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- PDB-6nbg: 2.05 Angstrom Resolution Crystal Structure of Hypothetical Protei... -

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Basic information

Entry
Database: PDB / ID: 6nbg
Title2.05 Angstrom Resolution Crystal Structure of Hypothetical Protein KP1_5497 from Klebsiella pneumoniae.
ComponentsGlucosamine-6-phosphate deaminase
KeywordsUNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Hypothetical Protein
Function / homology
Function and homology information


glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine metabolic process / carbohydrate metabolic process
Similarity search - Function
Glucosamine-6-phosphate isomerase, conserved site / Glucosamine/galactosamine-6-phosphate isomerases signature. / Glucosamine-6-phosphate isomerase / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / NagB/RpiA transferase-like
Similarity search - Domain/homology
PHOSPHATE ION / Glucosamine-6-phosphate deaminase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionDec 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosamine-6-phosphate deaminase
B: Glucosamine-6-phosphate deaminase
C: Glucosamine-6-phosphate deaminase
D: Glucosamine-6-phosphate deaminase
E: Glucosamine-6-phosphate deaminase
F: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,28415
Polymers160,4896
Non-polymers7959
Water13,745763
1
A: Glucosamine-6-phosphate deaminase
B: Glucosamine-6-phosphate deaminase
C: Glucosamine-6-phosphate deaminase
E: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4089
Polymers106,9934
Non-polymers4155
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-65 kcal/mol
Surface area37120 Å2
MethodPISA
2
D: Glucosamine-6-phosphate deaminase
F: Glucosamine-6-phosphate deaminase
hetero molecules

D: Glucosamine-6-phosphate deaminase
F: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,75312
Polymers106,9934
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9160 Å2
ΔGint-94 kcal/mol
Surface area37040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.482, 123.806, 299.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-541-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLNGLNAA-1 - 2382 - 241
21ASNASNGLNGLNBB-1 - 2382 - 241
12ASNASNLEULEUAA-1 - 2372 - 240
22ASNASNLEULEUCC-1 - 2372 - 240
13ALAALALEULEUAA0 - 2373 - 240
23ALAALALEULEUDD0 - 2373 - 240
14ASNASNLEULEUAA-1 - 2372 - 240
24ASNASNLEULEUEE-1 - 2372 - 240
15ALAALAGLNGLNAA0 - 2383 - 241
25ALAALAGLNGLNFF0 - 2383 - 241
16ASNASNLEULEUBB-1 - 2372 - 240
26ASNASNLEULEUCC-1 - 2372 - 240
17ALAALALEULEUBB0 - 2373 - 240
27ALAALALEULEUDD0 - 2373 - 240
18ASNASNLEULEUBB-1 - 2372 - 240
28ASNASNLEULEUEE-1 - 2372 - 240
19ALAALAGLNGLNBB0 - 2383 - 241
29ALAALAGLNGLNFF0 - 2383 - 241
110ALAALALEULEUCC0 - 2373 - 240
210ALAALALEULEUDD0 - 2373 - 240
111ASNASNGLNGLNCC-1 - 2382 - 241
211ASNASNGLNGLNEE-1 - 2382 - 241
112ALAALALEULEUCC0 - 2373 - 240
212ALAALALEULEUFF0 - 2373 - 240
113ALAALALEULEUDD0 - 2373 - 240
213ALAALALEULEUEE0 - 2373 - 240
114ALAALALEULEUDD0 - 2373 - 240
214ALAALALEULEUFF0 - 2373 - 240
115ALAALALEULEUEE0 - 2373 - 240
215ALAALALEULEUFF0 - 2373 - 240

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Glucosamine-6-phosphate deaminase


Mass: 26748.199 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: nagB_2, DM059_30720, SAMEA4364603_04465 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) magic
References: UniProt: A0A332QZQ2, glucosamine-6-phosphate deaminase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein: 8.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCl pH 8.3; Screen: Classics II (D7), 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG3350;

