[English] 日本語
Yorodumi
- PDB-6wn8: 2.70 Angstrom Resolution Crystal Structure of Uracil Phosphoribos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wn8
Title2.70 Angstrom Resolution Crystal Structure of Uracil Phosphoribosyl Transferase from Klebsiella pneumoniae
ComponentsUracil phosphoribosyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Uracil Phosphoribosyl Transferase
Function / homology
Function and homology information


uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / UMP salvage / GTP binding / magnesium ion binding
Similarity search - Function
Uracil phosphoribosyltransferase, bacterial-type / Uracil phosphoribosyl transferase / Uracil phosphoribosyltransferase / : / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / beta-D-fructopyranose / Uracil phosphoribosyltransferase / Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F. / 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
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jun 14, 2023Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_abbrev ..._chem_comp.pdbx_synonyms / _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
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase
C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase
E: Uracil phosphoribosyltransferase
F: Uracil phosphoribosyltransferase
G: Uracil phosphoribosyltransferase
H: Uracil phosphoribosyltransferase
I: Uracil phosphoribosyltransferase
J: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,466130
Polymers228,66610
Non-polymers10,800120
Water8,521473
1
A: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase
C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,03754
Polymers91,4664
Non-polymers4,57150
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22410 Å2
ΔGint-699 kcal/mol
Surface area31120 Å2
MethodPISA
2
E: Uracil phosphoribosyltransferase
F: Uracil phosphoribosyltransferase
G: Uracil phosphoribosyltransferase
H: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,91151
Polymers91,4664
Non-polymers4,44547
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22120 Å2
ΔGint-667 kcal/mol
Surface area31110 Å2
MethodPISA
3
I: Uracil phosphoribosyltransferase
J: Uracil phosphoribosyltransferase
hetero molecules

I: Uracil phosphoribosyltransferase
J: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,03750
Polymers91,4664
Non-polymers3,57046
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area21340 Å2
ΔGint-685 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.349, 203.349, 157.775
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Uracil phosphoribosyltransferase / UMP pyrophosphorylase / UPRTase


Mass: 22866.570 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: upp, C4Y86_021390, C4Z38_007125, E3U37_17930, E3U38_17635, E9161_15415, E9167_16225, EJ893_03135, FAT88_15980, NCTC9504_02023, RJA_06790
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (DE3)magic
References: UniProt: A0A1Y0PUH0, UniProt: A6TCB0*PLUS, uracil phosphoribosyltransferase

-
Sugars , 2 types, 6 molecules

#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 587 molecules

#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 91 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein: 10.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen (AmSO4, H2): 0.1M Sodium acetate pH 4.6, 2.0M Ammonium sulfate; Cryo: 25% Sucrose, 2.0M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2019 / Details: BE
