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- PDB-7np8: Crystal structure of the Coenzyme F420-dependent sulfite reductas... -

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Basic information

Entry
Database: PDB / ID: 7np8
TitleCrystal structure of the Coenzyme F420-dependent sulfite reductase from Methanocaldococcus jannaschii at 2.3-A resolution
ComponentsCoenzyme F420-dependent sulfite reductase
KeywordsOXIDOREDUCTASE / Sulfite detoxification / Sulfur metabolism / sulfide / hydrogenotrophic methanogens / iron-sulfur cluster / sulfite-reductase evolution / sulfite/nitrite reductase / siroheme / flavin / ferredoxin / F420 / hyperthermophile
Function / homology
Function and homology information


sulfite reductase (coenzyme F420) / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / 4 iron, 4 sulfur cluster binding / heme binding / metal ion binding
Similarity search - Function
Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily ...Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / 4Fe-4S binding domain / 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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / IRON/SULFUR CLUSTER / SULFITE ION / SIROHEME / Coenzyme F420-dependent sulfite reductase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJespersen, M. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society/ Germany
German Research Foundation (DFG)Schwerpunktprogram 1927 Iron-sulfur for Life WA 4053/1-1 Germany
Citation
Journal: Nat.Chem.Biol. / Year: 2023
Title: Structures of the sulfite detoxifying F 420 -dependent enzyme from Methanococcales.
Authors: Jespersen, M. / Pierik, A.J. / Wagner, T.
#1: Journal: Biorxiv / Year: 2022
Title: The structure of the F420-dependent sulfite-detoxifying enzyme from Methanococcales reveals a prototypical sulfite-reductase with assimilatory traits
Authors: Jespersen, M. / Pierik, A.J. / Wagner, T.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Revision 2.0Dec 6, 2023Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coenzyme F420-dependent sulfite reductase
B: Coenzyme F420-dependent sulfite reductase
C: Coenzyme F420-dependent sulfite reductase
D: Coenzyme F420-dependent sulfite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,34493
Polymers279,6084
Non-polymers19,73689
Water13,908772
1
A: Coenzyme F420-dependent sulfite reductase
B: Coenzyme F420-dependent sulfite reductase
hetero molecules

A: Coenzyme F420-dependent sulfite reductase
B: Coenzyme F420-dependent sulfite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,49782
Polymers279,6084
Non-polymers18,88978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area49840 Å2
ΔGint-807 kcal/mol
Surface area88120 Å2
MethodPISA
2
C: Coenzyme F420-dependent sulfite reductase
D: Coenzyme F420-dependent sulfite reductase
hetero molecules

C: Coenzyme F420-dependent sulfite reductase
D: Coenzyme F420-dependent sulfite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,191104
Polymers279,6084
Non-polymers20,582100
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area54020 Å2
ΔGint-865 kcal/mol
Surface area88470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.258, 172.202, 195.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1273-

HOH

21B-1296-

HOH

31C-1211-

HOH

41D-1368-

HOH

51D-1377-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Coenzyme F420-dependent sulfite reductase / Sulfite reductase (coenzyme F420)


Mass: 69902.047 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Methanocaldococcus jannaschii DSM 2661 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: /
References: UniProt: Q58280, sulfite reductase (coenzyme F420)

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Non-polymers , 10 types, 861 molecules

#2: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical
ChemComp-SO3 / SULFITE ION / Sulfite


Mass: 80.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SRM / SIROHEME / Siroheme


Mass: 916.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H44FeN4O16 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.53 Å3/Da / Density % sol: 51.34 % / Description: Black, long plate-shaped crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Purified Fsr from Methanocaldococcus jannaschii was crystallized anaerobically under yellow light at a concentration of 6.1 mg ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol and 2 mM ...Details: Purified Fsr from Methanocaldococcus jannaschii was crystallized anaerobically under yellow light at a concentration of 6.1 mg ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol and 2 mM dithiothreitol. 0.5 ul protein sample was mixed with 0.5 ul reservoir of crystallization solution containing 45% v/v 2-Methyl-2,4-pentandiol, 100 mM Bis-Tris pH 5.5 and 200 mM Calcium chloride. Crystals appeared after a few days.
PH range: / / Temp details: +/- 1 degree of oscillation

