, ygcY / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q46915, Lyases; Carbon-oxygen lyases; Hydro-lyases

-
Non-polymers , 7 types, 1464 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#8: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1450 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop
Details: Protein solution was at 12.5 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME. Mother liqueur contained 0.17 M Ammonium acetate, 0.085 M Na-citrate tribasic, ...Details: Protein solution was at 12.5 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME. Mother liqueur contained 0.17 M Ammonium acetate, 0.085 M Na-citrate tribasic, dihydrate (pH 5.6), 25.5% PEG 4,000 and 15% v/v glycerol, vapor diffusion, sitting drop, temperature 282K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 15, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionNumber: 1029210 / Rmerge(I) obs: 0.148 / D res high: 2.1 Å / Num. obs: 244679 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
9.3930263895.810.037
6.649.39503499.710.045
5.426.64651399.810.058
4.75.42769199.710.052
4.24.7868099.910.052
3.834.2966199.710.057
3.553.831048399.810.069
3.323.551125999.810.088
3.133.321198199.410.109
2.973.131264299.410.143
2.832.971325199.510.173
2.712.831385898.910.207
2.62.711450199.410.244
2.512.61497299.210.274
2.422.511563599.510.321
2.352.421613399.410.36
2.282.351673199.510.405
2.212.281717399.610.471
2.152.211776899.910.525
2.12.151807599.810.609
ReflectionResolution: 2.1→30 Å / Num. obs: 118199 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.762 Å2 / Rsym value: 0.148 / Net I/σ(I): 9.24
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.150.6092.447769118075199.8
2.15-2.210.5252.827628417768199.9
2.21-2.280.4713.197369817173199.6
2.28-2.350.4053.77181316731199.5
2.35-2.420.364.176948116133199.4
2.42-2.510.3214.696712415635199.5
2.51-2.60.2745.476403714972199.2
2.6-2.710.2446.176207014501199.4
2.71-2.830.2077.265892313858198.9
2.83-2.970.1738.65612713251199.5
2.97-3.130.14310.155303912642199.4
3.13-3.320.10912.734947711981199.4
3.32-3.550.08815.244626611259199.8
3.55-3.830.06918.094248010483199.8
3.83-4.20.05720.58387879661199.7
4.2-4.70.05221.87350348680199.9
4.7-5.420.05221.64308627691199.7
5.42-6.640.05820.33263556513199.8
6.64-9.390.04524.18198195034199.7
9.39-300.03727.3898432638195.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8_1066refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EC7

1ec7


Resolution: 2.1→29.965 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9051 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 17.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 6221 5 %random
Rwork0.1486 ---
all0.172 ---
obs0.1505 118199 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.71 Å2 / Biso mean: 16.293 Å2 / Biso min: 2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13568 0 102 1450 15120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814035
X-RAY DIFFRACTIONf_angle_d1.02919050
X-RAY DIFFRACTIONf_chiral_restr0.0722065