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 103165 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Rsym value: 0.09 / Χ2: 1.006 / Net I/σ(I): 20.3
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5133 / CC1/2: 0.737 / CC star: 0.921 / Rpim(I) all: 0.332 / Rrim(I) all: 0.857 / Rsym value: 0.79 / Χ2: 1.001 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ehj
Resolution: 2.7→29.71 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 19.449 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.389 / ESU R Free: 0.25
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 5203 5 %RANDOM
Rwork0.1888 ---
obs0.1903 97876 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 157.93 Å2 / Biso mean: 55.587 Å2 / Biso min: 30.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 2.7→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15854 0 561 473 16888
Biso mean--90.02 53.56 -
Num. residues----2087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01316597
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716101
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.63722542
X-RAY DIFFRACTIONr_angle_other_deg0.2911.57637410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.15952085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.32623.435655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.445152990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.7921570
X-RAY DIFFRACTIONr_chiral_restr0.050.22209
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.0217725
X-RAY DIFFRACTIONr_gen_planes_other0.0530.022865
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 355 -
Rwork0.291 7134 -
all-7489 -
obs--99.63 %
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)
13.4910.0702-0.54584.7821-1.49323.3229-0.05510.2604-0.7852-0.1975-0.0666-0.47780.14830.31930.12170.36330.01450.01630.1944-0.05020.232392.886135.650518.2784
29.95282.98825.72162.12362.28143.7740.08810.191-0.05190.0247-0.16270.155-0.0320.17280.07460.1836-0.020.04820.16950.00350.050588.813642.072224.69
33.5682-0.29675.98191.2449-1.35710.9695-0.02670.04690.105-0.0637-0.1165-0.1231-0.24160.23480.14320.2162-0.03790.03850.0319-0.02870.116196.81853.304334.7816
44.0782-0.09641.18792.07940.24856.58020.1440.01390.3909-0.32080.1712-0.233-0.3696-0.0312-0.31520.3097-0.02060.04350.036-0.00170.097487.480555.379615.5514
52.1833-0.3618-0.32354.43660.91753.66780.05530.26310.0682-0.49570.018-0.1877-0.29310.3915-0.07330.2815-0.04830.07430.15420.03230.040796.0150.681813.0595
64.8916-2.705-2.98725.55473.86073.0294-0.18510.17530.0050.0282-0.00970.3440.0665-0.04370.19480.2493-0.0187-0.01770.11280.04170.065478.902143.50611.9631
72.60241.7489-0.80061.9847-1.87664.0360.1139-0.03980.0225-0.1048-0.0831-0.4168-0.25370.5707-0.03090.526-0.13650.14690.5435-0.05860.7324101.206741.579242.1405
81.6861-2.7659-3.46385.73827.660511.1503-0.11520.0681-0.1262-0.1312-0.08850.3226-0.20780.22930.20370.16860.0049-0.04440.24740.01240.220191.922938.769637.7687
90.1013-0.01470.35141.55120.61028.61530.00840.0008-0.1038-0.1058-0.15130.02190.0970.09130.1430.0666-0.0028-0.03020.10020.00020.159586.27128.752329.4808
