[English] 日本語
Yorodumi
- PDB-7l6c: Crystal Structure of Enoyl-[acyl-carrier-protein] reductase InhA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l6c
TitleCrystal Structure of Enoyl-[acyl-carrier-protein] reductase InhA from Mycobacterium abscessus in complex with NAD
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / SSGCID / Enoyl-[acyl-carrier-protein] reductase / InhA / MAB_2722c / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologytrans-2-enoyl-CoA reductase (NADH) activity / Enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / Enoyl-(Acyl carrier protein) reductase / fatty acid biosynthetic process / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Function and homology information
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Efficacy and Mode of Action of a Direct Inhibitor of Mycobacterium abscessus InhA.
Authors: Alcaraz, M. / Roquet-Baneres, F. / Leon-Icaza, S.A. / Abendroth, J. / Boudehen, Y.M. / Cougoule, C. / Edwards, T.E. / Kremer, L.
History
DepositionDec 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,65014
Polymers118,7804
Non-polymers2,87010
Water15,601866
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.660, 92.630, 98.130
Angle α, β, γ (deg.)90.000, 118.318, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-446-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 18 or resid 20...
d_2ens_1(chain "B" and (resid 3 through 18 or resid 20...
d_3ens_1(chain "C" and (resid 3 through 18 or resid 20...
d_4ens_1(chain "D" and (resid 3 through 18 or resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYASPA1 - 16
d_12ens_1SERALAA18 - 32
d_13ens_1LEUASPA34 - 40
d_14ens_1LEUPROA42 - 53
d_15ens_1PROGLYA55 - 100
d_16ens_1PHEALAA106 - 152
d_17ens_1PROALAA154 - 155
d_18ens_1ASNALAA157 - 174
d_19ens_1GLUMETA176 - 197
d_110ens_1ALAVALA199 - 201
d_111ens_1ALAGLNA204 - 211
d_112ens_1METGLNA213 - 222
d_113ens_1ALAALAA224 - 237
d_114ens_1THRLEUA239 - 267
d_115ens_1NADNADB
d_21ens_1GLYASPF2 - 17
d_22ens_1SERALAF19 - 33
d_23ens_1LEUASPF35 - 41
d_24ens_1LEUPROF43 - 54
d_25ens_1PROGLYF56 - 101
d_26ens_1PHEALAF107 - 153
d_27ens_1PROALAF155 - 156
d_28ens_1ASNALAF158 - 175
d_29ens_1GLUMETF177 - 198
d_210ens_1ALAVALF200 - 202
d_211ens_1ALAGLNF205 - 212
d_212ens_1METGLNF214 - 223
d_213ens_1ALAALAF225 - 238
d_214ens_1THRLEUF240 - 268
d_215ens_1NADNADG
d_31ens_1GLYASPI1 - 16
d_32ens_1SERALAI18 - 32
d_33ens_1LEUASPI34 - 40
d_34ens_1LEUPROI42 - 53
d_35ens_1PROGLYI55 - 100
d_36ens_1PHEALAI106 - 152
d_37ens_1PROALAI154 - 155
d_38ens_1ASNALAI157 - 174
d_39ens_1GLUMETI176 - 197
d_310ens_1ALAVALI199 - 201
d_311ens_1ALAGLNI204 - 211
d_312ens_1METGLNI213 - 222
d_313ens_1ALAALAI224 - 237
d_314ens_1THRLEUI239 - 267
d_315ens_1NADNADJ
d_41ens_1GLYASPL1 - 16
d_42ens_1SERALAL18 - 32
d_43ens_1LEUASPL34 - 40
d_44ens_1LEUPROL42 - 53
d_45ens_1PROGLYL55 - 100
d_46ens_1PHEALAL106 - 152
d_47ens_1PROALAL154 - 155
d_48ens_1ASNALAL157 - 174
d_49ens_1GLUMETL176 - 197
d_410ens_1ALAGLNL199 - 209
d_411ens_1METGLNL211 - 220
d_412ens_1ALAALAL222 - 235
d_413ens_1THRLEUL237 - 265
d_414ens_1NADNADM

NCS oper:
IDCodeMatrixVector
1given(-0.773335035658, 0.527069939099, -0.352349545085), (0.52610506753, 0.223369536192, -0.820560484194), (-0.353788609968, -0.819941052515, -0.450033654139)-100.860291896, 106.422645258, 94.122869887
2given(-0.744994968365, -0.441427374178, -0.500124354973), (-0.445735280365, -0.228370961898, 0.865544200835), (-0.496288783824, 0.867749144101, -0.0266245368554)-50.1092658976, -18.6305859055, -9.20446254033
3given(0.527670972992, -0.0958757070437, 0.844020848712), (-0.0984318797456, -0.993817887018, -0.0513534077954), (0.843726560748, -0.0559808560253, -0.533846077486)-67.4299352317, 82.7894559819, 131.630993097

-
Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 29695.074 Da / Num. of mol.: 4 / Fragment: MyabA.00170.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: MAB_2722c / Plasmid: MyabA.00170.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1MC30, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 866 / 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: 3.48 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.27
Details: Optimization condition around RigakuReagents JCSG+ E1: 100mM Sodium cacodylate / HCl pH 6.27, 1090mM sodium citrate tribasic: MyabA.00710.a.B1.PS38577 at 23.06mg/ml + 4mM NAD: tray: 319064 ...Details: Optimization condition around RigakuReagents JCSG+ E1: 100mM Sodium cacodylate / HCl pH 6.27, 1090mM sodium citrate tribasic: MyabA.00710.a.B1.PS38577 at 23.06mg/ml + 4mM NAD: tray: 319064 c9: cryo: 20% EG + 4mM NAD: puck: ZXC1-5.

-
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: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 138659 / % possible obs: 99.7 % / Redundancy: 16.298 % / Biso Wilson estimate: 33.792 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.076 / Χ2: 0.926 / Net I/σ(I): 25.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.99.2920.5933.14101000.9050.62799.3
1.9-1.959.6290.4544.16100010.9410.47999.8
1.95-2.0110.0260.3585.596290.9620.376100
2.01-2.0711.2520.2757.7594320.980.28899.7
2.07-2.1413.5020.2310.4191880.9890.23999.9
2.14-2.2114.870.17514.5188240.9940.18299.8
2.21-2.2915.5650.15217.0785050.9950.15799.8
2.29-2.3916.4090.13120.3881950.9970.13599.8
2.39-2.4917.5420.11923.2978790.9970.12399.8
2.49-2.6219.4990.10727.6275420.9980.1199.8
2.62-2.7622.2550.09434.371950.9980.09699.7
2.76-2.9322.2230.08438.7567440.9990.08699.8
2.93-3.1321.890.07943.463870.9990.08199.7
3.13-3.3821.5030.0749.8159490.9990.07299.8
3.38-3.721.0110.06454.255030.9990.06699.7
3.7-4.1420.8220.06157.6449350.9990.06399.8
4.14-4.7820.8650.05859.3244020.9990.05999.6
4.78-5.8520.9640.05758.6137190.9990.05999.7
5.85-8.2720.8750.05259.0829110.9990.05499.5
8.27-5020.3490.04660.516190.9980.04798.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc 4035refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure, PDB code 7KLI
Resolution: 1.85→46.31 Å / SU ML: 0.2007 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 2015 1.45 %0
Rwork0.1896 136621 --
obs0.19 138636 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.79 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7867 0 188 866 8921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00828365
X-RAY DIFFRACTIONf_angle_d0.954311405
X-RAY DIFFRACTIONf_chiral_restr0.05961305
X-RAY DIFFRACTIONf_plane_restr0.011555
X-RAY DIFFRACTIONf_dihedral_angle_d11.66363115
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.880105021145
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.14048313825
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.74620616986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.27641080.23239605X-RAY DIFFRACTION99.42
1.9-1.950.28351020.22759788X-RAY DIFFRACTION99.91
1.95-20.30961200.22239721X-RAY DIFFRACTION99.99
2-2.070.23951280.20639743X-RAY DIFFRACTION99.98
2.07-2.140.23181450.19729778X-RAY DIFFRACTION99.98
2.14-2.230.22441730.18989688X-RAY DIFFRACTION99.96
2.23-2.330.22831420.18869771X-RAY DIFFRACTION99.93
2.33-2.450.21061650.19149723X-RAY DIFFRACTION99.95
2.45-2.610.22011700.19959680X-RAY DIFFRACTION99.98
2.61-2.810.2311570.19499781X-RAY DIFFRACTION99.97
2.81-3.090.24031510.19429814X-RAY DIFFRACTION99.97
3.09-3.540.20551250.18669791X-RAY DIFFRACTION99.99
3.54-4.460.19361590.16949796X-RAY DIFFRACTION100
4.46-46.310.20931700.18389942X-RAY DIFFRACTION99.88
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)
