[English] 日本語
Yorodumi
- PDB-8egl: Crystal Structure of Guanylate kinase from Pseudomonas aeruginosa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8egl
TitleCrystal Structure of Guanylate kinase from Pseudomonas aeruginosa PAO1 in complex with GMP and ADP
ComponentsGuanylate kinase
KeywordsTRANSFERASE / SSGCID / ATP-binding / Nucleotide-binding / GMP kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


guanylate kinase / guanylate kinase activity / phosphorylation / ATP binding / cytosol
Similarity search - Function
Guanylate kinase / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / ADENOSINE-5'-DIPHOSPHATE / Guanylate kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of Guanylate kinase from Pseudomonas aeruginosa PAO1 in complex with GMP and ADP
Authors: Abendroth, J. / DeBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Guanylate kinase
B: Guanylate kinase
C: Guanylate kinase
D: Guanylate kinase
E: Guanylate kinase
F: Guanylate kinase
G: Guanylate kinase
H: Guanylate kinase
I: Guanylate kinase
J: Guanylate kinase
K: Guanylate kinase
L: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,70136
Polymers288,21612
Non-polymers9,48524
Water8,305461
1
A: Guanylate kinase
B: Guanylate kinase
C: Guanylate kinase
J: Guanylate kinase
K: Guanylate kinase
L: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,85118
Polymers144,1086
Non-polymers4,74312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Guanylate kinase
E: Guanylate kinase
F: Guanylate kinase
G: Guanylate kinase
H: Guanylate kinase
I: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,85118
Polymers144,1086
Non-polymers4,74312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.280, 72.370, 144.730
Angle α, β, γ (deg.)81.603, 87.997, 60.003
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 15 or (resid 16...
d_2ens_1(chain "B" and (resid 3 through 15 or (resid 16...
d_3ens_1(chain "C" and (resid 3 through 15 or (resid 16...
d_4ens_1(chain "D" and (resid 3 through 15 or (resid 16...
d_5ens_1(chain "E" and (resid 3 through 15 or (resid 16...
d_6ens_1(chain "F" and (resid 3 through 15 or (resid 16...
d_7ens_1(chain "G" and (resid 3 through 15 or (resid 16...
d_8ens_1(chain "H" and (resid 3 through 15 or (resid 16...
d_9ens_1(chain "I" and (resid 3 through 15 or (resid 16...
d_10ens_1(chain "J" and (resid 3 through 15 or (resid 16...
d_11ens_1(chain "K" and (resid 3 through 15 or (resid 16...
d_12ens_1(chain "L" and (resid 3 through 45 or (resid 46...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYTHRA2 - 37
d_12ens_1GLUPHEA44 - 52
d_13ens_1PHEGLUA58 - 66
d_14ens_1HISGLUA70 - 72
d_15ens_1LEULEUA77 - 110
d_16ens_1PROPHEA112 - 118
d_17ens_1LEUSERA120 - 123
d_18ens_1GLUARGA125 - 134
d_19ens_1ARGPHEA144 - 179
d_110ens_1ALAARGA181 - 182
d_111ens_1LEUGDPA184
d_112ens_1ADPADPB
d_21ens_1GLYTHRC2 - 37
d_22ens_1GLUPHEC44 - 52
d_23ens_1PHEGLUC58 - 66
d_24ens_1HISGLUC70 - 72
d_25ens_1LEULEUC77 - 110
d_26ens_1PROPHEC112 - 118
d_27ens_1LEUSERC120 - 123
d_28ens_1GLUPHEC125 - 170
d_29ens_1ALAARGC172 - 173
d_210ens_1LEUGDPC175
d_211ens_1ADPADPD
d_31ens_1GLYTHRE2 - 37
d_32ens_1GLUPHEE44 - 52
d_33ens_1PHEGLUE58 - 66
d_34ens_1HISGLUE70 - 72
d_35ens_1LEULEUE77 - 110
d_36ens_1PROPHEE112 - 118
d_37ens_1LEUSERE120 - 123
d_38ens_1GLUARGE125 - 134
d_39ens_1ARGPHEE144 - 179
d_310ens_1ALAARGE181 - 182
d_311ens_1LEUALAE184 - 202
d_312ens_1GDPGDPE
d_313ens_1ADPADPF
d_41ens_1GLYTHRG2 - 37
d_42ens_1GLUPHEG44 - 52