X-RAY DIFFRACTIONf_plane_restr0.0052507
X-RAY DIFFRACTIONf_dihedral_angle_d13.0035122
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
2.1-2.12390.24222070.182839394146
2.1239-2.14890.26142060.178439094115
2.1489-2.17510.22522070.173239304137
2.1751-2.20260.21582050.169739054110
2.2026-2.23150.2312080.169139504158
2.2315-2.26210.23552070.170439284135
2.2621-2.29440.25752080.173539424150
2.2944-2.32860.23852050.169938974102
2.3286-2.3650.22662060.164539194125
2.365-2.40380.2282080.158239604168
2.4038-2.44520.22592060.164239114117
2.4452-2.48970.20952060.159239064112
2.4897-2.53750.20042070.156539474154
2.5375-2.58930.20892090.152939534162
2.5893-2.64560.20912050.149639044109
2.6456-2.70710.20862050.155738954100
2.7071-2.77470.20542070.153339404147
2.7747-2.84970.18782080.149839474155
2.8497-2.93350.19082060.148739184124
2.9335-3.02810.20972080.153839414149
3.0281-3.13620.17732070.149739434150
3.1362-3.26160.19572070.142839274134
3.2616-3.40980.16352080.13639584166
3.4098-3.58930.15492080.133439554163
3.5893-3.81380.15082090.124539544163
3.8138-4.10760.15522070.120539494156
4.1076-4.51970.15122090.124539734182
4.5197-5.17080.12192100.130539714181
5.1708-6.50370.15792090.158739894198
6.5037-29.96780.16382130.157340434256
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)
10.72750.41620.06790.2515-0.02330.6919-0.0752-0.0054-0.03890.0878-0.0562-0.3068-0.04010.07370.13460.03990.01280.0130.0691-0.01630.0855.285455.2871107.2595
20.48150.1731-0.27830.6579-0.29560.4262-0.0092-0.07260.07280.05550.0276-0.0006-0.05580.0179-0.00150.0736-0.0202-0.02560.1079-0.01010.065949.270551.2806113.6301
30.1970.03770.00020.7297-0.240.5344-0.03770.0070.0245-0.02030.0053-0.0249-0.03220.02480.03530.0511-0.0351-0.00750.08290.00340.081348.382353.9665100.6601
40.4950.00340.0920.4050.16920.28330.00380.18330.0985-0.10570.0359-0.2108-0.09310.0664-0.02670.1-0.0782-0.00030.18550.06360.262565.272367.554786.1751
51.3886-1.3345-0.35613.48160.61081.45760.03440.2080.1883-0.1895-0.0357-0.0201-0.0921-0.0654-0.0190.0665-0.07070.00440.14840.04440.104350.795967.788779.9947
62.5391-0.2262-0.45290.76360.16381.4960.01240.17940.2127-0.221-0.04330.01-0.15860.01720.01380.0799-0.0344-0.02590.0840.03650.091442.180367.954680.4971
70.3877-0.2507-0.03040.3664-0.11760.1473-0.0010.064-0.0167-0.01070.0130.03920.0009-0.0283-0.00850.0696-0.0228-0.00530.09510.01140.071338.600857.673591.4844
80.82140.6435-0.12731.31020.07780.7233-0.06730.0907-0.0019-0.09220.0522-0.13560.05420.08310.00480.0782-0.03190.00090.08320.0130.109858.282852.996892.5605
90.5854-0.2790.19880.6749-0.32870.4062-0.0646-0.0470.20770.123-0.0548-0.2118-0.12130.04640.10360.1256-0.0395-0.03730.12970.00650.174156.790666.3212102.3411
100.7540.04330.0750.34630.02330.23070.0653-0.0043-0.24380.01050.10030.00190.29910.0318-0.09740.1355-0.0661-0.01320.0630.03930.178329.383819.6461103.3568
112.01971.66120.35052.26810.56681.3746-0.0460.2061-0.0889-0.23960.0624-0.04480.17770.0508-0.01930.1532-0.00310.0190.0776-0.01320.095939.679123.995394.6452
