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- PDB-8a36: Crystal structure of PpSB1-LOV-K117E mutant (dark state), monocli... -

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Basic information

Entry
Database: PDB / ID: 8a36
TitleCrystal structure of PpSB1-LOV-K117E mutant (dark state), monoclinic form
ComponentsSensory box protein
KeywordsSIGNALING PROTEIN / LOV domain / short LOV / PAS domain / Photocycle / Dimerization / Signaling blue light photoreceptor
Function / homology
Function and homology information


PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBatra-Safferling, R. / Granzin, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchFKZ 031A16 Germany
CitationJournal: To Be Published
Title: Crystal structure of PpSB1-LOV-K117E mutant (dark state), monoclinic form
Authors: Batra-Safferling, R. / Granzin, J. / Krauss, U.
History
DepositionJun 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Refinement description / Category: struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Feb 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: Sensory box protein
B: Sensory box protein
C: Sensory box protein
D: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2968
Polymers74,4714
Non-polymers1,8254
Water0
1
A: Sensory box protein
B: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1484
Polymers37,2362
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Sensory box protein
D: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1484
Polymers37,2362
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.754, 80.929, 94.370
Angle α, β, γ (deg.)90.000, 93.846, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 133 or resid 500))
d_2ens_1(chain "B" and (resid 2 through 133 or resid 500))
d_3ens_1chain "C"
d_4ens_1(chain "D" and (resid 2 through 133 or resid 500))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ILEILEARGARGAA2 - 13322 - 153
d_12FMNFMNFMNFMNAE500
d_21ILEILEARGARGBB2 - 13322 - 153
d_22FMNFMNFMNFMNBF500
d_31ILEILEARGARGCC2 - 13322 - 153
d_32FMNFMNFMNFMNCG500
d_41ILEILEARGARGDD2 - 13322 - 153
d_42FMNFMNFMNFMNDH500

NCS oper:
IDCodeMatrixVector
1given(-0.758957524553, 0.233586010979, -0.607800173905), (0.114548416749, -0.870985857871, -0.477768035357), (-0.640985285435, -0.432228193045, 0.634284362878)-35.4606200466, 7.78407787689, -11.7550230366
2given(0.724365210431, -0.0107442184629, 0.689332723499), (-0.447392899157, -0.768069342845, 0.45815835512), (0.524532778482, -0.640276538967, -0.561169598203)-37.0643169964, 7.48470649017, -11.1667789795
3given(-0.995408598977, -0.0892812044424, -0.0345048926493), (-0.0676931652522, 0.40178035434, 0.913230629274), (-0.0676709425202, 0.911373366629, -0.405979346936)-70.6145968199, 12.665599841, -25.7432520128

