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- PDB-7r39: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Sul... -

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Basic information

Entry
Database: PDB / ID: 7r39
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Sulfolobus acidocaldarius in complex with adenosine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Complex / S-adenosyl-L-homocysteine (SAH) / S-adenosyl-L-methionine (SAM)
Function / homology
Function and homology information


adenosylhomocysteinase / adenosylhomocysteinase activity / one-carbon metabolic process / cytoplasm
Similarity search - Function
Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSaleem-Batcha, R. / Popadic, D. / Andexer, J.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)235777276/RTG1976 Germany
European Research Council (ERC)ERC project 716966 Germany
CitationJournal: To Be Published
Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Sulfolobus acidocaldarius in complex with adenosine
Authors: Saleem-Batcha, R. / Popadic, D. / Andexer, J.N.
History
DepositionFeb 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
E: Adenosylhomocysteinase
F: Adenosylhomocysteinase
G: Adenosylhomocysteinase
H: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,04324
Polymers389,5978
Non-polymers7,44516
Water5,116284
1
A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules

E: Adenosylhomocysteinase
G: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,52112
Polymers194,7994
Non-polymers3,7238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area28030 Å2
ΔGint-126 kcal/mol
Surface area51790 Å2
MethodPISA
2
B: Adenosylhomocysteinase
H: Adenosylhomocysteinase
hetero molecules

D: Adenosylhomocysteinase
F: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,52112
Polymers194,7994
Non-polymers3,7238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area28140 Å2
ΔGint-129 kcal/mol
Surface area51800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.362, 88.364, 138.537
Angle α, β, γ (deg.)78.863, 74.849, 64.843
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Adenosylhomocysteinase / / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 48699.668 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: ahcY, Saci_0646 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4JAZ7, adenosylhomocysteinase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350 with 200 mM ammonium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.86 Å / Num. obs: 107558 / % possible obs: 89.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 39.32 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.4
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.24 / Num. unique obs: 15731 / CC1/2: 0.936

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H9U
Resolution: 2.5→46.16 Å / SU ML: 0.3752 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.7492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2817 5267 5.01 %
Rwork0.2292 99957 -
obs0.2318 105224 87.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25760 0 504 284 26548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004826688
X-RAY DIFFRACTIONf_angle_d0.958636096
X-RAY DIFFRACTIONf_chiral_restr0.05594136
X-RAY DIFFRACTIONf_plane_restr0.0084576
X-RAY DIFFRACTIONf_dihedral_angle_d19.52449864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.4191460.30332996X-RAY DIFFRACTION79
2.53-2.560.37161790.30493215X-RAY DIFFRACTION84.07
2.56-2.590.35771900.29253595X-RAY DIFFRACTION94.11
2.59-2.620.33881690.30693585X-RAY DIFFRACTION94.04
2.62-2.660.38961890.32613435X-RAY DIFFRACTION89.24
2.66-2.690.40721790.33193189X-RAY DIFFRACTION84.88
2.69-2.730.32641770.2963577X-RAY DIFFRACTION92.94
2.73-2.770.34062010.27983507X-RAY DIFFRACTION93.4