102.59850.0177-1.06662.759-1.970411.07090.015-0.0818-0.50030.17650.05880.25490.0820.1866-0.07380.0854-0.0453-0.00820.04880.03440.127185.762924.723549.1842
112.89521.42961.5032.82830.84033.22920.15450.0407-0.16940.11540.0247-0.13530.17230.3635-0.17920.02590.0148-0.02450.0680.01450.067897.52826.618446.93
1211.5963-0.4662-0.14380.2401-0.02610.0137-0.058-0.37820.44430.05530.08250.0947-0.02290.0253-0.02450.178-0.01-0.02410.1691-0.00390.136492.619242.152955.3168
133.1137-1.60020.85233.02940.61071.02140.20970.0621-0.2378-0.072-0.43490.831-0.191-0.45760.22530.41650.1245-0.00720.4231-0.00070.486759.028739.142638.5767
141.3674-2.704-1.277210.63794.5542.7947-0.03650.0899-0.0428-0.01170.15190.066-0.07430.1297-0.11550.0907-0.00040.02520.09710.03170.104468.911340.906538.8556
150.60011.4850.27057.0994-1.07851.0201-0.0097-0.11580.02150.42940.02960.1078-0.2531-0.2027-0.01990.22260.023-0.00730.0697-0.00560.081974.181354.481648.9241
162.85930.9678-1.46495.2755-1.99613.8004-0.0055-0.4131-0.01540.0412-0.16550.06030.1247-0.04520.1710.1544-0.0269-0.05310.09480.01310.126372.863733.273852.3981
172.17730.70080.2741.806-0.1692.8040.0967-0.39810.30590.4285-0.20440.3174-0.0761-0.24180.10770.2154-0.02090.05320.1309-0.00990.196964.515538.092954.8378
188.78910.2913-0.14240.1920.5923.93360.17640.2884-0.60670.1834-0.00420.01220.2771-0.0996-0.17220.2529-0.0150.00170.01760.0110.213264.49724.119742.3118
193.3575-0.04030.26322.0135-0.78525.7691-0.1993-0.58870.40990.22250.13170.3296-0.555-0.38430.06760.44250.1001-0.00810.1306-0.03690.366768.11962.828438.7274
2010.50077.76940.98516.18811.06530.6532-0.01180.0935-0.02940.0210.15710.0667-0.14490.1063-0.14520.2980.05590.0390.043-0.02620.189870.901653.861333.4738
212.56322.5978-0.02377.828-1.51371.1499-0.08140.26230.3001-0.12560.36520.8313-0.1999-0.1095-0.28390.18220.0420.02150.07920.01760.149964.259542.795524.9653
225.30581.6866-1.27968.5529-6.25068.1292-0.01810.4844-0.0349-0.18450.39480.1821-0.2314-0.5042-0.37670.21160.02850.03530.06560.01750.024272.253457.612417.609
232.3298-0.3241.22465.1760.59693.1195-0.13690.16690.2968-0.2730.0070.4418-0.1753-0.17950.12980.30570.0158-0.06090.04810.05350.206164.091962.607320.596
240.4941-1.7457-0.49886.22531.78220.5190.062-0.01980.1431-0.39440.0571-0.4072-0.12530.0574-0.11920.52530.001-0.04280.16720.02890.332775.519770.546632.0398
254.7088-0.3495-0.8861.959-1.0092.8022-0.0365-0.29470.10330.0676-0.09850.0851-0.0927-0.21820.13490.17980.094-0.00240.15380.02150.180970.1968-9.190335.5777
260.4981.1022-0.214211.218-0.30760.0957-0.02970.03110.0296-0.30190.0498-0.06440.0107-0.0146-0.02010.11410.0898-0.03710.10780.00280.060172.1745-7.118725.6119
271.7452-2.90121.06517.4597-2.45351.0336-0.05130.09340.0662-0.02940.0906-0.036-0.04460.0966-0.03930.15920.06260.05660.16550.05060.107780.81841.472119.3635
2811.834613.30173.015119.56894.62961.10640.3235-0.20480.19321.3376-0.39210.24820.3091-0.12650.06860.55510.171-0.02550.3285-0.01510.075499.4974-20.624334.786
291.4142-0.30870.19141.7703-0.35563.66760.1330.0430.12420.1856-0.0852-0.2734-0.02640.3958-0.04790.12420.0774-0.02850.14850.04810.182187.1129-8.656332.7464
301.3147-0.5792-1.32010.34061.39459.1778-0.04270.0111-0.02550.0702-0.02710.00570.5873-0.1360.06980.16430.0273-0.00770.08570.03970.158976.3707-23.014530.4098
