[English] 日本語
Yorodumi
- PDB-5upb: Swit_4259, an Acetoacetate Decarboxylase-like Enzyme from Sphingo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5upb
TitleSwit_4259, an Acetoacetate Decarboxylase-like Enzyme from Sphingomonas wittichii RW1
ComponentsAcetoacetate decarboxylase
KeywordsLYASE / Acetoacetate Decarboxylase-like Enzyme
Function / homologyAcetoacetate decarboxylase / Acetoacetate decarboxylase domain superfamily / Acetoacetate decarboxylase (ADC) / carboxy-lyase activity / Acetoacetate decarboxylase
Function and homology information
Biological speciesSphingomonas wittichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.912 Å
AuthorsMydy, L.S. / Silvaggi, N.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1157392 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Swit_4259, an acetoacetate decarboxylase-like enzyme from Sphingomonas wittichii RW1.
Authors: Mydy, L.S. / Mashhadi, Z. / Knight, T.W. / Fenske, T. / Hagemann, T. / Hoppe, R.W. / Han, L. / Miller, T.R. / Schwabacher, A.W. / Silvaggi, N.R.
History
DepositionFeb 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2017Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.3Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetoacetate decarboxylase
B: Acetoacetate decarboxylase
C: Acetoacetate decarboxylase
D: Acetoacetate decarboxylase


Theoretical massNumber of molelcules
Total (without water)110,8974
Polymers110,8974
Non-polymers00
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19630 Å2
ΔGint-116 kcal/mol
Surface area32740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.040, 75.040, 179.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 20 through 33 or (resid 34...
21(chain B and (resid 20 through 33 or (resid 34...
31(chain C and (resid 20 through 33 or (resid 34...
41(chain D and (resid 20 through 33 or (resid 34...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEU(chain A and (resid 20 through 33 or (resid 34...AA20 - 3319 - 32
12ARGARGARGARG(chain A and (resid 20 through 33 or (resid 34...AA3433
13ALAALALEULEU(chain A and (resid 20 through 33 or (resid 34...AA4 - 2593 - 258
14ALAALALEULEU(chain A and (resid 20 through 33 or (resid 34...AA4 - 2593 - 258
15ALAALALEULEU(chain A and (resid 20 through 33 or (resid 34...AA4 - 2593 - 258
16ALAALALEULEU(chain A and (resid 20 through 33 or (resid 34...AA4 - 2593 - 258
21ALAALALEULEU(chain B and (resid 20 through 33 or (resid 34...BB20 - 3319 - 32
22ARGARGARGARG(chain B and (resid 20 through 33 or (resid 34...BB3433
23ALAALALEULEU(chain B and (resid 20 through 33 or (resid 34...BB4 - 2593 - 258
24ALAALALEULEU(chain B and (resid 20 through 33 or (resid 34...BB4 - 2593 - 258
25ALAALALEULEU(chain B and (resid 20 through 33 or (resid 34...BB4 - 2593 - 258
26ALAALALEULEU(chain B and (resid 20 through 33 or (resid 34...BB4 - 2593 - 258
31ALAALALEULEU(chain C and (resid 20 through 33 or (resid 34...CC20 - 3319 - 32
32ARGARGARGARG(chain C and (resid 20 through 33 or (resid 34...CC3433
33ALAALALEULEU(chain C and (resid 20 through 33 or (resid 34...CC2 - 2591 - 258
34ALAALALEULEU(chain C and (resid 20 through 33 or (resid 34...CC2 - 2591 - 258
35ALAALALEULEU(chain C and (resid 20 through 33 or (resid 34...CC2 - 2591 - 258
36ALAALALEULEU(chain C and (resid 20 through 33 or (resid 34...CC2 - 2591 - 258
41ALAALALEULEU(chain D and (resid 20 through 33 or (resid 34...DD20 - 3319 - 32
42ARGARGARGARG(chain D and (resid 20 through 33 or (resid 34...DD3433
43ALAALAGLUGLU(chain D and (resid 20 through 33 or (resid 34...DD2 - 2571 - 256
44ALAALAGLUGLU(chain D and (resid 20 through 33 or (resid 34...DD2 - 2571 - 256
45ALAALAGLUGLU(chain D and (resid 20 through 33 or (resid 34...DD2 - 2571 - 256
46ALAALAGLUGLU(chain D and (resid 20 through 33 or (resid 34...DD2 - 2571 - 256