2.77-2.820.31671770.27663655X-RAY DIFFRACTION94.06
2.82-2.860.33541950.27763549X-RAY DIFFRACTION94.21
2.86-2.910.34641940.26623597X-RAY DIFFRACTION93.49
2.91-2.960.35531950.2723500X-RAY DIFFRACTION93.33
2.96-3.020.32851790.26583630X-RAY DIFFRACTION93.45
3.02-3.080.33892070.26623491X-RAY DIFFRACTION93.03
3.08-3.150.3561880.26013529X-RAY DIFFRACTION92.49
3.15-3.220.31471780.26183485X-RAY DIFFRACTION91.23
3.22-3.30.33771720.25543496X-RAY DIFFRACTION91.22
3.3-3.390.34551730.25623365X-RAY DIFFRACTION87.79
3.39-3.490.32911190.25382581X-RAY DIFFRACTION68.16
3.49-3.610.32211480.25113113X-RAY DIFFRACTION81.4
3.61-3.730.3217930.24712191X-RAY DIFFRACTION56.55
3.73-3.880.31471530.23482811X-RAY DIFFRACTION74.03
3.88-4.060.27961710.20462830X-RAY DIFFRACTION74.56
4.06-4.270.23452050.193549X-RAY DIFFRACTION93.71
4.27-4.540.22791860.17823562X-RAY DIFFRACTION93.7
4.54-4.890.22312020.17463539X-RAY DIFFRACTION92.74
4.89-5.380.20331990.19263427X-RAY DIFFRACTION90.65
5.38-6.160.27371850.20683398X-RAY DIFFRACTION89.24
6.16-7.760.20881870.19143157X-RAY DIFFRACTION82.92
7.76-46.160.15831310.1593403X-RAY DIFFRACTION88.33
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)
11.417945657841.13355719135-0.3124335794461.98848190029-0.427850474962.384221410370.0365787023924-0.02178807492180.1655407448080.340941104247-0.08078127885180.0775015018058-0.443223185316-0.2356335091530.06311572350380.4171478984930.154039026754-0.005348033095410.239242332099-0.02502259605320.299172309405-27.40820764176.11068622958-73.8768486082
22.26933063084-0.1946245403450.6564596921242.277545249380.9446839030692.161303850680.0975049380045-0.2656486456130.2419002196630.4986655415880.1393104940670.114791017525-0.185674591108-0.563602489611-0.2122611014140.5740885148040.1315913569370.1095788525280.43355531191-0.01719050961180.278784010638-29.0029269013-0.123182341509-56.5778167892
32.04412973161-0.8111323438960.06675614070611.298219152040.1470073175561.80556079384-0.11126601719-0.00741073678915-0.1644818602310.3036730998960.0237220060403-0.03199144298-0.168443976067-0.1525687598320.09268971051590.248295848544-0.01811029705240.02788608471920.149460939448-0.02070617997130.194616562249-10.6610843125-15.3601458473-66.162083562
43.43184129105-0.0335848551337-0.7857335742683.08380281499-0.5321425740693.78990735655-0.130787801237-0.4007786182370.375814014320.06051425984470.0609287728301-0.059890846175-1.192000358980.1636823971790.03973775324270.586264277537-0.0403966882947-0.1342816758140.201781294028-0.007576925568640.3223615910711.01930806-2.96434891011-61.2173332714
56.759308002120.2369532648821.261960990354.56169850506-0.5633003715924.93662878967-0.0484455150225-0.568383425820.07512409900240.1501821130140.160940990349-0.404615792193-1.023387830260.40569943128-0.05112330998240.517534361697-0.0512204002677-0.02396023242740.375528719123-0.1060151978610.2565815076684.43930181457-0.0947782547803-67.5280789167
62.859146360040.6657356327480.3338719568352.017203289050.3271789804731.337486308670.0312885008349-0.313174156641-0.1048799741570.1658226854020.02408514228870.2653336927790.030564345786-0.269988568548-0.05568035988270.256500417150.03753128082640.03816628907050.2426091009320.004358161585250.395950423565-31.1513603663-9.22638607102-69.8671559
72.033683858950.2668096502760.5371098429721.25137998542-0.4152981974762.772988902620.103671446096-0.1819573655920.00130053830588-0.5894490605140.2656158820530.6524569602580.426518986403-0.932370344784-0.2300019433020.427023631249-0.112061609735-0.01951134712710.395978945833-0.04826380044730.464645204156-40.1157957582-38.1529470197-74.0357238619