d_43ens_1PHEGLUG58 - 66
d_44ens_1HISGLUG70 - 72
d_45ens_1LEULEUG77 - 110
d_46ens_1PROPHEG112 - 118
d_47ens_1LEUSERG120 - 123
d_48ens_1GLUARGG125 - 134
d_49ens_1ARGPHEG144 - 179
d_410ens_1ALAARGG181 - 182
d_411ens_1LEUGDPG184
d_412ens_1ADPADPH
d_51ens_1GLYTHRI2 - 37
d_52ens_1GLUPHEI44 - 52
d_53ens_1PHEGLUI58 - 66
d_54ens_1HISGLUI70 - 72
d_55ens_1LEULEUI77 - 110
d_56ens_1PROPHEI112 - 118
d_57ens_1LEUSERI120 - 123
d_58ens_1GLUARGI125 - 134
d_59ens_1ARGPHEI144 - 179
d_510ens_1ALAARGI181 - 182
d_511ens_1LEUALAI184 - 202
d_512ens_1GDPGDPI
d_513ens_1ADPADPJ
d_61ens_1GLYTHRK2 - 37
d_62ens_1GLUPHEK44 - 52
d_63ens_1PHEGLUK58 - 66
d_64ens_1HISGLUK70 - 72
d_65ens_1LEULEUK77 - 110
d_66ens_1PROPHEK112 - 118
d_67ens_1LEUSERK120 - 123
d_68ens_1GLUARGK125 - 134
d_69ens_1ARGPHEK144 - 179
d_610ens_1ALAARGK181 - 182
d_611ens_1LEUGDPK184
d_612ens_1ADPADPL
d_71ens_1GLYTHRM2 - 37
d_72ens_1GLUPHEM44 - 52
d_73ens_1PHEGLUM58 - 66
d_74ens_1HISGLUM70 - 72
d_75ens_1LEULEUM77 - 110
d_76ens_1PROPHEM112 - 118
d_77ens_1LEUSERM120 - 123
d_78ens_1GLUARGM125 - 134
d_79ens_1ARGPHEM144 - 179
d_710ens_1ALAARGM181 - 182
d_711ens_1LEUALAM184 - 202
d_712ens_1GDPGDPM
d_713ens_1ADPADPN
d_81ens_1GLYTHRO2 - 37
d_82ens_1GLUPHEO44 - 52
d_83ens_1PHEGLUO58 - 66
d_84ens_1HISGLUO70 - 72
d_85ens_1LEULEUO77 - 110
d_86ens_1PROPHEO112 - 118
d_87ens_1LEUSERO120 - 123
d_88ens_1GLUARGO125 - 134
d_89ens_1ARGPHEO141 - 176
d_810ens_1ALAARGO178 - 179
d_811ens_1LEUALAO181 - 199
d_812ens_1GDPGDPO
d_813ens_1ADPADPP
d_91ens_1GLYTHRQ2 - 37
d_92ens_1GLUPHEQ44 - 52
d_93ens_1PHEGLUQ58 - 66
d_94ens_1HISGLUQ70 - 72
d_95ens_1LEULEUQ77 - 110
d_96ens_1PROPHEQ112 - 118
d_97ens_1LEUSERQ120 - 123
d_98ens_1GLUARGQ125 - 134
d_99ens_1ARGPHEQ144 - 179
d_910ens_1ALAARGQ181 - 182
d_911ens_1LEUGDPQ184
d_912ens_1ADPADPR
d_101ens_1GLYTHRS2 - 37
d_102ens_1GLUPHES44 - 52
d_103ens_1PHEGLUS58 - 66
d_104ens_1HISGLUS70 - 72
d_105ens_1LEULEUS77 - 110
d_106ens_1PROPHES112 - 118
d_107ens_1LEUSERS120 - 123
d_108ens_1GLUARGS125 - 134
d_109ens_1ARGPHES141 - 176
d_1010ens_1ALAARGS178 - 179
d_1011ens_1LEUGDPS181
d_1012ens_1ADPADPT
d_111ens_1GLYTHRU1 - 36
d_112ens_1GLUPHEU43 - 51
d_113ens_1PHEGLUU57 - 65
d_114ens_1HISGLUU69 - 71
d_115ens_1LEULEUU76 - 109
d_116ens_1PROPHEU111 - 117
d_117ens_1LEUSERU119 - 122
d_118ens_1GLUARGU124 - 133
d_119ens_1ARGPHEU143 - 178
d_1110ens_1ALAARGU180 - 181
d_1111ens_1LEUGDPU183
d_1112ens_1ADPADPV
d_121ens_1GLYLEUW2 - 92
d_122ens_1PROPHEW94 - 100
d_123ens_1LEUSERW102 - 105
d_124ens_1GLUARGW107 - 116
d_125ens_1ARGPHEW126 - 161
d_126ens_1ALAARGW163 - 164
d_127ens_1LEUALAW166 - 184
d_128ens_1GDPGDPW
d_129ens_1ADPADPX

NCS oper:
IDCodeMatrixVector
1given(0.947023967709, 0.317138922873, -0.050680451697), (0.316676376901, -0.94837907814, -0.0171229804583), (-0.0534946436391, 0.000166571069522, -0.998568122541)-1.54351787426, 14.7538944619, 36.4871448451
2given(-0.50622400046, 0.860582342977, 0.0559936810297), (-0.86144638192, -0.507651833014, 0.0141332060961), (0.0405880824279, -0.0410809858042, 0.998331087451)-35.0783544699, -11.4627470349, 0.683164651067
3given(-0.514025635082, 0.85204970233, 0.0989391289544), (0.855331528315, 0.517840091569, -0.0157992479249), (-0.0646963920889, 0.0765045379303, -0.994968056033)-113.527865805, -1.64284131713, -36.2260868079
4given(0.998124362835, 0.0320960277548, -0.0521306178559), (0.0316760566377, -0.999458893846, -0.00886267163292), (-0.0523868662124, 0.00719475607286, -0.998600947192)-77.3567157326, -12.2892313481, -35.4144053553