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.05
ReflectionResolution: 2.299→78.823 Å / Num. obs: 104064 / % possible obs: 96 % / Redundancy: 13.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.07 / Rrim(I) all: 0.261 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.41 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.623 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5203 / CC1/2: 0.629 / Rpim(I) all: 0.459 / Rrim(I) all: 1.688 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
CRANK22.0.227phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→78.82 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.55 / Stereochemistry target values: TWIN_LSQ_F
Details: Refinement was performed with the twin law:-k,-h,-l
RfactorNum. reflection% reflection
Rfree0.2047 5313 5.11 %
Rwork0.1817 98850 -
obs0.1829 104063 83.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.85 Å2 / Biso mean: 42.4377 Å2 / Biso min: 16.19 Å2
Refinement stepCycle: final / Resolution: 2.3→78.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19545 0 920 772 21237
Biso mean--46.27 39.71 -
Num. residues----2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0120891
X-RAY DIFFRACTIONf_angle_d1.38428290
X-RAY DIFFRACTIONf_chiral_restr0.3053066
X-RAY DIFFRACTIONf_plane_restr0.0053506
X-RAY DIFFRACTIONf_dihedral_angle_d21.9768159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2992-2.33890.2988790.27461692177127
2.3389-2.38140.31741260.28161926205231
2.3814-2.42720.3117980.25572282238037
2.4272-2.47670.26771340.26362815294945
2.4767-2.53060.29631580.24683402356055
2.5306-2.58940.28162150.2534100431566
2.5894-2.65410.29682730.25345168544183
2.6541-2.72590.27692870.24695883617095
2.7259-2.80610.28353030.22825903620695
2.8061-2.89660.26413150.22765911622695
2.8966-3.00010.26433250.20795899622495
3.0001-3.12010.24762910.20155917620895
3.1201-3.2620.22863410.19635909625095
3.262-3.43390.21683010.18385981628295
3.4339-3.64880.20143120.17265928624095
3.6488-3.93020.1683290.15995906623595
3.9302-4.32510.16733020.14745995629795
4.3251-4.94960.15263230.13735991631495
4.9496-6.23050.17673210.16186035635695
6.2305-35.66390.1593370.15996207654495
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)
11.687-0.36430.01390.9522-0.17581.0264-0.0014-0.2216-0.01270.02080.04430.1154-0.047-0.0624-0.03540.31080.0221-0.00340.2635-0.02540.271455.72818.9832140.5133
21.559-0.4657-0.8022.02251.36522.54910.008-0.28820.16930.17870.07270.0723-0.13940.0014-0.07370.28990.0226-0.00380.2872-0.00620.321654.701524.5303144.2046
30.52140.1773-0.43770.1999-0.21351.02580.10610.00030.16770.0785-0.00720.098-0.308-0.066-0.12150.36480.05330.00830.2394-0.02190.387761.212234.2547123.4612
40.15970.0012-0.30580.4701-0.00641.5236-0.05140.02490.0351-0.04050.00180.0691-0.0581-0.0890.050.2175-0.0033-0.01920.1834-0.00440.311361.693813.161393.3764
50.77420.58090.06881.47090.09171.4513-0.0153-0.01640.0294-0.22730.0410.0616-0.0782-0.1624-0.01460.3609-0.03770.01490.21390.00980.332184.409128.446965.0716
62.02620.29081.70643.9517-1.3532.7904-0.0130.2756-0.0474-0.47010.2427-0.3065-0.30330.5239-0.20660.4746-0.08970.16930.3714-0.08630.3582107.042828.884656.0108
73.2471-0.5348-1.33432.24290.65264.3933-0.0130.0104-0.2562-0.0685-0.0734-0.04220.10190.13820.07530.35910.0044-0.00980.18780.00320.308495.474426.466160.6611
83.88783.275-0.67714.84490.76911.237-0.03820.0993-0.3322-0.27240.1611-0.3772-0.09150.034-0.08240.38090.0298-0.02660.24070.0630.383988.895618.071267.5398
91.3627-0.238-0.3792.609-1.56154.01830.11380.16910.3047-0.43530.0718-0.1403-0.31220.2496-0.19520.6056-0.0770.04520.2458-0.01160.427395.813146.240555.0264
105.4714-1.2774-0.5192.08030.420.68930.1332-0.16010.4199-0.11270.0409-0.3214-0.30890.1569-0.19690.4689-0.10360.06560.25960.00310.2967100.821141.792471.3024
110.81430.0156-0.26461.8012-1.81273.88230.04170.01230.16310.05340.07130.0599-0.32720.0015-0.08980.33540.0051-0.01240.2001-0.01470.382477.706737.774289.1299
120.23790.0593-0.34620.3926-0.16271.4385-0.0268-0.03630.04340.00580.0186-0.0482-0.01190.0730.01910.18050.0012-0.01530.17430.01680.285186.899911.7038105.592
131.5132-0.2944-0.35761.65810.72431.97360.13780.15480.0102-0.1521-0.0016-0.08420.05850.2933-0.08520.19340.0379-0.01150.278-0.05180.2135103.135565.5309107.7686