81.107355903170.3899455180481.169986401241.61185002062-0.08595259617352.37479408146-0.406394498446-0.08458379673240.8476986748030.588571946158-0.200062697161-0.706233066285-0.9117881499980.444843234450.457891778310.582333082367-0.118049389229-0.2388110254390.5697776222010.06767799641530.71852070588733.4619427985.03633162831-20.210293631
92.3095162924-0.6165156503590.4860304066342.008298530130.3339976017061.894491626210.06010442215230.4488217956290.8472673961650.126665049076-0.389368937736-0.404629563465-0.6365243743630.2855802008470.3102612821290.672702684006-0.0387661434532-0.2910803035680.6152664855810.1613544700970.70350046568729.71860497056.96191200368-24.7994835387
102.288524022220.347024251962-0.4821276498931.23642376966-0.2241073050030.320563125441-0.0247385216720.1901724941270.37832605756-0.178629293756-0.091227063416-0.175755538589-0.1905930471350.1839523238920.1228895015150.551501544366-0.0321906725593-0.07269950131740.3900486704590.0736895728220.33591474610422.6560489282-4.59397663548-32.6333227149
112.39393446773-0.199746514042-0.01399106348092.390409997270.1115707048092.71711492965-0.02546947727640.1302422077240.15635898014-0.000965786889918-0.0587651205392-0.0992323677545-0.238806182612-0.05986217917060.07922687492070.5785601457010.0279342249054-0.09058367813950.2427952985480.003241020893330.2533544580273.68683111371-10.2590434253-34.4158815257
124.33023745309-0.8565755663360.04636364820952.82341859211-0.3311986543122.76005978710.2675966513720.3782772717390.432123693432-0.23727923729-0.3034918374530.292128422609-0.215047261889-0.1693321246130.07294303802360.6645461783290.0607775328545-0.1237334021620.2734099321240.05095075345790.379899565875-1.788043444791.76697523739-30.6346970151
133.31621982614-1.235216199430.3683695214772.5963209758-0.2806179785450.299774745531-0.02488513250360.1919063038560.137645862725-0.150892506128-5.48407892885E-5-0.499062022020.005170144747070.105652224370.01332516682030.402708768525-0.0545072178157-0.007267159615210.3738819628930.07395839891410.33851910987133.2900422987-8.69128606832-25.8651546827
142.8117863674-2.3731195356-0.2634972333154.663595360941.1928440092.80988472085-0.413083910990.256045530640.0009717640518970.9184302430860.576532348707-0.6854808417490.9439907797510.968637964794-0.1319734600310.5951911760210.1181708823890.03834729574950.674132507071-0.05613411373250.47474621470440.1194035436-36.5649074366-15.9891747624
151.53836574387-0.09413005534210.009704801804921.661624861850.0556332637722.20801705284-0.02168351771990.1096390614120.335808024695-0.196987914293-0.00654820985228-0.141641773731-0.6035026597640.2695169372830.03232911479740.47528816425-0.135292506104-0.0256452713860.2601843103040.01671032138490.34461091388112.44210109892.82268737967-92.2247184662
162.31909248858-0.07513295716-0.3303222847191.8185746739-0.09608978500181.401956106450.006054690189160.3256263977850.0404113972116-0.2001562850820.112830157612-0.259568791936-0.4105608120270.129594934052-0.1028991948440.466738622478-0.1610676755580.04303733907620.400852989250.002343191946660.27969470053712.8495321854-10.268238714-105.210458117
172.299475365230.1352058737680.1044053083811.662993065570.09791370084412.06329063387-0.0567651746694-0.0200836596271-0.133489338319-0.02721757775440.0385406670560.0281214522836-0.316075315201-0.01722481875770.01021344460590.269333635644-0.007598502388310.03200090957260.1211063733460.0112641629510.200228242526-10.7316474065-19.301298229-93.9147348896
183.62218135945-0.3183724478780.1105532772143.650899364360.4899642106633.73977822708-9.87940772192E-50.5705808478080.399323700287-0.474823165940.09932440893270.129410014079-1.03146654207-0.171002664389-0.06544650860060.5229447758270.00705977593326-0.0096985553680.2575261083450.05278149939220.261594804995-16.6021122992-6.97040463485-102.810456317