120.91050.12620.33080.2670.00670.44580.0432-0.048-0.1251-0.050.04630.05920.1028-0.0821-0.06530.1014-0.0353-0.00470.07450.03180.112726.072429.5326101.9838
130.2711-0.0850.11970.36830.0790.3553-0.0144-0.3381-0.13280.0052-0.01850.36220.0188-0.4655-0.04210.1032-0.17230.04510.2060.22890.21063.156125.8794109.1806
141.1963-0.241-0.68850.8842-0.36791.64090.0032-0.04540.00670.09630.02480.2759-0.0925-0.04840.00240.0714-0.03590.00820.10390.01720.16192.879241.27898.9691
150.1929-0.13510.10160.2165-0.22010.3618-0.00760.00560.00050.0060.02940.0473-0.0038-0.0212-0.01910.0803-0.0379-0.00530.09650.01340.084419.443940.449997.2504
161.0280.484-0.13411.07780.28530.51440.009-0.1274-0.08320.10990.06290.13350.131-0.0591-0.08160.1169-0.0404-0.01080.14620.04840.098219.500327.5146112.8012
171.72080.9871.24352.9271.0442.18370.0998-0.1093-0.33860.30.0192-0.08820.39190.0162-0.12690.139-0.03740.00940.15120.0720.139928.835116.344110.2572
180.15330.0323-0.06261.0568-0.29810.6182-0.06460.117-0.1042-0.0871-0.0053-0.00680.1835-0.06710.06870.1559-0.0773-0.0350.14730.02980.21316.420920.213490.128
191.8009-1.3035-0.16881.00770.0630.11520.0630.138-0.0486-0.0495-0.08850.07630.007-0.0250.00230.0758-0.0052-0.03560.0733-0.01090.08110.203558.562553.6843
201.0456-0.2443-0.2493.58262.45251.986-0.0097-0.2168-0.2790.46090.01240.10250.3952-0.0484-0.0210.1113-0.0051-0.00920.07130.03320.1366-8.429459.689966.1568
210.591-0.4272-0.29930.5120.44290.47530.0134-0.00970.0135-0.0176-0.00830.02080.0544-0.0253-0.00820.066-0.0033-0.00570.06810.01310.05078.474665.127359.5421
220.67480.45680.41582.77390.07791.13140.01370.34110.0684-0.5268-0.0832-0.0402-0.0880.17610.04230.13840.04750.01490.1632-0.01010.049322.388753.207342.4071
230.8353-0.02290.08291.2861-0.37211.15410.08430.01660.00920.0224-0.0746-0.12740.03270.1703-0.00730.0620.01530.00740.0786-0.00110.066529.778351.241859.772
241.11690.7192-0.92391.4154-1.4342.8288-0.0093-0.0719-0.0852-0.0204-0.0159-0.13370.0890.15710.04370.07970.0067-0.00540.05290.00320.084427.405149.029172.8541
250.0685-0.05880.06330.1768-0.17180.29090.015-0.0324-0.036-0.0164-0.0324-0.03120.0366-0.02960.01650.06760.00310.00470.06640.00310.057514.75958.856271.7565
261.1172-0.5788-0.53791.1225-0.05170.40130.06690.0806-0.0167-0.133-0.06310.0372-0.0147-0.065-0.02130.0531-0.00450.00520.05570.00640.069313.464463.854256.1004
270.85170.0241-0.07611.84110.10870.5728-0.08750.21950.137-0.2165-0.02650.2573-0.1066-0.060.11440.08330.0295-0.01040.12670.01180.07344.974566.690348.2409
282.1525-0.38051.65271.3947-0.44672.9403-0.0769-0.0425-0.07670.14410.00440.12250.0915-0.160.06650.1557-0.02160.0050.0906-0.01810.174614.093738.01954.7051
290.34360.10250.07370.5732-0.40551.6047-0.0517-0.0340.03850.0079-0.03440.0267-0.1574-0.03040.07490.09520.00030.00920.048-0.01340.08743.848691.378586.427
303.9317-0.01124.3790.05850.00064.8679-0.00370.1928-0.03830.0581-0.0286-0.1769-0.04510.39080.04950.089-0.0281-0.00490.11590.00850.14614.583682.017878.9541
310.30230.0159-0.06510.2857-0.04651.0720.0197-0.02070.06920.0561-0.02630.0195-0.0373-0.02650.00860.06290.00970.00530.0474-0.00160.0660.103279.447188.0709