142.11350.3490.39191.65520.50643.57460.0710.1409-0.31920.04120.0875-0.03440.45630.2372-0.12980.30610.1174-0.0670.2933-0.04630.2982100.775948.0926100.9813
154.6045-3.3257-0.88653.90631.56691.12120.28950.3034-0.3277-0.0148-0.24350.16930.09410.0645-0.03060.28840.0185-0.03450.22510.01150.263993.600561.1229112.7228
161.09930.6023-0.11041.9381.15672.8841-0.1250.1864-0.1264-0.17030.3444-0.37810.17830.9143-0.21830.32480.10950.0070.6296-0.11570.3922118.076454.306293.7105
170.12690.34590.18220.5620.88831.66810.11390.203-0.18160.02940.1433-0.15550.36210.6846-0.23480.34770.2004-0.07150.5788-0.07360.3617116.258657.8123116.2898
182.00240.39-1.65911.6849-0.47695.59140.05590.2373-0.17260.0821-0.0253-0.46490.09450.73030.00230.19470.0515-0.03050.5924-0.05030.3079120.946672.58131.9613
190.3283-0.00730.12850.22310.27261.97860.06680.0365-0.06420.0133-0.027-0.03860.18640.1964-0.04190.25180.024-0.03020.225700.277196.832463.1627151.4477
201.9730.73590.26280.62320.32921.5954-0.0182-0.00180.0056-0.07310.0066-0.0153-0.02430.2043-0.00850.2196-0.0375-0.03910.25070.00010.1958112.054286.2777179.7338
213.15020.57451.14332.3074-0.57572.8793-0.19660.09140.55490.0644-0.03680.0908-0.87820.170.14950.5448-0.0678-0.11370.2391-0.0160.4418112.2325108.9299188.6181
222.22071.27191.00211.65790.79471.8463-0.0922-0.04670.3608-0.110.030.2007-0.1869-0.00520.06580.2693-0.016-0.06040.22860.00610.3216106.152794.2293180.9524
232.3740.41562.34751.80040.84855.1536-0.20870.13560.18490.00630.205-0.2843-0.45790.4740.00290.2648-0.1077-0.00210.40180.00970.3499129.698197.926189.5317
241.6351-1.18910.67675.4593-0.28411.3302-0.20330.34850.4242-0.1751-0.0212-0.425-0.49990.540.13080.4622-0.2709-0.08080.53750.07260.3247124.9087102.7366173.2788
251.0835-0.14981.89090.54350.2014.66630.0250.2673-0.02-0.05810.0314-0.0787-0.08330.7806-0.02570.1934-0.0430.00390.4087-0.01010.3003121.386879.4382155.6197
261.99280.80792.62731.03631.664.568-0.01430.31680.0669-0.12740.0222-0.1262-0.24660.54680.00220.2676-0.0445-0.00990.2980.00950.2645108.130188.4037142.1936
270.30280.04830.50480.29040.18872.62320.00310.02040.0308-0.0035-0.0535-0.037-0.2290.0850.06760.2649-0.0102-0.02840.19970.01750.280392.385588.3449138.4882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 129 )A1 - 129
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 268 )A130 - 268
3X-RAY DIFFRACTION3chain 'A' and (resid 269 through 411 )A269 - 411
4X-RAY DIFFRACTION4chain 'A' and (resid 412 through 619 )A412 - 619
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 77 )B1 - 77
6X-RAY DIFFRACTION6chain 'B' and (resid 78 through 129 )B78 - 129
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 169 )B130 - 169
8X-RAY DIFFRACTION8chain 'B' and (resid 170 through 199 )B170 - 199
9X-RAY DIFFRACTION9chain 'B' and (resid 200 through 268 )B200 - 268
10X-RAY DIFFRACTION10chain 'B' and (resid 269 through 328 )B269 - 328
11X-RAY DIFFRACTION11chain 'B' and (resid 329 through 411 )B329 - 411
12X-RAY DIFFRACTION12chain 'B' and (resid 412 through 620 )B412 - 620
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 77 )C1 - 77
14X-RAY DIFFRACTION14chain 'C' and (resid 78 through 169 )C78 - 169
15X-RAY DIFFRACTION15chain 'C' and (resid 170 through 199 )C170 - 199
16X-RAY DIFFRACTION16chain 'C' and (resid 200 through 268 )C200 - 268
17X-RAY DIFFRACTION17chain 'C' and (resid 269 through 365 )C269 - 365
18X-RAY DIFFRACTION18chain 'C' and (resid 366 through 411 )C366 - 411
19X-RAY DIFFRACTION19chain 'C' and (resid 412 through 619 )C412 - 619
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 77 )D1 - 77
21X-RAY DIFFRACTION21chain 'D' and (resid 78 through 129 )D78 - 129
22X-RAY DIFFRACTION22chain 'D' and (resid 130 through 199 )D130 - 199
23X-RAY DIFFRACTION23chain 'D' and (resid 200 through 268 )D200 - 268
24X-RAY DIFFRACTION24chain 'D' and (resid 269 through 328 )D269 - 328
25X-RAY DIFFRACTION25chain 'D' and (resid 329 through 411 )D329 - 411
26X-RAY DIFFRACTION26chain 'D' and (resid 412 through 452 )D412 - 452
27X-RAY DIFFRACTION27chain 'D' and (resid 453 through 620 )D453 - 620

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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