194.647789699410.02710361518931.057469087163.753949615190.8442695605724.018601599110.05944822080640.0240241222846-0.0226696153136-0.1614817960320.0601249623220.384421929574-0.768677943055-0.57320660144-0.002762248066210.4588501061550.1196050511530.07104855383740.2595585364980.03394732783840.281546509591-19.8422536342-2.4070186101-97.2273644136
203.05093470001-0.768050393920.5211126219541.85148878351-0.4414006554850.5684248876570.04029548349650.346986102894-0.00654471416107-0.1061951852750.0185919073155-0.282881419861-0.03262375190080.155838375919-0.0587434026990.302753294276-0.09235328563860.02633852107850.319142162815-0.0100405973540.30827833338115.0831988451-13.1206321651-92.9527780965
212.22119058327-1.247373776970.01105987783993.940450402482.891019470964.74438514818-0.3790513893330.217359790592-0.008252716043470.6789237396050.796249415947-0.3334341768040.6398854984050.385752439509-0.3716857660130.3238465620330.01251135778280.1078645141440.4936549148190.01242046703890.31800126695122.1733665558-41.0598418324-82.7741114082
222.490976064980.404847929138-0.415638019550.5188805733330.2945936912531.567252569130.3941490873030.235267326496-0.647992201265-0.540517108243-0.1679336854180.3200036659790.620169218357-0.095749711001-0.1653636050350.8462552831460.151772115826-0.2241467998440.419612772425-0.08153234796790.450506538237-34.33069439926.8822220449-32.9933934555
232.21751077628-0.6314012860770.2724477008191.52141624762-1.040848222620.7841417973690.1065633662530.207981648674-0.5200945356890.1052947910590.0390521480765-0.0431456881070.3651241424660.226200846898-0.1175026204550.8172344601450.163631576472-0.1937022854910.408015796899-0.100397521640.583249545227-25.44514582322.0734678051-27.2963018134
243.12907279544-1.69113959944-0.4915717190962.75031068369-0.3434086877121.957107960320.2641315821520.581364498372-0.222014849381-0.57182768496-0.277835163881-0.09707370469210.2766360955750.302504918404-0.01757807947480.6371213406720.1459337251460.0002758726167350.524153151428-0.03013864808260.340659839983-14.942436449935.3239993228-32.2811321788
251.836550395090.31352800216-0.1382945911941.92769249930.2722026652671.125629547170.0681786338852-0.1093577651890.0627362643668-0.000947607209466-0.02588665687850.0113847730736-0.01328540692320.0827283329265-0.02541443881980.3998733399870.0370946310945-0.08246122334320.235427009157-0.002260862004220.252743457279-24.180021047548.9809643587-9.9075158834
264.224080366160.5224458211870.6968385361333.74186218045-0.4508033468833.758896515970.313950552553-0.154416226616-0.7263229669110.567596451172-0.0236882074101-0.4202705433510.7980945171660.327179999713-0.2721756395240.6310545633520.0805392429043-0.1709481565840.280363042115-0.01295105725440.42157130123-19.168075802935.1784319554-0.964080590694
271.01807555961-0.0317615758473-0.4586274777810.914490007229-0.148753977392.267354794250.07834910246290.3526217260870.0633324628854-0.290047887022-0.162364623124-0.104427847528-0.06554305205940.04488455928990.05939796743740.7648681483540.14791759655-0.1373655972390.4335760902650.01421764221280.407793934298-26.653438143739.5481582289-34.7918979449
285.958705132153.76386767403-1.858385541894.36936195262-1.93542469594.04304731173-0.41655345741.343183735030.115595097365-0.7253350305940.6535595683070.181687349672-0.1543147901090.0381183958257-0.2977085233290.6033937783350.0292886501637-0.1098506684240.6169076935350.05765236598810.324427053576-33.08315393167.0327202672-45.677493251
292.48124880804-0.134068372824-0.1045934457092.75462581798-0.7818273475422.935484440850.1485595135340.103855391806-0.295462166983-0.257047159793-0.1256651598830.1821814477480.4248953770120.0266828949054-0.0474122696590.3077801326630.0435136213792-0.03854729612790.179438653504-0.02554627888850.245777232757-50.897904081621.5595844466-98.1059045147