5given(0.94987112449, 0.308486448621, -0.0508031286254), (-0.307312234138, 0.951145400367, 0.02969205465), (0.0574807586076, -0.0125912023798, 0.998267210727)-79.2779757893, -27.560333063, -71.5416606963
6given(-0.478674351841, -0.877954305708, -0.00819157971192), (-0.876502730137, 0.477298050865, 0.0626860008465), (-0.0511256193208, 0.0371861228063, -0.997999681022)-104.133612661, -37.7790528617, -36.0685859597
7given(-0.212975365373, -0.976145934914, -0.0421972451233), (0.975317596271, -0.209821430238, -0.0687790216388), (0.0582844760562, -0.0558039529464, 0.996739102617)-97.4859333451, 4.65989382018, -71.4891601735
8given(-0.741014259871, 0.670781429061, 0.0308243587869), (-0.671330137579, -0.741057043975, -0.012259851244), (0.0146189276675, -0.0297780456209, 0.999449626021)-116.284309176, -27.3074395997, -72.1171803257
9given(-0.205781428212, -0.978127220266, -0.0303503669958), (-0.977366051386, 0.203867800179, 0.0565112524041), (-0.0490877316737, 0.0412923845786, -0.997940546112)-19.8339254099, -17.4484087429, 36.385544436
10given(-0.745956428212, 0.665416287147, 0.027751973061), (0.665828790489, 0.746052990124, 0.00877255284683), (-0.0148670429399, 0.0250220048448, -0.999576345412)-38.6954064972, 14.4502739713, 36.6480175608
11given(-0.491997571271, -0.870549043277, 0.00909687386695), (0.869863708729, -0.491985222968, -0.0358840997942), (0.0357143962624, -0.00974184950621, 0.999314554216)-27.1057054434, 24.5413857278, 0.326884151686

-
Components

#1: Protein
Guanylate kinase / / GMP kinase


Mass: 24017.996 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: gmk, PA5336 / Plasmid: Psaea.01463.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HTM2, guanylate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: RigakuReagents. JCSG+ screen, condition G7: 100mM succinic acid pH 7.0, 15% PEG 3350; PsaeA.01463.a.AE1.PW38943 at 20mg/ml + 5mM ATP + 5mM GMP + 5mM MgCl2; tray 320335g7; cryo: 20%EG; puck xhd7-11

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 18, 2022 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 103118 / % possible obs: 98.6 % / Redundancy: 7.459 % / Biso Wilson estimate: 51.475 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 0.893 / Net I/σ(I): 26.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.416.2780.6073.2974340.8240.66394.9
2.41-2.486.930.5314.172710.9060.57498
2.48-2.557.3280.4474.9671910.9290.48197.9
2.55-2.637.5980.3546.3769840.960.37998.2
2.63-2.717.6270.3077.1468280.9690.32998.4
2.71-2.817.6240.2558.3965630.9820.27398.4
2.81-2.917.6580.1811.4664130.9880.19398.7
2.91-3.037.6680.14314.0661210.9930.15398.9
3.03-3.177.6940.10718.2858620.9950.11599.1
3.17-3.327.6790.08323.1456130.9970.08999.2
3.32-3.57.6520.06430.2853400.9980.06999.3
3.5-3.727.6120.04640.7951060.9990.04999.4
3.72-3.977.6080.03748.1747650.9990.0499.5
3.97-4.297.6370.02958.94450310.03199.6
4.29-4.77.6240.02567.96405810.02699.8
4.7-5.257.5930.02566.85374610.02799.9
5.25-6.077.5760.02960.03329210.03299.7
6.07-7.437.5680.02566.9274010.02799.7
7.43-10.517.5070.01790.77215010.018100
10.51-507.380.016102.64113810.01798.4

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1 4674refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 7u5f, GMP-bound structure
Resolution: 2.35→48.15 Å / SU ML: 0.3025 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.8897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1986 1.93 %0