-
Components

#1: Protein
Acetoacetate decarboxylase


Mass: 27724.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas wittichii (bacteria) / Strain: RW1 / DSM 6014 / JCM 10273 / Gene: Swit_4259 / Production host: Escherichia coli (E. coli) / References: UniProt: A5VE83
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.64 Å3/Da / Density % sol: 53.45 % / Description: Long, hexagonal rods
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG 10000, 0.1M Tris pH 8.0, 0.3M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.91→44.96 Å / Num. obs: 87644 / % possible obs: 100 % / Redundancy: 5.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.106 / Net I/av σ(I): 6.8 / Net I/σ(I): 13.92
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4465 / CC1/2: 0.8 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
MOSFLM7.0.7data reduction
Aimless0.1.27data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZBO, 4JM3

4zbo

4jm3


Resolution: 1.912→44.064 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.62 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 5983 3.44 %
Rwork0.1716 167702 -
obs0.1726 173685 99.11 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 398.65 Å2 / Biso mean: 53.1377 Å2 / Biso min: 20.65 Å2
Refinement stepCycle: final / Resolution: 1.912→44.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7752 0 0 428 8180
Biso mean---45.25 -
Num. residues----1021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117965
X-RAY DIFFRACTIONf_angle_d1.17610863
X-RAY DIFFRACTIONf_chiral_restr0.071178
X-RAY DIFFRACTIONf_plane_restr0.0081423
X-RAY DIFFRACTIONf_dihedral_angle_d11.3024595
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5223X-RAY DIFFRACTION7.254TORSIONAL
12B5223X-RAY DIFFRACTION7.254TORSIONAL
13C5223X-RAY DIFFRACTION7.254TORSIONAL
14D5223X-RAY DIFFRACTION7.254TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9115-1.97990.30715610.2737160601662195
1.9799-2.05910.27495930.2386167361732999
2.0591-2.15280.24866060.2154167991740599
2.1528-2.26630.22296150.1857168011741699
2.2663-2.40830.21175940.17441689717491100
2.4083-2.59420.22245780.1771689817476100
2.5942-2.85530.21966000.17771684417444100
2.8553-3.26830.19266190.17111694417563100
3.2683-4.11730.19626040.15991691017514100
4.1173-44.07590.16566130.1498168131742699
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)
10.58270.0674-0.57471.01560.31832.09710.2004-0.47410.072-0.01970.0499-0.386-0.99040.63-0.30630.4958-0.1303-0.02530.4826-0.07090.52763.14313.66594.021
22.18610.107-0.0011.66080.90921.51920.02360.1511-0.01130.1307-0.20560.06380.03270.36370.16440.2591-0.0199-0.00240.35050.02750.2-4.2855-7.278920.5171
32.70250.979-1.57574.3232-1.75534.8309-0.2659-0.1961-0.34560.136-0.0155-0.76190.68570.33350.21970.40830.08790.04850.30010.02620.52489.0026-19.653214.6197
41.4439-1.39840.31061.7083-0.14081.61860.01640.10120.24670.3353-0.2584-0.2102-0.21290.16680.21710.2043-0.0608-0.03920.2396-0.0050.2845-5.94646.111715.4624
51.1369-0.2882-0.16830.76270.14531.2095-0.0143-0.208-0.07790.0925-0.053-0.11760.20150.10540.02410.239-0.0260.00530.2996-0.02090.2726-5.2937-5.078815.7454
60.83710.2724-0.39460.3293-0.04622.02180.025-0.1052-0.1058-0.0064-0.03530.04090.370.04760.10670.3283-0.03260.03620.2353-0.01610.3064-13.2729-12.946215.1726
70.98940.3247-0.49620.56390.31542.00460.0446-0.0008-0.05850.0298-0.0838-0.1657-0.08080.42690.07010.25110.05220.01480.3634-0.01020.30659.3049-5.557511.1397
80.6070.0561-0.05631.24890.36531.0999-0.1078-0.1407-0.15780.04290.1064-0.06460.28910.09830.00050.3252-0.01910.01280.26010.00370.2595-6.6147-7.798825.068