300.66070641655-0.5496766252920.2532156164081.549703199120.1306609551822.152004067070.09435250002290.145410309961-0.141931323952-0.159644660657-0.0728644485082-0.08372152682430.2966450566940.188685479501-0.02947089725510.2413097406740.03813254035910.04785186710990.201471627274-0.01965141756140.270516899892-38.713634994631.467220959-90.5199191553
312.287769155850.2521132231550.6412906852522.91596748891-1.533862922582.582478620380.07939185971250.0347612179615-0.3736695787450.28495961605-0.0633306887049-0.2581933782410.3295139796880.172832001365-0.04825570525520.3679902153190.0667830973286-0.008012652226050.20889437883-0.0340123056520.320899310607-35.605789209939.5199541626-72.4366802862
321.29389579735-0.2102259175320.1782098338921.293916644920.132428293324.2555699142-0.004231828504840.019947431759-0.02266883682610.0492593817-0.0740824389535-0.01401697335090.1378018907850.2771154866680.1167029080.2668825609140.005221900855520.003428091891520.156677858114-0.01504082432430.273908883345-43.773619325933.2450103576-91.3900639922
336.599077607440.755609875825-0.5939215943871.4771095931-0.1584711665364.98371440798-0.1726077110320.2527962890370.759943842773-0.3432223541360.309313119280.144878974727-0.3703677865960.466630054144-0.2157814855830.579987986354-0.07746253431530.01220480560590.4246710355020.06488538154090.240131494871-51.444039028662.9543056675-112.592353376
342.40483706027-0.441909090682-0.08326000133721.052768621530.5870932325982.902138579370.143326341817-0.721626689098-0.6628403191010.393331262639-0.097881328093-0.3193161061680.474212749931-0.0685872235746-0.02797563048520.759185343291-0.19421911509-0.2268678179320.64776144890.2071840007410.457800339074-43.540105936730.884456891611.3270065464
353.93002445064-0.2310240451470.7350779421381.613250222871.335591512971.57193773348-0.103322572828-0.675308232247-0.7953735821740.652950165812-0.0927902097826-0.1338155134080.358137252526-0.2201840165650.1803254617680.975834630944-0.2874907704-0.2099248026870.6155938689060.1772026391630.600365264069-56.374315199623.52641781896.56972621846
363.312068099171.82524123101-0.06233375210063.9578180918-1.636048856274.738397129590.247786905305-0.6280272754-0.2999410548810.131269265075-0.2452823156010.0937877944870.979536463587-0.07064959913180.002913609533570.592074060098-0.157731297252-0.01438942082920.8040703424920.1108718552640.390446675598-63.104599559837.572045778811.0004951229
372.1676748910.04537463101540.1985189969921.08884143421-0.07237999098851.836394870790.126439210122-0.428567654474-0.1538925950730.18567017272-0.09284564060960.1221983164080.08296862503730.0103965375647-0.02368812012690.386985636108-0.0717258550349-0.01971008079750.2487529217830.0584183355750.258612429157-49.899444682847.2769510127-5.86128026187
381.88719012552-0.2325368736680.421448999713.692797757671.340210593992.269386890270.163890163192-0.0806476648681-0.3280396881790.0245486623108-0.007815111521620.1096724708560.391151613109-0.44429428695-0.1510247044470.554007800382-0.0301391690832-0.1137167903250.3233473059570.04379809289920.326184925283-57.722143252643.8980531696-17.6488132855
394.01746622484-0.2695152983352.317424417340.6435786088490.6370926884073.23427620140.363231001763-0.146808036844-0.783939435786-1.072458593140.03384048941390.5929258907490.680603206804-0.158018407946-0.3404869406730.794592496062-0.0292444447484-0.1525989188240.2706432129080.1018059758280.479822760819-53.249296465131.8661302708-22.3731951096
401.225704997970.5488666604950.6898149748612.188756299720.1335921474591.634559073070.12778719341-0.608046600055-0.1851165155790.328472330489-0.0412511187960.2836189615090.188211950377-0.456217799263-0.09435125945620.59112902113-0.0274208000336-0.03532038055310.6132746900390.1148295060820.331500251077-48.717841794345.097452877111.9080656104