Rwork0.1962 101110 --
obs0.1968 103096 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.41 Å2
Refinement stepCycle: LAST / Resolution: 2.35→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18544 0 324 461 19329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005419323
X-RAY DIFFRACTIONf_angle_d0.725226353
X-RAY DIFFRACTIONf_chiral_restr0.04582987
X-RAY DIFFRACTIONf_plane_restr0.00783729
X-RAY DIFFRACTIONf_dihedral_angle_d13.04387198
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.527849380945
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.474611874349
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.637613325856
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.525368527063
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.457944013861
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.636946553555
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.611900672357
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS0.582953587923
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS0.566824897666
ens_1d_11AX-RAY DIFFRACTIONTorsion NCS0.600351828034
ens_1d_12AX-RAY DIFFRACTIONTorsion NCS1.10544436194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.30851350.27247035X-RAY DIFFRACTION94.77
2.41-2.470.28611460.24927028X-RAY DIFFRACTION97.81
2.47-2.550.27621340.23947179X-RAY DIFFRACTION97.99
2.55-2.630.27181160.22427236X-RAY DIFFRACTION98.28
2.63-2.720.27991250.23967233X-RAY DIFFRACTION98.32
2.72-2.830.28841470.24277189X-RAY DIFFRACTION98.5
2.83-2.960.27391340.23287282X-RAY DIFFRACTION98.75
2.96-3.120.26811350.22467237X-RAY DIFFRACTION98.97
3.12-3.310.24381530.20457286X-RAY DIFFRACTION99.21
3.31-3.570.22431480.19637248X-RAY DIFFRACTION99.28
3.57-3.930.22331500.17857264X-RAY DIFFRACTION99.41
3.93-4.490.20931740.16457310X-RAY DIFFRACTION99.73
4.49-5.660.19591410.17127294X-RAY DIFFRACTION99.87
5.66-48.150.1891480.17737289X-RAY DIFFRACTION99.56
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)
12.80564484978-0.0399954707223-1.189211224772.073856695141.172078832452.75509393975-0.2198261981070.447997684041-0.0672206367918-0.4999307559450.335895402875-0.113054685447-0.1211667695190.437485529-0.1162734527880.392700937231-0.0919802724929-0.005935106293160.565939322408-0.02998413668060.306820595622-0.5302770331031.964656204511.24328750274
24.220429300581.816448739021.643931797683.912815545940.1558065291762.523799170060.352254257112-0.7564631082350.5831465988320.733885611933-0.507107238721-0.011883595501-0.08221748610680.07894977430080.1099042515130.412794895051-0.09383055921040.03917732664380.617682422704-0.03019865635790.381965283162-1.218368965711.526433266134.1259570609
30.795363362180.01315246118581.606777013181.468838961490.6137959699794.441149868950.0858086059008-0.0726644807537-0.0583848380282-0.0200993543968-0.0717657015030.01920662446920.161787064079-0.288875078799-0.02220457429270.308364837186-0.05657424519230.05395195147250.3449393317-0.02592188209890.340477613473-32.7274914458-11.95558976691.943790243
41.38959622422-0.214221688932-0.400715755851.83263481178-0.3654262109091.625261649320.00851638702352-0.1333851798030.2789922144010.2415418968780.00783625088027-0.107650610815-0.273881838434-0.125728378962-0.02927487176220.2741830976890.0692745223429-0.03156665477860.268099142041-0.04279257884980.428650432702-111.275268873-1.17418786987-37.3770983244