315.476-0.9026-0.77212.21380.5333.44410.07150.04190.4483-0.03290.0825-0.1985-0.03880.5239-0.1540.1630.0544-0.03220.12190.01930.189367.448312.197821.6762
320.58410.617-1.58872.6046-5.547112.0649-0.11110.1111-0.0959-0.0027-0.0377-0.0289-0.0103-0.09280.14880.1150.0681-0.01670.1452-0.03810.185264.12212.282820.6055
331.7647-2.05171.06585.4391-2.78531.4467-0.0034-0.1144-0.1231-0.21350.20790.3830.1556-0.1511-0.20450.2467-0.0037-0.08310.1841-0.00720.335757.3699-9.238328.6534
343.5309-0.56610.15687.4642-3.69972.78210.08080.1242-0.2806-0.25570.08430.43890.2915-0.2637-0.16510.16180.0341-0.06250.1033-0.04520.066552.47632.168716.089
352.0315-0.6658-0.01112.5227-0.11881.63770.0345-0.0203-0.02480.0943-0.01720.26630.0297-0.1255-0.01740.08270.0503-0.06530.088-0.00310.1849.600110.079822.5538
363.93080.9646-0.084711.86815.83384.2496-0.07810.56960.1815-0.43490.08640.1876-0.28820.2673-0.00830.14110.04320.01140.22560.07190.120359.242316.09598.9124
372.2321-0.82150.57744.07-0.8975.50350.350.2559-0.5956-0.0515-0.18640.29490.79610.1502-0.16360.21760.1246-0.16010.1337-0.15770.285255.49-21.34572.944
386.18683.5304-6.48913.0549-3.87579.49280.41770.2723-0.21-0.0096-0.23880.11430.14470.1859-0.17890.2060.1954-0.14250.2397-0.10820.218461.1825-13.40561.5591
397.85992.1928-1.14681.6679-0.26510.34180.03340.3485-0.1728-0.45-0.20750.1453-0.03920.15790.17420.32210.1731-0.09170.42220.1140.146369.5109-1.9637-5.2069
409.64960.9839-1.571.523-0.88362.12410.17790.1446-0.1374-0.1991-0.06160.1121-0.1698-0.0056-0.11630.17970.1224-0.06910.1153-0.06480.092750.6672-4.07832.5808
413.0648-0.31960.71082.452-0.19231.95240.20540.6175-0.298-0.602-0.13710.24910.15970.0659-0.06830.29910.1893-0.19910.2773-0.16560.186748.3387-7.2995-5.836
422.46490.55354.07049.07113.59767.54540.2684-0.1537-0.36090.78090.07280.49720.6131-0.2574-0.34110.13320.0228-0.10890.1482-0.04480.380643.3833-15.92349.4067
433.2356-0.92021.94211.2702-1.43022.39570.2380.4744-0.1832-0.6085-0.29850.04510.10960.20470.06060.87470.312-0.10510.6179-0.05010.398478.2996-12.6611-6.1834
447.40594.9791.763910.27042.06932.45710.1010.33460.4023-0.3607-0.23620.4127-0.3442-0.02190.13520.21050.2110.01350.27040.02930.047175.8844-10.97043.124
455.08650.283-0.59263.147-0.52634.0421-0.08130.126-0.4028-0.0629-0.00140.35680.4212-0.07280.08270.171-0.0166-0.0630.0253-0.04980.207351.9545-30.95237.7499
4610.02851.8350.14391.75-0.43770.33940.03950.3417-0.5268-0.306-0.0972-0.04840.18560.15080.05770.20420.1503-0.03830.1296-0.02830.101471.2149-23.309710.0083
473.5928-0.3939-0.03133.7444-0.50193.39490.07240.3252-0.2852-0.4386-0.3168-0.34120.51880.26720.24440.32690.30050.04120.3162-0.02220.244687.269-24.1794.4462
480.2036-0.347-0.77950.97990.32788.37180.06210.05880.03120.0515-0.0608-0.1276-0.27460.2855-0.00130.13590.1228-0.00120.17470.03860.186490.3494-7.65524.1221
495.7895-2.24130.44532.07770.2795.52680.0239-0.3752-0.54450.09390.12020.41760.2934-0.8498-0.14410.1337-0.0164-0.0450.360.29070.406910.243810.238819.3951
501.87360.92391.364712.23066.40653.8641-0.2136-0.06-0.24610.25130.19710.53080.11180.06870.01650.14920.0641-0.0690.25390.10830.269113.924817.29812.7012
511.8475-2.33020.72056.4472-0.11060.4757-0.1337-0.1349-0.04690.25130.12460.003-0.0372-0.04250.00910.04060.0491-0.01770.1170.05020.123421.678528.745611.9824
