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- PDB-7q5y: Structure of NADH:ubichinon oxidoreductase (complex I) of the hyp... -

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Basic information

Entry
Database: PDB / ID: 7q5y
TitleStructure of NADH:ubichinon oxidoreductase (complex I) of the hyperthermophilic eubacterium Aquifex aeolicus
Components
  • (NADH-quinone oxidoreductase subunit ...) x 5
  • NADH dehydrogenase I chain G
KeywordsOXIDOREDUCTASE / complex I
Function / homology
Function and homology information


NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdenum ion binding / anaerobic respiration / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding ...NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdenum ion binding / anaerobic respiration / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / aerobic respiration / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / iron ion binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
NADH-quinone oxidoreductase subunit CD / Soluble ligand binding domain / SLBB domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I ...NADH-quinone oxidoreductase subunit CD / Soluble ligand binding domain / SLBB domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / NADH dehydrogenase I chain G / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit C/D 2 / NADH-quinone oxidoreductase subunit I
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsWarkentin, E. / Ermler, U. / Peng, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Structure of NADH:ubichinon oxidoreductase (complex I) of the hyperthermophilic eubacterium Aquifex aeolicus
Authors: Warkentin, E. / Ermler, U. / Peng, G.
History
DepositionNov 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH dehydrogenase I chain G
B: NADH-quinone oxidoreductase subunit C/D 2
C: NADH-quinone oxidoreductase subunit F
D: NADH-quinone oxidoreductase subunit I
E: NADH-quinone oxidoreductase subunit E
F: NADH-quinone oxidoreductase subunit B
G: NADH dehydrogenase I chain G
H: NADH-quinone oxidoreductase subunit C/D 2
I: NADH-quinone oxidoreductase subunit F
J: NADH-quinone oxidoreductase subunit I
K: NADH-quinone oxidoreductase subunit E
L: NADH-quinone oxidoreductase subunit B
M: NADH dehydrogenase I chain G
N: NADH-quinone oxidoreductase subunit C/D 2
O: NADH-quinone oxidoreductase subunit F
P: NADH-quinone oxidoreductase subunit I
Q: NADH-quinone oxidoreductase subunit E
R: NADH-quinone oxidoreductase subunit B
S: NADH dehydrogenase I chain G
T: NADH-quinone oxidoreductase subunit C/D 2
U: NADH-quinone oxidoreductase subunit F
V: NADH-quinone oxidoreductase subunit I
W: NADH-quinone oxidoreductase subunit E
X: NADH-quinone oxidoreductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,015,90568
Polymers1,001,42124
Non-polymers14,48444
Water6,503361
1
A: NADH dehydrogenase I chain G
B: NADH-quinone oxidoreductase subunit C/D 2
C: NADH-quinone oxidoreductase subunit F
D: NADH-quinone oxidoreductase subunit I
E: NADH-quinone oxidoreductase subunit E
F: NADH-quinone oxidoreductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,97617
Polymers250,3556
Non-polymers3,62111
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27230 Å2
ΔGint-349 kcal/mol
Surface area75100 Å2
MethodPISA
2
G: NADH dehydrogenase I chain G
H: NADH-quinone oxidoreductase subunit C/D 2
I: NADH-quinone oxidoreductase subunit F
J: NADH-quinone oxidoreductase subunit I
K: NADH-quinone oxidoreductase subunit E
L: NADH-quinone oxidoreductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,97617
Polymers250,3556
Non-polymers3,62111
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27320 Å2
ΔGint-344 kcal/mol
Surface area75620 Å2
MethodPISA
3
M: NADH dehydrogenase I chain G
N: NADH-quinone oxidoreductase subunit C/D 2
O: NADH-quinone oxidoreductase subunit F
P: NADH-quinone oxidoreductase subunit I
Q: NADH-quinone oxidoreductase subunit E
R: NADH-quinone oxidoreductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,97617
Polymers250,3556
Non-polymers3,62111
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27480 Å2
ΔGint-347 kcal/mol
Surface area75380 Å2
MethodPISA
4
S: NADH dehydrogenase I chain G
T: NADH-quinone oxidoreductase subunit C/D 2
U: NADH-quinone oxidoreductase subunit F
V: NADH-quinone oxidoreductase subunit I
W: NADH-quinone oxidoreductase subunit E
X: NADH-quinone oxidoreductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,97617
Polymers250,3556
Non-polymers3,62111
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27410 Å2
ΔGint-352 kcal/mol
Surface area75190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.880, 240.240, 230.920
Angle α, β, γ (deg.)90.000, 95.566, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44
15
25
35
45
16
26
36
46