52.901406504011.735358596841.432488906882.503160766910.2374245347021.608598909510.14835473646-0.3913200539840.1975347835410.432424239014-0.2141874759170.0278949741281-0.1082627665130.02767512756170.05845178566620.277818034705-0.02560560188210.02277454687520.379509414704-0.00104677048360.339731460217-78.0337616269-14.5241494566-36.8634444587
63.12798235859-1.73730641227-1.118683264482.948589850490.653756248831.790885424040.2075819454190.623508133716-0.238868411001-0.56241141101-0.3449297490640.01514800630210.0582302745716-0.1301069671980.1360453314030.3190243093310.0711789860896-0.03483055387290.4478998243060.003267457921860.412467180121-79.3632038672-25.3976523544-70.1816621394
72.02331581747-0.193710424550.1606868428491.78776547301-0.1477083749151.6009074842-0.112809043488-0.203780253401-0.1077445631710.2569225266230.04865256276690.103019993150.303564140459-0.07544800952530.04162346544850.343568178252-0.003911745664970.01956534619990.2209893153360.02596702725020.385712272149-105.56078533-36.1322245211-37.2938491952
82.40245313581-0.01522505258390.7539020390213.99750100771-0.8385810537481.58731192874-0.1204574354670.5469448328910.55291268196-0.826340636375-0.0998641080337-0.523526516485-0.08622575062250.179336350330.1856663476730.4842436010150.02304212209460.01872772489850.3714140633490.08544584661570.584155631805-100.1859727113.39509287147-69.8691308105
93.30715931051-0.8630277496241.159699318451.308020693490.1346035959182.400620338520.1377083952530.567337513745-0.34550053489-0.278932305538-0.1479887304450.2203719962950.0703233438197-0.0278751506132-0.0004862541909280.277617326702-0.0315224300446-0.01985851643170.35058007493-0.03435621844890.475112749097-114.219825518-28.3000741726-70.6589216634
102.93900700901-0.407989200659-0.8413785467643.81158111807-0.7135456139682.67282816586-0.442014552467-0.599715281756-0.5404486331760.8825757176240.209325652422-0.4518651426480.2167284366980.1352939153970.1943507789620.6297605930210.106884174425-0.001754736914810.4028075988870.03811575142460.433792799426-22.6894130169-16.018216817234.6711733917
113.192641029170.157889729277-1.271459038771.542419197070.6044711196343.70037865629-0.0282343400027-0.6915218769830.5086398016980.1552286064820.05776574363540.111687941396-0.259814168325-0.0714871927566-0.01281935902740.3923887035870.105301481978-0.03486152481760.461813614053-0.08124727133980.607994861037-36.803423037515.296273889335.4857847426
121.98809738387-0.04538039490470.8186102968452.635903056180.1657703241552.73714919146-0.2565693619460.4595431714460.31149147799-1.050327589710.02452807229920.165279686403-0.9474521607960.1053254297210.1630948136491.03611050397-0.0117191843834-0.1082619672880.4090293790350.07860601174580.612285778662-28.883259815121.96807707164.00522908861
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain 'A' and resid 2 through 302)AA - B2 - 302
22(chain 'B' and resid 2 through 302)BC - D2 - 302
33(chain 'C' and resid 2 through 302)CE - F2 - 302
44(chain 'D' and resid 2 through 302)DG - H2 - 302
55(chain 'E' and resid 2 through 302)EI - J2 - 302
66(chain 'F' and resid 2 through 302)FK - L2 - 302
77(chain 'G' and resid 2 through 302)GM - N2 - 302
88(chain 'H' and resid 2 through 302)HO - P2 - 302
99(chain 'I' and resid 2 through 302)IQ - R2 - 302
1010(chain 'J' and resid 2 through 302)JS - T2 - 302
1111(chain 'K' and resid 3 through 302)KU - V3 - 302
1212(chain 'L' and resid 2 through 302)LW - X2 - 302

+
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