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Components

#1: Protein
Sensory box protein


Mass: 18617.764 Da / Num. of mol.: 4 / Mutation: K117E
Source method: isolated from a genetically manipulated source
Details: K117E ENGINEERED MUTATION / Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria)
Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
Gene: PP_4629
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q88E39
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Sodium acetate, 24% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2018
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.7→49.27 Å / Num. obs: 20405 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 91.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Net I/σ(I): 10.7
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.062 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2685 / CC1/2: 0.878 / Rpim(I) all: 0.433 / Rrim(I) all: 1.148 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J3W
Resolution: 2.7→42.5 Å / SU ML: 0.4315 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.6719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2718 956 4.72 %
Rwork0.2252 19312 -
obs0.2273 20268 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 132.96 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4307 0 124 0 4431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00364495
X-RAY DIFFRACTIONf_angle_d0.71696073
X-RAY DIFFRACTIONf_chiral_restr0.0475643
X-RAY DIFFRACTIONf_plane_restr0.006803
X-RAY DIFFRACTIONf_dihedral_angle_d10.74131767
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.86966153861
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.958506094624
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.02467436112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.46431560.38912706X-RAY DIFFRACTION98.45
2.84-3.020.43771600.35262700X-RAY DIFFRACTION98.11
3.02-3.250.30871250.28772742X-RAY DIFFRACTION98.52
3.25-3.580.28931190.26482770X-RAY DIFFRACTION99.04
3.58-4.10.29441240.22882773X-RAY DIFFRACTION99.08
4.1-5.160.22881360.20492780X-RAY DIFFRACTION99.25
5.16-42.50.24721360.19492841X-RAY DIFFRACTION99.1
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)
12.58131125986-1.46763296743.991581263340.835188680297-2.616691983365.952990785211.34627378957-4.27702575209-4.39003388404-0.4013936762410.02900916560440.7336511340931.65645003201-0.181989679034-0.6359626206420.9041691759920.2538460719310.1528884347552.242223774280.5805199618521.40505194523-23.2984497493-0.4607527301790.475428604768
28.783905723142.64129170268-0.5732626912632.55277065006-0.9347336596048.13238553058-0.502139219561-1.79315098073-0.6247710177060.162530203968-0.7274075963780.04323838442980.3756382873520.8386341365341.035202824280.8661327853640.2154227910640.07814982233511.483973738730.4043452345231.22737294068-38.9899228036-4.026872124433.77761322478
30.8780679408111.91061537695-2.992807376681.4426426811-3.35014306277.62643298505-0.013635996807-1.91608456559-1.177701100170.233645790723-1.19128346712-0.2525968556870.01039299926173.611803714260.9856058369530.9460067852720.2158884883130.1464660144492.186484697720.8450684397021.63677048563-34.412672882-2.3149418218812.1487554331
48.935725099935.543110541754.975642536931.999516827756.32009193543.78028624887-1.13427708998-0.256919468083-0.0289231587404-1.100128302470.2982040066332.725769901593.2760364873-0.5414309942870.730705152471.005387139110.4151769223180.2603477252181.66996151720.5225210763741.01689210784-41.1327240653-1.812351902763.87167543501
53.0419320507-0.273380241703-2.673392708862.414600161181.076048323423.10751638149-1.495733432111.199920879271.009068406881.085951117230.546530699683-0.144662231887-0.580581289895-0.6976329770170.7711966059341.06292685220.0346424696268-0.08608108876261.182350722270.3867731221451.42455752986-22.96109559555.97045974264-1.68184423614
64.006619445933.288739048290.4674169609555.572996465131.143137475497.15295412441-0.637281821447-0.9560161298160.599433256490.4028519106750.1257943899810.414744506058-1.1433291589-0.2093760885340.2229420062841.091306039730.1928154683150.04674528666070.829389204104-0.06098706038480.874795269168-12.59916231077.7270324833211.0492526032
76.015513047381.23424157491-2.279180242978.57002579438-1.596035520827.148550274540.382489879453-0.6789322925120.6722425724420.914505880307-0.3578496693530.383234522417-0.891951530519-0.335532573399-0.08145822671541.053734968450.1243818055460.05371106659220.826434636789-0.1593522775520.657501205272-6.842690378835.763358073519.0376523432