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A4 - 629
121chain 'A'A717
231chain 'G'G4 - 629
241chain 'G'G717
351chain 'M'M4 - 629
361chain 'M'M717
471chain 'S'S4 - 629
481chain 'S'S717
192chain 'B'B1 - 585
2102chain 'H'H1 - 585
3112chain 'N'N1 - 585
4122chain 'T'T1 - 585
1133chain 'C'C1 - 419
1143chain 'C'C500
2153chain 'I'I1 - 419
2163chain 'I'I500
3173chain 'O'O1 - 419
3183chain 'O'O500
4193chain 'U'U1 - 419
4203chain 'U'U500
1214chain 'D'D5 - 200
2224chain 'J'J5 - 200
3234chain 'P'P5 - 200
4244chain 'V'V5 - 200
1255chain 'E'E6 - 160
1265chain 'E'E720
2275chain 'K'K6 - 160
2285chain 'K'K720
3295chain 'Q'Q6 - 160
3305chain 'Q'Q720
4315chain 'W'W6 - 160
4325chain 'W'W720
1336chain 'F'F20 - 154
2346chain 'L'L20 - 154
3356chain 'R'R20 - 154
4366chain 'X'X20 - 154

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules AGMS

#1: Protein
NADH dehydrogenase I chain G


Mass: 72875.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5 / References: UniProt: O66748

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NADH-quinone oxidoreductase subunit ... , 5 types, 20 molecules BHNTCIOUDJPVEKQWFLRX

#2: Protein
NADH-quinone oxidoreductase subunit C/D 2 / NADH dehydrogenase I subunit C/D 2 / NDH-1 subunit C/D 2


Mass: 67991.797 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
References: UniProt: O67335, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#3: Protein
NADH-quinone oxidoreductase subunit F / NADH dehydrogenase I subunit F / NDH-1 subunit F


Mass: 47566.301 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
References: UniProt: O66841, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#4: Protein
NADH-quinone oxidoreductase subunit I / NADH dehydrogenase I subunit I / NDH-1 subunit I


Mass: 23446.473 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
References: UniProt: O67337, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#5: Protein
NADH-quinone oxidoreductase subunit E / NADH dehydrogenase I subunit E / NDH-1 subunit E


Mass: 18573.619 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
References: UniProt: O66842, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein
NADH-quinone oxidoreductase subunit B / NADH dehydrogenase I subunit B / NDH-1 subunit B


Mass: 19901.324 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
References: UniProt: O67334, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Non-polymers , 4 types, 405 molecules