90.9057-0.4190.08450.20580.06530.89840.0149-0.0694-0.11140.0243-0.0079-0.10920.29680.2082-0.01130.3818-0.02280.02630.31530.00370.33860.6001-10.928115.2116
100.4249-0.4630.37890.76980.29291.83010.02560.1214-0.0729-0.0678-0.0452-0.20180.41960.46420.0180.3330.09590.04230.4769-0.03480.4005-0.0225-4.282-9.6955
116.7738-1.93372.4115.5694-2.26185.9544-0.38560.26370.9781-0.16770.1408-0.6817-1.12730.12710.05950.5614-0.0851-0.00460.40710.02570.46185.405221.2792-12.9985
121.02540.3482-0.22260.59280.36041.7951-0.06090.077-0.1752-0.1597-0.1072-0.36280.21630.16040.14330.28370.05290.05370.28090.01420.2806-4.0284-1.6725-13.4972
131.24840.0892-0.32860.77180.27951.4647-0.06660.25050.0412-0.14520.0274-0.1148-0.04050.08890.0150.30850.01190.02180.3238-0.01920.2667-7.54943.8848-13.7697
140.5925-0.01170.09180.22150.01751.2890.06530.1670.1342-0.1426-0.061-0.0167-0.1497-0.1883-0.01950.31120.0784-0.00330.3321-0.01120.2686-15.318411.3792-12.9879
151.2391-0.51361.26930.37370.05522.71590.0309-0.02160.0526-0.1473-0.0311-0.1581-0.0310.26690.10270.295-0.03570.04260.3959-0.00920.3288.21417.2761-9.2533
160.6071-0.3899-0.10491.21160.39880.8503-0.01560.22810.0629-0.0638-0.04060.0532-0.1067-0.13590.0360.35060.01890.00770.35870.01290.2632-8.29787.201-23.0565
170.57750.3603-0.0540.25960.10781.4975-0.0251-0.00130.2326-0.12520.0444-0.1012-0.34940.2236-0.01440.35860.00210.01520.3029-0.0050.3267-1.282111.4063-13.2138
180.83430.51580.19110.31390.01781.9655-0.0223-0.1548-0.09670.1335-0.1990.22310.3253-0.61570.15740.2678-0.09580.07320.5282-0.09950.3998-32.7415-1.319213.0891
192.74811.30781.40313.37591.19991.37180.0695-0.01820.3688-0.0322-0.05040.3712-0.3254-0.6699-0.02360.31880.2149-0.06850.7689-0.0070.6947-41.466821.58967.1318
201.6338-0.8115-0.14092.3454-0.95231.974-0.06-0.2244-0.1044-0.0277-0.03920.3398-0.0036-0.59590.03630.2694-0.03660.01920.4861-0.09080.3589-29.54033.219816.6486
211.6935-0.42260.21031.3528-0.34141.0580.056-0.0817-0.01070.027-0.12840.16320.0537-0.42390.09620.2209-0.04360.00110.4274-0.08650.283-28.90080.990114.2318
220.85260.2639-0.12390.6582-0.40430.2462-0.0732-0.10370.2580.11680.01110.28550.0032-0.58670.03710.24150.0130.01410.5759-0.09930.3667-32.41376.08419.5877
232.0456-2.28010.59742.7761-0.69950.1959-0.1696-0.19880.39820.45950.0812-0.4101-0.4428-0.07020.05710.3844-0.0549-0.0630.3708-0.07020.37-8.98511.885225.1762
241.2026-0.16460.05090.82520.14821.22410.0848-0.10750.20580.1585-0.0962-0.0535-0.306-0.35710.00440.27490.0196-0.01620.3368-0.05990.2791-19.678415.292710.0228
251.3933-0.03890.73330.1652-0.33691.31130.0938-0.3557-0.0562-0.02410.23930.0156-0.2672-0.6341-0.04780.29980.08150.05140.8728-0.14310.4227-37.826312.012916.1376
260.3222-0.18940.07291.42611.79426.54910.00940.27610.1933-0.02010.10090.15130.4367-0.7126-0.05530.3288-0.0654-0.04391.0812-0.08620.4374-47.43221.36240.0623
271.939-0.13970.05121.4201-0.39592.2579-0.0995-0.28840.23630.4084-0.01870.2338-0.2731-0.68540.11050.2880.04290.03790.4624-0.12230.3624-26.293113.774721.1733
280.8704-0.39990.45350.1936-0.14441.19610.02640.00250.06890.0347-0.0660.0381-0.1587-0.43-00.28830.05360.00480.5203-0.09250.376-33.482813.404210.757
290.43160.11560.57930.33661.00963.1349-0.12910.37180.111-0.35490.20210.1306-0.4802-1.08480.00170.35530.0627-0.03680.8351-0.02450.4346-38.09419.0366-6.3684
301.47680.7931-0.47792.0064-0.00210.9141-0.07640.2381-0.1261-0.2416-0.10570.4460.6108-0.89190.00360.4883-0.30020.03390.6761-0.18140.3919-32.0396-16.2303-10.7452
311.38470.5809-0.33011.8184-0.09820.7961-0.00120.2949-0.0582-0.1772-0.15120.14710.2355-0.67120.04660.343-0.0718-0.00850.5314-0.12420.2719-27.7917-3.511-11.6744
320.2619-0.47420.19720.7972-0.36490.1651-0.08520.2816-0.2475-0.0929-0.07720.22780.423-0.69230.11610.3328-0.16050.02790.5803-0.14670.3151-29.4483-9.606-8.4334