414.59910285613-1.42123859866-1.682455045171.153602810121.955404500343.46709183088-0.0923073620364-0.8093363298440.8146581230230.02685634788090.395352856497-0.355447924749-0.402022850443-0.311300119961-0.2756837719590.6488576339830.149178843135-0.03145815957790.533450669178-0.08499316325020.448494255287-40.780937602873.720922089617.067274459
422.31014607347-0.08418299977280.02009827027471.95254539517-0.009966337096232.652086132190.0739968775799-0.105858245594-0.3753445478390.28659950183-0.0518510779769-0.0341593726940.5346258145590.0840426160964-0.02782708345240.585087447832-0.0413268946902-0.02900037558740.2288252622730.0006272102116250.259877968044-59.673390885627.4841650667-53.9982049699
432.428820251510.002931820137040.9522323522.471784909591.090575204192.94984631561-0.00890747862224-0.1726205762470.0395540011231-0.3581372645080.006847912093520.156702955110.685169825596-0.321357168005-0.03863589289630.379384333201-0.08175309400060.004606623365040.2907253978530.0403224755150.258261053293-64.147429560424.8647166306-57.4486708813
442.66047914303-0.0678274351323-0.3238514936310.7659766133670.01674657477440.3186104907670.354240635421-0.132985876459-0.5468716143770.599019092028-0.275598903886-0.1491425997340.838129740232-0.299628135397-0.07462697361920.914684111422-0.231455026294-0.01761929766920.4176414650610.02358390771080.467496752136-74.29301978119.1483354983-59.8910505661
452.641681619491.446198100490.6934495173883.59031782473-1.368607782944.101820825970.163043772378-0.1616136922820.2459580781710.1997054328160.09157495234420.4729401513390.381193713246-0.931543570109-0.2206182142560.456286568975-0.0674701388210.1337192134230.49485027346-0.03352678248450.351186662806-80.986925926433.1768808301-55.422172179
460.5248831031120.1058302585090.1048889886481.62315309002-0.6456390483272.830013632820.013286732432-0.2337453740340.01628101699380.1185274624790.007908729070050.07776708770920.06079058103090.00130631881682-0.02024845402140.225366686657-0.03362345822090.05209615059850.246680259056-0.005986896022390.307762120271-67.867871155742.8962443912-72.4593577176
471.59566623928-0.1298399834811.465528350023.133413602910.1448894168832.01515148943-0.115834464367-0.113888069955-0.113904625887-0.1217900236090.03548617645050.04683866025210.0731349998487-0.2782284893380.08348437700810.20107657191-0.02064336439280.07428580854160.285453010433-0.0004190910770520.342634887697-74.452997677147.5392962323-82.5969014716
483.6542181442-0.0599791324590.2696564373093.856625164140.8663201812083.27615483398-0.0546312225969-0.0608638560762-0.205697731581-0.0196293406109-0.1122589675430.5420066192870.620011674511-0.3416304724690.1895793237290.345574683843-0.0668281384913-0.003923570376510.2691606258840.03057167326360.287931307688-77.121089078231.6039951832-85.665173892
493.61016229861-0.05315439490980.3056708273133.093210781610.4245755939194.13303726521-0.08132841281890.246053805715-0.477257851136-0.700157310850.2019991881020.5862718959040.602711935673-0.103578195741-0.05346700968860.597153576759-0.03124396455-0.03233470615080.289972636813-0.03407124885610.394631063287-71.455985920427.3680162906-88.8455512436
500.6362097670360.6350562805030.9360292048532.585720734430.6924685954482.28327079696-0.0155990250263-0.2477575580330.01738751518480.378475818287-0.04229876776540.3141998551150.121701553825-0.2499164532030.08405443347810.3510885543350.01599998467130.06192502738590.2920171136680.01952434231110.282323474963-66.54822302640.5550322581-54.7437065353
515.86425182911-1.70865472423-0.04673901687733.439895128150.3200823986572.820826201390.237263849836-0.3123521818010.3123212508740.01097643509550.260070749282-0.262426580038-0.281947945067-0.224879685018-0.523515161850.4167459865970.0951846615936-0.05356866333510.52560831715-0.06344448131540.321040633047-58.310053540469.6629132348-49.989862251