12.826610399810.55434796599-0.3014883134863.57887758670.3515915933472.195177138460.02780091527360.204035046703-0.170954537859-0.232407582182-0.047656367012-0.2422508809050.2496704327250.0806471926856-0.002068242559830.2270349602980.03356320493340.05654249843090.258130126551-0.01230494019330.164214226209-35.845201283336.959641222230.3907083541
24.734773537932.97458197762-0.569139052256.40964207094-0.4765476631111.52102255062-0.1348195019960.4245595519020.0880382800987-0.375058799250.0837714182214-0.5045954624330.005262465100690.2691018619950.0798520855480.206811719810.04827310844490.05474091762530.3493464529270.0109425926470.204924244917-30.108164287544.295464885726.4181236657
32.91639335234-2.707870975880.1327708565646.072891762511.204068378441.863312886090.02947180680690.4055021636450.190447168214-0.6881979885250.051191403811-0.132045583724-0.17018266025-0.0639144663394-0.1006795047580.218699741087-0.00735414066570.0687725977230.3407357446190.05879338949680.201373300763-34.981598452447.177041565225.0673718682
41.986648344430.1547688576811.714697239079.716418540093.313189347462.522692062260.1095644738050.4359838253470.208380844833-0.906999672496-0.092801843983-0.213291143294-0.558178395216-0.03843621976180.0370324444050.381644065030.05321625125850.03747598874610.4216892608820.07818862019780.226451021239-42.527830230650.674827090819.423733129
50.197573037923-0.620619487677-0.7184412287843.332570044322.427083885794.27471526685-0.08397201587340.5811138486010.152726624935-0.4054450544890.208890554190.00503544319928-0.2223097224950.061739926008-0.1070647163830.197047920974-0.02062795133180.02197287031530.351121118730.03165775066750.128045379554-42.518864038445.749319527129.1786146029
60.805620207596-0.527066615793-0.7239509445051.906777970690.7571679558212.71130926650.0276743908707-0.006272749790510.19405713955-0.0879608942333-0.0461716055963-0.159647944653-0.048303428553-0.08160640055030.01136861901450.115723781758-0.0005215483445570.0102462024010.1921729438430.03937294236760.228852591492-43.263327455352.649448152541.1440938237
75.002629532863.953208119333.30411307036.246931168724.862902671694.75379951584-0.0612033931990.2357334292920.0749865511257-0.03514880796790.03588218863360.130662544836-0.1231706116890.07421022315320.02766838685820.1725991136740.01861710946480.01785215559410.1313214995680.03158879719680.135199823266-51.561903667249.751435670140.3016201983
84.523666746161.12526300831.3839965971.05167699226-0.04245741151680.585586339785-0.106502976792-0.0146412117892-0.083106269148-0.05646074715780.0627812669567-0.149943866153-0.1519234419520.1361745111330.02507796788540.1897180863780.01500580308110.01808218447980.280368933432-0.0150139587880.191595219915-35.98448751145.538482516343.7859818456
91.561126278561.678454466760.3982214263544.318600400531.612629497441.896215573010.126738806395-0.001582714875920.1126431999140.2201258863970.0598803016026-0.2554824328790.005720864592780.322809963676-0.1531929368950.1977625192670.0233258649937-0.02276117676140.36444892457-0.0001110342448520.262308093454-32.093816644340.796454911354.6705166777
104.792058192950.0535564188595-0.3149063688821.512481873280.1536852340850.929317269156-0.197391020510.0958660149034-0.316289751829-0.1559449917120.101280657981-0.05409217318310.1038968441170.1115376641080.1039066576090.244132817974-0.009334296504580.02723709382520.208028406771-0.02153263923220.195401798782-45.903049756632.622933902636.4959125859
114.82174174551-0.480614330421-2.169492756125.9475442456-0.6953027285181.237386140970.0769049882081-0.162306580235-0.1662377080860.224965463563-0.0564557599536-0.1126159650130.1340895627110.316881424334-0.01611771751170.149358906654-0.015163915245-0.006094481272350.1751698959740.00557996495160.150929632158-44.966067181936.818834148352.3264430091