330.7877-0.12730.54491.20030.02770.55880.010.1448-0.2327-0.2673-0.1989-0.06490.8004-0.15620.16260.5662-0.06540.09550.3116-0.08870.3528-14.5705-16.7195-12.4317
340.4439-0.1808-0.01960.8608-0.25570.1444-0.05710.0211-0.201-0.53220.30120.01610.1438-0.13420.15190.546-0.3376-0.01260.8965-0.25350.4161-36.3542-16.423-13.3387
350.2795-0.3552-0.11820.4942-0.08091.9236-0.28430.2573-0.2196-0.30390.19060.3210.1683-0.66430.23760.3407-0.20870.01320.9474-0.14860.444-47.0795-6.82914.1033
361.49020.2691-0.55891.2514-0.65212.2111-0.12530.4399-0.1982-0.4871-0.19340.04210.8032-0.42510.32320.5351-0.14160.04170.4542-0.16590.3323-24.6446-16.8357-18.4615
372.1157-0.1001-0.02410.89581.74824.15130.1548-0.3365-0.328-0.1163-0.2441-0.12360.9879-0.3586-0.00890.6184-0.21770.11190.4041-0.05720.4491-26.0557-22.7222.5616
381.93350.8236-0.85841.5801-0.1450.4232-0.0770.27520.0756-0.1943-0.00920.01050.4726-0.8845-0.00910.5523-0.1846-0.0250.7391-0.18420.313-33.8034-14.1294-15.6241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 21 )A4 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 35 )A22 - 35
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 53 )A36 - 53
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 80 )A54 - 80
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 146 )A81 - 146
6X-RAY DIFFRACTION6chain 'A' and (resid 147 through 169 )A147 - 169
7X-RAY DIFFRACTION7chain 'A' and (resid 170 through 203 )A170 - 203
8X-RAY DIFFRACTION8chain 'A' and (resid 204 through 222 )A204 - 222
9X-RAY DIFFRACTION9chain 'A' and (resid 223 through 259 )A223 - 259
10X-RAY DIFFRACTION10chain 'B' and (resid 4 through 34 )B4 - 34
11X-RAY DIFFRACTION11chain 'B' and (resid 35 through 53 )B35 - 53
12X-RAY DIFFRACTION12chain 'B' and (resid 54 through 93 )B54 - 93
13X-RAY DIFFRACTION13chain 'B' and (resid 94 through 146 )B94 - 146
14X-RAY DIFFRACTION14chain 'B' and (resid 147 through 169 )B147 - 169
15X-RAY DIFFRACTION15chain 'B' and (resid 170 through 203 )B170 - 203
16X-RAY DIFFRACTION16chain 'B' and (resid 204 through 222 )B204 - 222
17X-RAY DIFFRACTION17chain 'B' and (resid 223 through 259 )B223 - 259
18X-RAY DIFFRACTION18chain 'C' and (resid 2 through 34 )C2 - 34
19X-RAY DIFFRACTION19chain 'C' and (resid 35 through 53 )C35 - 53
20X-RAY DIFFRACTION20chain 'C' and (resid 54 through 69 )C54 - 69
21X-RAY DIFFRACTION21chain 'C' and (resid 70 through 93 )C70 - 93
22X-RAY DIFFRACTION22chain 'C' and (resid 94 through 131 )C94 - 131
23X-RAY DIFFRACTION23chain 'C' and (resid 132 through 146 )C132 - 146
24X-RAY DIFFRACTION24chain 'C' and (resid 147 through 169 )C147 - 169
25X-RAY DIFFRACTION25chain 'C' and (resid 170 through 187 )C170 - 187
26X-RAY DIFFRACTION26chain 'C' and (resid 188 through 203 )C188 - 203
27X-RAY DIFFRACTION27chain 'C' and (resid 204 through 222 )C204 - 222
28X-RAY DIFFRACTION28chain 'C' and (resid 223 through 259 )C223 - 259
29X-RAY DIFFRACTION29chain 'D' and (resid 2 through 21 )D2 - 21
30X-RAY DIFFRACTION30chain 'D' and (resid 22 through 69 )D22 - 69
31X-RAY DIFFRACTION31chain 'D' and (resid 70 through 92 )D70 - 92
32X-RAY DIFFRACTION32chain 'D' and (resid 93 through 135 )D93 - 135
33X-RAY DIFFRACTION33chain 'D' and (resid 136 through 169 )D136 - 169
34X-RAY DIFFRACTION34chain 'D' and (resid 170 through 187 )D170 - 187
35X-RAY DIFFRACTION35chain 'D' and (resid 188 through 202 )D188 - 202
36X-RAY DIFFRACTION36chain 'D' and (resid 203 through 222 )D203 - 222
37X-RAY DIFFRACTION37chain 'D' and (resid 223 through 236 )D223 - 236
38X-RAY DIFFRACTION38chain 'D' and (resid 237 through 257 )D237 - 257

+
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