521.67241.1225-2.531714.4165-7.90476.7548-0.0766-0.0565-0.1061-0.12810.0749-0.1320.17960.0750.00170.1170.0467-0.08490.1881-0.00630.39231.8239-1.374115.2931
533.0181-0.3010.17681.4543-0.98332.57810.0968-0.2599-0.23680.21850.16760.17250.0219-0.1505-0.26440.13960.0796-0.08780.25130.11110.278827.525613.293420.5557
542.29730.421-1.87951.8596-3.39526.9282-0.10870.1042-0.365-0.09930.0685-0.00160.2124-0.24310.04030.122-0.0091-0.06960.05780.04530.272419.305-1.238512.9977
556.1837-0.7603-0.28653.19420.92553.6609-0.1053-0.89450.07850.20290.1905-0.1809-0.16850.3102-0.08520.13650.1112-0.03380.33480.05720.14277.55935.764217.0999
560.4681-0.11860.59764.6453-1.68592.0223-0.0474-0.1938-0.4047-0.08510.30740.177-0.0022-0.3426-0.25990.06710.09830.0250.34760.17550.47662.554719.711710.922
572.5502-1.5828-0.09796.1964-0.13741.98560.0507-0.0516-0.10810.05070.08790.02420.1765-0.3204-0.13870.10750.0461-0.07040.27340.13230.2008-4.595432.10173.8901
581.8104-0.39541.19910.98690.49342.69210.1252-0.4985-0.46960.13540.10550.19020.1021-0.6526-0.23070.08440.0817-0.01770.50350.25820.375-11.652429.78078.4424
597.7550.9722-1.09915.0643-2.68772.4861-0.0802-0.4830.23460.05570.1076-0.0584-0.046-0.137-0.02740.09570.1277-0.02310.29220.00630.0362-3.028241.177215.6168
607.51413.8605-2.44254.1351-3.07672.49590.3404-0.18310.06650.1412-0.19530.1431-0.19470.267-0.14510.2018-0.0116-0.020.2138-0.01640.14044.891740.7796-1.4588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 22
2X-RAY DIFFRACTION2A23 - 49
3X-RAY DIFFRACTION3A50 - 85
4X-RAY DIFFRACTION4A86 - 115
5X-RAY DIFFRACTION5A116 - 194
6X-RAY DIFFRACTION6A195 - 208
7X-RAY DIFFRACTION7B-1 - 23
8X-RAY DIFFRACTION8B24 - 50
9X-RAY DIFFRACTION9B51 - 89
10X-RAY DIFFRACTION10B90 - 117
11X-RAY DIFFRACTION11B118 - 191
12X-RAY DIFFRACTION12B192 - 208
13X-RAY DIFFRACTION13C-1 - 21
14X-RAY DIFFRACTION14C22 - 49
15X-RAY DIFFRACTION15C50 - 85
16X-RAY DIFFRACTION16C86 - 114
17X-RAY DIFFRACTION17C115 - 184
18X-RAY DIFFRACTION18C185 - 208
19X-RAY DIFFRACTION19D-1 - 23
20X-RAY DIFFRACTION20D24 - 50
21X-RAY DIFFRACTION21D51 - 84
22X-RAY DIFFRACTION22D85 - 115
23X-RAY DIFFRACTION23D116 - 178
24X-RAY DIFFRACTION24D179 - 208
25X-RAY DIFFRACTION25E-1 - 22
26X-RAY DIFFRACTION26E23 - 50
27X-RAY DIFFRACTION27E51 - 102
28X-RAY DIFFRACTION28E103 - 110
29X-RAY DIFFRACTION29E111 - 191
30X-RAY DIFFRACTION30E192 - 208
31X-RAY DIFFRACTION31F0 - 23
32X-RAY DIFFRACTION32F24 - 50
33X-RAY DIFFRACTION33F51 - 84
34X-RAY DIFFRACTION34F85 - 106
35X-RAY DIFFRACTION35F107 - 188
36X-RAY DIFFRACTION36F189 - 208
37X-RAY DIFFRACTION37G0 - 26
38X-RAY DIFFRACTION38G27 - 49
39X-RAY DIFFRACTION39G50 - 83
40X-RAY DIFFRACTION40G84 - 109
41X-RAY DIFFRACTION41G110 - 188
42X-RAY DIFFRACTION42G189 - 208
43X-RAY DIFFRACTION43H0 - 21
44X-RAY DIFFRACTION44H22 - 47
45X-RAY DIFFRACTION45H48 - 59
46X-RAY DIFFRACTION46H60 - 94
47X-RAY DIFFRACTION47H95 - 191
48X-RAY DIFFRACTION48H192 - 208
49X-RAY DIFFRACTION49I-1 - 23
50X-RAY DIFFRACTION50I24 - 50
51X-RAY DIFFRACTION51I51 - 99
52X-RAY DIFFRACTION52I100 - 109
53X-RAY DIFFRACTION53I110 - 185
54X-RAY DIFFRACTION54I186 - 208
55X-RAY DIFFRACTION55J-1 - 22
56X-RAY DIFFRACTION56J23 - 81
57X-RAY DIFFRACTION57J82 - 110
58X-RAY DIFFRACTION58J111 - 155
59X-RAY DIFFRACTION59J156 - 199
60X-RAY DIFFRACTION60J200 - 208

+
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