#7: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2S2
#9: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate (pH 5.0), 40% methylpentanediol (MPD), 0.05% decyl-beta-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 393067 / % possible obs: 98.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 64.94 Å2 / Rrim(I) all: 0.128 / Net I/σ(I): 8.03
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.7 % / Num. unique obs: 20959 / Rrim(I) all: 1.689 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XDSdata scaling
SHARPv2006/3phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.95 Å / SU ML: 0.3537 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 19447 5.02 %
Rwork0.1694 367799 -
obs0.1714 387246 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.51 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms68252 0 412 361 69025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008770603
X-RAY DIFFRACTIONf_angle_d1.298895668
X-RAY DIFFRACTIONf_chiral_restr0.072710320
X-RAY DIFFRACTIONf_plane_restr0.008520616
X-RAY DIFFRACTIONf_dihedral_angle_d14.803942204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.3556170.319712189X-RAY DIFFRACTION98.12
2.73-2.760.33856760.305212253X-RAY DIFFRACTION98.58
2.76-2.80.33926520.312210X-RAY DIFFRACTION98.85
2.8-2.830.33086440.288512368X-RAY DIFFRACTION98.85
2.83-2.870.30835990.273712324X-RAY DIFFRACTION99.06
2.87-2.910.31686490.271912280X-RAY DIFFRACTION99.14
2.91-2.950.31396940.268312329X-RAY DIFFRACTION99.13
2.95-2.990.29316610.25512303X-RAY DIFFRACTION99.17
2.99-3.040.28696120.24912380X-RAY DIFFRACTION99.11
3.04-3.090.29955920.239212382X-RAY DIFFRACTION99.22
3.09-3.140.28786220.236512299X-RAY DIFFRACTION99.11
3.14-3.20.27536600.221412354X-RAY DIFFRACTION99.25
3.2-3.260.26186380.208812380X-RAY DIFFRACTION99.28
3.26-3.330.24886360.204812335X-RAY DIFFRACTION99.2
3.33-3.40.23226250.193212395X-RAY DIFFRACTION99.29
3.4-3.480.23226810.185312270X-RAY DIFFRACTION99.28
3.48-3.570.2196510.176212379X-RAY DIFFRACTION99.35
3.57-3.660.2166710.168312369X-RAY DIFFRACTION99.31
3.66-3.770.20626350.160412326X-RAY DIFFRACTION99.18
3.77-3.890.1966880.151712312X-RAY DIFFRACTION99.16
3.89-4.030.18436640.146912362X-RAY DIFFRACTION99
4.03-4.190.17596520.141212291X-RAY DIFFRACTION98.94
4.19-4.380.17346670.133412295X-RAY DIFFRACTION98.75
4.38-4.610.17146590.130812290X-RAY DIFFRACTION98.56
4.61-4.90.17726410.133912296X-RAY DIFFRACTION98.3
4.9-5.280.18236840.140712124X-RAY DIFFRACTION97.77
5.28-5.80.18696570.151312145X-RAY DIFFRACTION97.5
5.8-6.640.18396730.147412115X-RAY DIFFRACTION96.88
6.64-8.330.17236580.140412012X-RAY DIFFRACTION95.77
8.33-29.950.15665890.12911432X-RAY DIFFRACTION90.42
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4026027548740.0666180823773-0.101496080080.62294878641-0.02619253021020.7801558586190.07805890184580.02953948410140.243316511610.0218796063756-0.01919902362960.141216624477-0.493268520114-0.133213486276-0.02902795441980.5824300493690.1051739562140.06174848183960.4834438846250.03822571620630.466958378452142.208665589237.009855897220.938076379
20.9411007716140.360201089145-0.2473714014830.475035626565-0.06067988546890.716924096261-0.1992486703290.117104893701-0.705718047272-0.09672230459280.00841315016881-0.3492989724520.391676778230.1142813465890.04815718772570.5096028159450.1150426848910.1086920381910.48509122401-0.0979414153620.83209642065199.9532681653143.916566622197.978979308
30.794988221224-0.098047782221-0.2053255399770.3301737681750.02803013171021.15598167928-0.119577132405-0.18331507992-0.2614599147070.05916307617230.09730226168380.01621826166110.5398596694420.1268329208950.007405817371680.6286323931110.04945680067110.009981441794830.6350947959470.1143492646050.42817714043164.5457773631137.984905018145.719883292
40.4127433346830.0472088968316-0.01264032255280.133818579044-0.2276555461930.7427948430020.043441794073-0.01655648358420.235205215075-0.009958838105250.06234232796160.069016100598-0.667480370671-0.22693779713-0.03147125047231.275746622330.2202368634380.1657725499860.698902211843-0.02822920429330.54744034860423.2209237451233.409613328119.428164773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' or chain 'B' or chain 'C' or (chain 'D' and ((resid 27 through 201) or (resid 301 through 302))) or chain 'E' or chain 'F' )
2X-RAY DIFFRACTION2((chain 'G' ) or (chain 'H' ) or (chain 'I' ) or (chain 'J' and ((resid 27 through 201) or (resid 301 through 302))) or chain 'K' or chain 'L' )
3X-RAY DIFFRACTION3((chain 'M' ) or (chain 'N' ) or (chain 'O' ) or (chain 'P' and ((resid 27 through 201) or (resid 301 through 302))) or chain 'Q' or chain 'R' )
4X-RAY DIFFRACTION4(chain 'S' or chain 'T' or chain 'U' or (chain 'V' and ((resid 27 through 201) or (resid 301 through 302))) or chain 'W' or chain 'X' )

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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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