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 11, 2018 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 87989 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.044 / Rrim(I) all: 0.105 / Rsym value: 0.095 / Χ2: 1.477 / Net I/σ(I): 20.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 2 / Num. unique obs: 4325 / CC1/2: 0.676 / Rpim(I) all: 0.393 / Rrim(I) all: 0.922 / Rsym value: 0.832 / Χ2: 1.002 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→29.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.822 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23131 4491 5.1 %RANDOM
Rwork0.20075 ---
obs0.20229 83398 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.545 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2--1.09 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 2.05→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11006 0 41 763 11810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01311299
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710607
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.64415337
X-RAY DIFFRACTIONr_angle_other_deg0.3771.56724595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.99851446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.3722.818543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.68151737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2821560
X-RAY DIFFRACTIONr_chiral_restr0.0670.21495
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.0212690
X-RAY DIFFRACTIONr_gen_planes_other0.0520.022190
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_it1.542.3325787
X-RAY DIFFRACTIONr_mcbond_other1.542.3325786
X-RAY DIFFRACTIONr_mcangle_it2.3833.4887232
X-RAY DIFFRACTIONr_mcangle_other2.3823.4887233
X-RAY DIFFRACTIONr_scbond_it1.982.5575512
X-RAY DIFFRACTIONr_scbond_other1.922.5285473
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9533.7048050
X-RAY DIFFRACTIONr_long_range_B_refined6.35429.76312559
X-RAY DIFFRACTIONr_long_range_B_other6.24529.37812401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A76760.07
12B76760.07
21A75450.09
22C75450.09
31A75560.07
32D75560.07
41A75630.08
42E75630.08
51A74070.1
52F74070.1
61B76220.09
62C76220.09
71B76060.06
72D76060.06
81B76590.07
82E76590.07
91B74350.1
92F74350.1
101C74300.09
102D74300.09
111C75040.09
112E75040.09
121C73240.11
122F73240.11
131D75010.08
132E75010.08
141D73150.11
142F73150.11
151E73510.11
152F73510.11
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 376 -
Rwork0.297 5835 -
obs--96.32 %
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)
12.86350.43250.45240.4531-0.21872.6162-0.0259-0.0796-0.1811-0.0467-0.0205-0.00550.26190.02460.04640.1669-0.01180.06770.0165-0.02940.1092-9.8681-14.745253.6832
22.2995-0.1107-0.88790.6716-0.27951.5036-0.1044-0.48070.03060.0250.0692-0.03730.020.12870.03520.118-0.00210.03680.1592-0.06610.0629-14.8514-9.093967.9161
30.43320.6372-1.10860.9835-1.90914.5189-0.03310.08170.1281-0.05320.15880.15360.1189-0.4436-0.12560.0329-0.0250.02750.1438-0.08890.152-32.1811-9.08162.0038
40.76840.0592-0.23150.7152-0.58221.5356-0.01040.00990.0772-0.1353-0.02630.1126-0.0758-0.20940.03670.1488-0.00950.02350.0971-0.07020.1107-24.6001-7.949849.7679
51.981-0.3712-1.25680.61890.67421.3068-0.08220.3295-0.06960.0458-0.05040.02790.1531-0.10810.13260.2104-0.0030.03980.12360.00870.10876.8246-15.317141.8616
65.69211.825-0.82363.70821.94631.93430.00110.87650.222-0.33980.0460.1117-0.078-0.3377-0.04710.18470.0384-0.00320.290.12810.07828.677-5.828630.1581
70.4798-0.1561-0.92110.58270.7942.2360.0361-0.03040.09420.02640.1242-0.0397-0.02440.2014-0.16030.18980.03410.04240.22120.08180.159923.8898-9.499739.2201