122.687897750170.284755980386-0.5526216634892.1581892958-0.1422821875673.18978694868-0.0850428611261-0.2538034337720.4369401492450.2253673330470.03014997897560.307877267785-0.147317810676-0.2389400347230.03961192214220.2734953184520.0745372954976-0.002310755646280.21426523996-0.09128273552570.358292717371-64.363187932570.850163399163.2994093326
132.66902433023-0.861728187067-0.3173310516862.34286325814-0.3574885331812.52481137214-0.167602070568-0.07548726707030.7223219480090.163207681895-0.02729900102710.283309708617-0.585322054529-0.04395657863210.1369393113120.3325995265310.0566237149524-0.08563313416270.211806811416-0.0715485735030.548560733839-63.479220509779.193860830557.0762533668
142.96143895819-0.313761712012-0.4652357618222.695181868151.51569969911.988908188390.057270552249-0.1595974507790.9569903150110.06237174144310.188094720939-0.407797823241-0.4796506382590.167307598324-0.2272122766560.3101541434220.0317406352538-0.05637899265710.184638280124-0.04551361576960.477735507432-53.13224587778.669872699958.0250504546
151.4321520226-0.356089296934-0.5016408669561.945224641010.4613489961781.95472864272-0.0337983992716-0.07796727388180.352295600457-0.008830194174770.00465607914447-0.0869175665884-0.209782065878-0.05726546821640.05110481955630.136647813840.026874367466-0.001885050611340.1149745981670.004761355126180.236418722287-53.343221097461.970415515950.0331231611
164.11209711554-0.03685012715760.3872330391852.57598098416-0.7058429779671.30973409335-0.2179635450950.3253501510360.535907524612-0.577261120250.1005929359810.576127710503-0.521559416568-0.4205635619930.1474054357620.3959141286030.101519093078-0.1086955588220.273428457866-0.02845091037740.425642722105-65.496346155960.911992081349.3306764141
172.246154409670.3393052300440.2786692958191.398040794571.01778555331.730729710130.001151691298260.1109953422820.188861125555-0.216896387036-0.05043257499850.231686110998-0.277180041463-0.2282860335140.09954663525410.2431843722930.06950916717850.008038543590260.2026146142050.008823652256250.260917930628-68.496346338756.131434226856.1438276101
184.42335666648-1.09977226753-1.818900715253.56955147533-1.758923478662.25522644894-0.114930077650.067907091157-0.0674165653595-0.2188291263330.03584875005660.324107286540.112377982279-0.2345967333180.06839327185340.1911299299640.0437716216744-0.002854520088790.200923926253-0.02613057266490.146112060678-65.152393436148.19745985656.3262841457
192.18614431739-0.04951717834-0.2999791717292.53029617936-0.183872492312.893933560490.02077710163090.286614501885-0.236654021463-0.2924923046210.03623233836-0.004673046649580.5481121478340.0212442095805-0.1073541766250.3239169961270.000568547387283-0.003843600795590.152066485253-0.04386825985440.300788260169-55.066149902815.284774065539.9008024085
200.6969434613620.8953181197960.5638696386721.339869413370.7405673921630.543481594516-0.05167087878910.156681626118-0.541348922809-0.286993639744-0.08729403467510.1606578359730.587931766102-0.267644864981-0.08276065420610.461140719602-0.051660362889-0.06177708448540.214569960614-0.02858066680170.416042119277-60.36987235257.7998745123643.2428684081
211.89673240024-0.0344739474062-0.0442187826172.13129116090.03489240274842.55870491674-0.0739556273801-0.126652206516-0.5399648721960.1247312732230.116577248479-0.1144655601570.8079442821540.0936322850599-0.03215687029690.461363344117-0.00965821534945-0.06794654798590.1953847526110.04996639332840.41919289639-53.97074633486.661194135852.0799866875
222.92655029201-0.600814359834-0.6344282927161.94386506770.4824901281831.901385865410.0129268476779-0.111776354062-0.2263581047030.0543690355297-0.01144284935220.07966160647380.203043387401-0.03898186424940.006979237672060.214706997702-0.0315224562857-0.02105011941830.1389493131380.0418930821880.166701928631-58.438109426823.677862097856.3928774556