522.165980981070.858405158816-0.1779785016082.148320480290.3483707269832.50565377899-0.0847938149409-0.0004437219513750.468077269089-0.222175896523-0.03618262096750.251752147226-0.348158513803-0.2033228284630.1139185291670.4844274601820.151038830755-0.1193210106640.284271908753-0.02036602919650.428506211798-12.34274654447.27646104739-11.8895254472
531.929874416491.278265582170.5451460473932.50681036353-0.06934772674222.0189972927-0.351001823001-0.2810051649970.4225695382980.384975473740.340104807178-0.255078245592-0.435720879527-0.08082701766940.04626099579410.5212469803190.107974906333-0.1759684994680.337297238244-0.08814961852050.460168289019-8.5595289627910.0572801843-7.77982218372
541.251306394110.252514442747-0.5409232730930.9682842030090.3443224187392.67312231966-0.066681387235-0.2455573264540.9079485501620.1681004203050.137954339377-0.256006331375-0.831897481511-0.27526831219-0.1323597328931.018547981930.209677199228-0.1349823313920.44243474742-0.1092971171380.608380543331-5.1554055885816.51548785471.51590780048
553.97253982127-0.975630557740.4167104546082.289511595170.5573532255652.32912685932-0.563846545537-0.8297419241530.3643873553810.8541791545550.4381648436780.110712269666-0.195034765584-0.1152438401180.06894482602390.7015503488650.2138637538866.63662583639E-60.627094957439-0.09468410681690.38190696533-11.11575709944.1906578280910.0332385466
562.49229125063-0.7686705832140.1918196495470.508857626139-0.6726906826050.685005541231-0.0604242588228-0.1549415791790.1591548805290.1937324186250.1173268549650.0664913776423-0.00591440220407-0.0517419577543-0.01546273190610.393869397102-0.00557696316796-0.05833126107940.23137488518-0.05539684783160.2546290805694.03559408695-9.29870502129-1.83997602439
571.518779653610.8851878902520.1316353136891.87835090489-0.2295136551311.93124503465-0.0169360494056-0.1683138034560.0532108193520.1430883759360.0386964228483-0.0255096117156-0.335047511511-0.0791449892541-0.006932295842490.4425438906260.074283768019-0.04105403198370.260425807725-0.03270040028680.25709807802313.6040262135-14.34554998515.36446353049
582.316145098850.9148343362370.4987110266291.8571224035-0.4755252762112.99230224764-0.193972388215-0.1743457249850.5456721426050.5105177883980.0584709779855-0.15396330582-0.8994415753730.1269145021780.09512136811310.617095367924-0.0246388258657-0.1517896909590.299042557946-0.05395953864550.41783980967718.72449652421.208249621615.85021099277
593.77416663902-0.2578225469020.5615473245732.60874630258-0.5899896269162.06812327783-0.281980468493-0.08355725014670.4976120889060.2119930094050.187967818784-0.537834645826-0.6454199990520.2394049996870.06680725419170.606396713482-0.0429649433927-0.1449750973280.292171413797-0.07526316165810.57248740404422.54477817014.20195680568-0.431138301714
603.596902275910.68863349571-0.319114401451.852696734890.8320329306090.668905938761-0.00715649204931-0.4623231037310.1666939783310.16938683421-0.04470713910060.2487702359590.0930670743772-0.2144460596610.01884248891910.4380176106960.0763139993013-0.07978199576170.409647625555-0.002399599966950.332417989865-13.2043656145-4.82537019779-3.31932989157
611.86220981949-0.1381930724890.5390843163093.09248094719-1.134979335212.700037194220.192627534835-0.148906729275-0.293433570109-0.191747292230.3680896122440.7326881605830.498277237601-0.674328594447-0.5306568675060.474652720528-0.184986921178-0.03439778633650.71242100091-0.001739747378490.468040084415-22.1208232009-33.8809116931-7.58501453773
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 116 )AA4 - 1161 - 113
22chain 'A' and (resid 117 through 160 )AA117 - 160114 - 157