320.88490.08150.1450.6378-0.36630.4153-0.0352-0.19210.01860.24210.05670.1394-0.0732-0.1137-0.02720.1995-0.00260.07520.1779-0.03270.1159-8.119182.8949110.6919
331.3377-0.1698-0.05310.58010.07510.6106-0.0371-0.1854-0.11970.2410.04010.01830.1148-0.06930.00290.19710.01330.02470.15410.03790.06923.357567.8917109.0841
344.0558-0.4265-0.6930.7980.41360.84520.0233-0.3099-0.25960.1207-0.01510.0510.0514-0.07590.00790.0994-0.0063-0.00520.12720.05610.070514.454362.9954102.6477
350.3866-0.05160.04230.1742-0.03810.2196-0.0382-0.0248-0.02250.03590.012-0.01590.00940.03730.02330.07050.0042-0.00250.072-0.00410.05256.844770.807489.0722
361.2601-0.2681-0.03320.7921-0.14151.4152-0.0076-0.16460.01070.03090.05940.1447-0.0334-0.1144-0.02470.06570.00140.01410.08410.00050.0791-8.073179.149894.1722
370.387-0.01920.37610.5196-0.07890.8596-0.049-0.060.08160.11280.0074-0.0418-0.20920.05450.04810.1621-0.01140.00990.1269-0.03030.13063.951389.837999.6469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3:34 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 35:90 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 91:159 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 160:199 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 200:226 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 227:251 )A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 252:357 )A0
8X-RAY DIFFRACTION8CHAIN A AND (RESID 358:391 )A0
9X-RAY DIFFRACTION9CHAIN A AND (RESID 392:446 )A0
10X-RAY DIFFRACTION10CHAIN B AND (RESID 4:58 )B0
11X-RAY DIFFRACTION11CHAIN B AND (RESID 59:90 )B0
12X-RAY DIFFRACTION12CHAIN B AND (RESID 91:159 )B0
13X-RAY DIFFRACTION13CHAIN B AND (RESID 160:226 )B0
14X-RAY DIFFRACTION14CHAIN B AND (RESID 227:254 )B0
15X-RAY DIFFRACTION15CHAIN B AND (RESID 255:357 )B0
16X-RAY DIFFRACTION16CHAIN B AND (RESID 358:391 )B0
17X-RAY DIFFRACTION17CHAIN B AND (RESID 392:416 )B0
18X-RAY DIFFRACTION18CHAIN B AND (RESID 417:446 )B0
19X-RAY DIFFRACTION19CHAIN C AND (RESID 6:57 )C0
20X-RAY DIFFRACTION20CHAIN C AND (RESID 58:106 )C0
21X-RAY DIFFRACTION21CHAIN C AND (RESID 107:158 )C0
22X-RAY DIFFRACTION22CHAIN C AND (RESID 159:198 )C0
23X-RAY DIFFRACTION23CHAIN C AND (RESID 199:247 )C0
24X-RAY DIFFRACTION24CHAIN C AND (RESID 248:281 )C0
25X-RAY DIFFRACTION25CHAIN C AND (RESID 282:343 )C0
26X-RAY DIFFRACTION26CHAIN C AND (RESID 344:376 )C0
27X-RAY DIFFRACTION27CHAIN C AND (RESID 377:414 )C0
28X-RAY DIFFRACTION28CHAIN C AND (RESID 415:446 )C0
29X-RAY DIFFRACTION29CHAIN D AND (RESID 6:75 )D0
30X-RAY DIFFRACTION30CHAIN D AND (RESID 76:100 )D0
31X-RAY DIFFRACTION31CHAIN D AND (RESID 101:158 )D0
32X-RAY DIFFRACTION32CHAIN D AND (RESID 159:198 )D0
33X-RAY DIFFRACTION33CHAIN D AND (RESID 199:247 )D0
34X-RAY DIFFRACTION34CHAIN D AND (RESID 248:281 )D0
35X-RAY DIFFRACTION35CHAIN D AND (RESID 282:356 )D0
36X-RAY DIFFRACTION36CHAIN D AND (RESID 357:390 )D0
37X-RAY DIFFRACTION37CHAIN D AND (RESID 391:445 )D0

+
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