230.619922699487-0.2332513144620.4329622256761.530132888480.04823140988791.557899294-0.16944474823-0.432166469311-0.5300503787670.04867630296090.01430142439870.4673959458730.21040292699-0.492494525363-0.04022842495940.238456464351-0.04475554812530.01599702713080.234171440304-0.02966899516390.314673786095-64.298453156325.343384670947.5978959417
243.976959421880.1952164289950.3531848573441.473688106-0.1238249858771.477802252520.1202078032710.064662946357-0.01208299634880.0763960680631-0.03451812054580.5622588182930.177007972356-0.5689415721630.01270746156860.257833612318-0.0477013198846-0.03488189046120.289570227437-0.02282008264670.3303555471-71.893120111333.166729113839.3235325015
253.03363878704-0.09239795469510.6467229393061.29708904971-0.1894456271031.597399295080.06694186246120.0198824276207-0.0884964031006-0.0662402994681-0.0534581766829-0.02187893300650.077550138461-0.0718143973396-0.007884574798910.191888383632-0.01239753636650.02090357426850.171564913215-0.01922467360620.150247973587-52.917759337931.090907132342.2073355929
261.879837758740.977822909729-0.2550397443091.859684159950.6300514872062.441906655760.164071588573-0.496977386224-0.008105045105020.309648209593-0.1606482658770.1048874277380.11472000811-0.4137470210310.01668662903520.297440854029-0.01031902309080.04409620947310.518112592734-0.009379909742470.18770571027-68.123424418842.111088429385.2543426799
271.35014020877-0.282231836723-0.196877952511.984680724370.3751811815641.7311956632-0.0292632734739-0.431238557744-0.07721489094780.1967001281540.05303994843820.06240574437560.060755460762-0.107178147619-0.007782267222960.211371908356-0.01146847851990.01194652267690.2864147285750.03540809650880.12823419797-63.056917766134.685718098769.9323061239
283.218547515470.313766510361-0.1146513669621.776054262570.2969935401171.81302628328-0.0540873951053-0.45928857869-0.1981313727930.3659502673220.0705240324881-0.2266397194850.2533685394680.207976176088-0.003202876661230.2894170430950.0588441524549-0.01044633464910.273667483443-0.02718581826190.161603958052-52.184358272645.754393130271.2534793383
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 31 )AA3 - 311 - 29
22chain 'A' and (resid 32 through 53 )AA32 - 5330 - 51
33chain 'A' and (resid 54 through 67 )AA54 - 6752 - 65
44chain 'A' and (resid 68 through 82 )AA68 - 8266 - 80
55chain 'A' and (resid 83 through 99 )AA83 - 9981 - 97
66chain 'A' and (resid 100 through 158 )AA100 - 15898 - 156
77chain 'A' and (resid 159 through 182 )AA159 - 182157 - 180
88chain 'A' and (resid 183 through 208 )AA183 - 208181 - 206
99chain 'A' and (resid 209 through 235 )AA209 - 235207 - 233
1010chain 'A' and (resid 236 through 255 )AA236 - 255234 - 253
1111chain 'A' and (resid 256 through 269 )AA256 - 269254 - 267
1212chain 'B' and (resid 2 through 31 )BF2 - 311 - 30
1313chain 'B' and (resid 32 through 53 )BF32 - 5331 - 52
1414chain 'B' and (resid 54 through 82 )BF54 - 8253 - 81
1515chain 'B' and (resid 83 through 182 )BF83 - 18282 - 181
1616chain 'B' and (resid 183 through 208 )BF183 - 208182 - 207
1717chain 'B' and (resid 209 through 255 )BF209 - 255208 - 254
1818chain 'B' and (resid 256 through 269 )BF256 - 269255 - 268
1919chain 'C' and (resid 3 through 31 )CI3 - 311 - 29
2020chain 'C' and (resid 32 through 53 )CI32 - 5330 - 51
2121chain 'C' and (resid 54 through 82 )CI54 - 8252 - 80
2222chain 'C' and (resid 83 through 182 )CI83 - 18281 - 180
2323chain 'C' and (resid 183 through 207 )CI183 - 207181 - 205
2424chain 'C' and (resid 208 through 235 )CI208 - 235206 - 233
2525chain 'C' and (resid 236 through 269 )CI236 - 269234 - 267
2626chain 'D' and (resid 3 through 82 )DL3 - 821 - 80
2727chain 'D' and (resid 83 through 182 )DL83 - 18281 - 180
2828chain 'D' and (resid 183 through 269 )DL183 - 269181 - 265

+
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