33chain 'A' and (resid 161 through 274 )AA161 - 274158 - 271
44chain 'A' and (resid 275 through 311 )AA275 - 311272 - 308
55chain 'A' and (resid 312 through 333 )AA312 - 333309 - 330
66chain 'A' and (resid 334 through 393 )AA334 - 393331 - 390
77chain 'A' and (resid 394 through 415 )AA394 - 415391 - 412
88chain 'B' and (resid 4 through 53 )BD4 - 531 - 50
99chain 'B' and (resid 54 through 90 )BD54 - 9051 - 87
1010chain 'B' and (resid 91 through 236 )BD91 - 23688 - 233
1111chain 'B' and (resid 237 through 311 )BD237 - 311234 - 308
1212chain 'B' and (resid 312 through 333 )BD312 - 333309 - 330
1313chain 'B' and (resid 334 through 393 )BD334 - 393331 - 390
1414chain 'B' and (resid 394 through 415 )BD394 - 415391 - 412
1515chain 'C' and (resid 4 through 116 )CG4 - 1161 - 113
1616chain 'C' and (resid 117 through 183 )CG117 - 183114 - 180
1717chain 'C' and (resid 184 through 274 )CG184 - 274181 - 271
1818chain 'C' and (resid 275 through 311 )CG275 - 311272 - 308
1919chain 'C' and (resid 312 through 333 )CG312 - 333309 - 330
2020chain 'C' and (resid 334 through 393 )CG334 - 393331 - 390
2121chain 'C' and (resid 394 through 415 )CG394 - 415391 - 412
2222chain 'D' and (resid 4 through 53 )DJ4 - 531 - 50
2323chain 'D' and (resid 54 through 116 )DJ54 - 11651 - 113
2424chain 'D' and (resid 117 through 183 )DJ117 - 183114 - 180
2525chain 'D' and (resid 184 through 274 )DJ184 - 274181 - 271
2626chain 'D' and (resid 275 through 333 )DJ275 - 333272 - 330
2727chain 'D' and (resid 334 through 393 )DJ334 - 393331 - 390
2828chain 'D' and (resid 394 through 415 )DJ394 - 415391 - 412
2929chain 'E' and (resid 4 through 90 )EM4 - 901 - 87
3030chain 'E' and (resid 91 through 236 )EM91 - 23688 - 233
3131chain 'E' and (resid 237 through 311 )EM237 - 311234 - 308
3232chain 'E' and (resid 312 through 393 )EM312 - 393309 - 390
3333chain 'E' and (resid 394 through 415 )EM394 - 415391 - 412
3434chain 'F' and (resid 4 through 90 )FP4 - 901 - 87
3535chain 'F' and (resid 91 through 116 )FP91 - 11688 - 113
3636chain 'F' and (resid 117 through 160 )FP117 - 160114 - 157
3737chain 'F' and (resid 161 through 236 )FP161 - 236158 - 233
3838chain 'F' and (resid 237 through 311 )FP237 - 311234 - 308
3939chain 'F' and (resid 312 through 333 )FP312 - 333309 - 330
4040chain 'F' and (resid 334 through 393 )FP334 - 393331 - 390
4141chain 'F' and (resid 394 through 415 )FP394 - 415391 - 412
4242chain 'G' and (resid 4 through 53 )GS4 - 531 - 50
4343chain 'G' and (resid 54 through 90 )GS54 - 9051 - 87
4444chain 'G' and (resid 91 through 116 )GS91 - 11688 - 113
4545chain 'G' and (resid 117 through 160 )GS117 - 160114 - 157
4646chain 'G' and (resid 161 through 236 )GS161 - 236158 - 233
4747chain 'G' and (resid 237 through 274 )GS237 - 274234 - 271
4848chain 'G' and (resid 275 through 311 )GS275 - 311272 - 308
4949chain 'G' and (resid 312 through 333 )GS312 - 333309 - 330
5050chain 'G' and (resid 334 through 393 )GS334 - 393331 - 390
5151chain 'G' and (resid 394 through 415 )GS394 - 415391 - 412
5252chain 'H' and (resid 4 through 53 )HV4 - 531 - 50
5353chain 'H' and (resid 54 through 90 )HV54 - 9051 - 87
5454chain 'H' and (resid 91 through 116 )HV91 - 11688 - 113
5555chain 'H' and (resid 117 through 160 )HV117 - 160114 - 157
5656chain 'H' and (resid 161 through 236 )HV161 - 236158 - 233
5757chain 'H' and (resid 237 through 274 )HV237 - 274234 - 271
5858chain 'H' and (resid 275 through 311 )HV275 - 311272 - 308
5959chain 'H' and (resid 312 through 333 )HV312 - 333309 - 330
6060chain 'H' and (resid 334 through 393 )HV334 - 393331 - 390
6161chain 'H' and (resid 394 through 415 )HV394 - 415391 - 412

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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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