81.108-0.126-0.3770.82520.36441.90040.0372-0.06880.09940.0674-0.0065-0.0374-0.03060.2422-0.03070.09660.00890.04220.06090.03120.06119.2249-7.968750.813
93.76120.6813-0.30321.7949-0.30080.8427-0.11130.75620.0953-0.330.11260.0715-0.2178-0.126-0.00130.34980.02720.02540.1620.02140.0142-14.008219.634638.3131
103.929-1.70570.984.4415-3.27374.8604-0.11320.64360.1609-0.39810.2550.6329-0.2579-0.3818-0.14180.38430.0536-0.19440.37010.01640.248-33.246518.033432.6016
111.66960.5962-0.26921.8211-0.41551.67520.02540.2486-0.1635-0.0704-0.02970.2836-0.2485-0.37610.00430.32480.08350.01180.1515-0.03590.1172-25.100913.864348.2647
126.5436-3.9148-0.33143.6610.62960.9406-0.2358-0.31360.10980.3080.27640.0351-0.21380.0032-0.04060.29410.08210.03120.0496-0.00750.0258-21.552922.156256.8349
132.22850.8538-0.65861.2642-0.2982.1705-0.2549-0.0043-0.2079-0.21760.1684-0.09410.28090.04210.08650.1713-0.03820.05260.0407-0.01060.0292-17.7058-17.294512.64
146.3053-1.77-2.15211.9979-0.49521.54590.0461-0.17940.5627-0.03440.2062-0.087-0.0296-0.0497-0.25220.1385-0.05290.00970.08330.01830.1099-20.4043-3.120314.2087
150.82590.2147-0.41391.1035-1.16992.091-0.10240.25590.0961-0.18170.17280.18210.1651-0.4849-0.07040.1732-0.08470.00270.2350.02630.1056-33.2173-11.20486.8791
164.4495-0.6078-0.39347.4627-2.48869.52160.36880.8385-0.4111-1.5377-0.28660.35960.504-0.0466-0.08210.551-0.0502-0.05590.3387-0.08040.1872-30.0264-22.0222-9.0191
172.64710.229-0.13310.09970.29281.19920.0033-0.23220.1375-0.07240.00580.0041-0.27150.0594-0.00910.4033-0.03350.06820.0522-0.02920.06843.856223.357152.1478
183.22260.9151.06551.9318-0.09952.2261-0.0152-1.0724-0.08830.2446-0.0598-0.0901-0.2993-0.23040.0750.38810.00320.06130.41190.02520.03049.690718.960467.0041
190.69650.00950.27241.81990.83450.50410.0655-0.1464-0.02790.05370.0488-0.1927-0.0190.0031-0.11430.3055-0.11070.05970.16150.00660.12523.257117.816358.3003
203.04540.3745-0.06071.2874-0.21080.97620.0350.0353-0.1183-0.211-0.0489-0.2053-0.20940.22310.01390.2767-0.07220.09410.0569-0.01310.092119.41515.233644.2385
214.2522-1.61953.38871.7457-2.00684.4791-1.1062-1.47950.70460.60610.4784-0.4161-1.1324-1.29450.62790.47640.2741-0.2020.734-0.2710.15083.047317.39859.0027
221.33081.64073.03028.32241.78877.5582-0.02220.1277-0.05680.4969-0.1715-1.2894-0.0850.30350.19360.1845-0.0567-0.17340.26630.05950.310822.41289.848113.1937
236.27895.5497-1.707212.98368.550612.99210.93030.58680.52040.3286-0.32590.0773-0.8796-1.2154-0.60430.28430.1645-0.03230.28440.05390.21322.120725.89915.3061
242.2053-0.56723.00681.1312-1.18835.5233-0.3894-0.04580.29320.0692-0.1136-0.3152-0.2896-0.02570.50310.1611-0.0576-0.04130.1786-0.01350.113813.743912.1291-1.2651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 55
2X-RAY DIFFRACTION2A56 - 124
3X-RAY DIFFRACTION3A125 - 170
4X-RAY DIFFRACTION4A171 - 239
5X-RAY DIFFRACTION5B-1 - 91
6X-RAY DIFFRACTION6B92 - 115
7X-RAY DIFFRACTION7B116 - 169
8X-RAY DIFFRACTION8B170 - 239
9X-RAY DIFFRACTION9C-1 - 139
10X-RAY DIFFRACTION10C140 - 173
11X-RAY DIFFRACTION11C174 - 223
12X-RAY DIFFRACTION12C224 - 238
13X-RAY DIFFRACTION13D0 - 105
14X-RAY DIFFRACTION14D106 - 124
15X-RAY DIFFRACTION15D125 - 229
16X-RAY DIFFRACTION16D230 - 238
17X-RAY DIFFRACTION17E-1 - 57
18X-RAY DIFFRACTION18E58 - 124
19X-RAY DIFFRACTION19E125 - 205
20X-RAY DIFFRACTION20E206 - 238
21X-RAY DIFFRACTION21F0 - 138
22X-RAY DIFFRACTION22F139 - 157
23X-RAY DIFFRACTION23F158 - 168
24X-RAY DIFFRACTION24F169 - 239

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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

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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

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