84.13151674955-1.72863331777-4.195109871783.406480253350.8956434816194.33147176577-0.0615982442671-1.20927351755-0.6852350053160.3919965168960.66635969239-0.6434797921230.7073124751520.42383644881-0.5477308108830.989561977440.06539363394690.03507406731381.04015632473-0.1095614972591.00261711845-10.8413115101-3.2944304899819.4692868948
91.75828190201-1.038763694110.6290137535686.16715160644-4.464209931116.33451744555-0.360856749144-1.093114006680.4485629096031.556339015161.188388722960.508237813755-0.02467212072270.449209144007-0.7601217749831.001382272650.1732808656510.174776217790.816025932902-0.1615106195830.869960486303-14.41217605543.3166356932617.9232423059
109.542836765460.983452822599-6.059681419542.531970954171.029315188824.735461365050.0889045247560.3564390128871.078870792410.03334847660610.748092448963-0.04931513770370.198824990259-0.258024830202-0.7574497251950.956671851540.218573596523-0.06749722135060.786821839160.01515908949780.829759331994-10.25153486471.065415404816.09987736232
113.23762534654.00986838296-2.738964190848.48368776227-4.471383029742.67020484563-0.302396750825-3.03644123948-0.480161350049-0.2710294713661.520144039540.4611644138911.31975129938-2.55894668563-1.325615620881.714927553660.06914314554210.2530851531372.286850025480.479245796021.26255349253-28.1488160332-4.3039353062133.6804416496
124.702917819282.489913031170.1121155876951.33281435337-0.005548157242982.233042182480.315454213698-1.53348741811.25491746285-0.9165336097710.164791620552-0.364633786526-1.470857008350.2159227420090.1135823936111.132458354040.2815935160730.1218135614050.7943443390370.09064462915651.1078105988-7.033044527752.7076266233817.7014053297
138.990418523464.77159009457-2.642368864923.42107859590.1202426512463.85155689622-0.0920708061633-2.130376836570.700820059618-0.05002147332651.74663253871.51076144899-0.313047424323-2.92727362584-1.471822366550.877150131154-0.0958391840571-0.005524513205631.969407346490.1862396077781.20569390902-48.051696498515.1404604057-18.4672235857
142.10933724655-2.414986271822.624937384929.44786252272-2.306261139756.26732820873-0.1837032462721.0468072957-0.513327484282-0.4214148947760.724810404251.383159542610.173707821773-0.608413693684-0.8238354225811.022133783090.00311442876657-0.1759308475620.9955120072950.03272074333021.1610070444-58.667423028622.8713394039-27.1968148463
156.39748067989-3.634186559933.161878302014.01114607041-3.65703861183.66175212531-0.867505761837-1.37151661913-0.512942423111-0.196163416141.469504259982.235177513360.235147231298-3.059939837560.1823290081891.292472545420.077800913819-0.2085407152721.347393890060.09283681662871.38087647197-66.61737394223.8323248166-26.8218422952
163.118678758750.3532749924422.563877872284.585049086272.608189030873.64894713269-0.06218578015760.8285996261891.220777575170.0736819365179-0.3549659754951.38966275162-0.0787628555058-1.316678591330.3776966980770.7863577758350.1573599113240.009497557750351.62040459097-0.04965154866971.40099057971-61.986244822632.5309068364-25.728529005
177.61894596644.075369948232.605125851319.16897362183-0.3277122004217.79018817218-0.5396375355851.816300369520.147272706468-2.248624236990.6621976710482.22921889098-0.711645336129-0.392459240433-0.364187632530.9078457090590.127673883879-0.1104303127571.733898567880.01129525481261.29096009524-61.029577873830.2998116778-37.7751872708
188.362015715014.13175290506-4.227417687262.29156807975-1.740981217778.00043229783-0.2198394693340.702398310211-0.1931530960520.5820308778170.618487421496-0.556295528391-0.654012480174-1.07896240879-0.4658103551671.108909928240.012112402745-0.1165914581640.963264955323-0.06377207847850.770273120087-56.481969796526.7918979777-34.748369034
190.9264679162030.311281309589-0.2422715206320.6749764154851.337496855073.62725217377-2.122450675270.629930494431-1.27302475435-1.594992158880.187592601932-1.664904806722.11063963541-0.286398482737-0.6892179262742.12668695162-1.97805058759-0.1267541388081.70225929172.295798944193.12665389055-66.93656923778.0520339387-27.2861362468
203.383678843640.005777361639061.512117886343.932445194341.801867377877.23012362021-0.5127230193872.33207272750.343802337385-0.8501462800031.41372376013-0.0852145369279-0.6046875161860.719210598767-0.8959555581261.35859155022-0.0714699203994-0.151402586141.587574947380.04291760375580.801600764177-48.828832110134.9279433232-37.835481007
213.07637701578-2.02106083603-0.3914289969483.68420836894-3.781105662317.675473515541.01349466190.586060263531.1821748055-1.27755666667-1.000331578761.35486558059-0.0453914322742-1.53541237782-0.5442891557561.098039465660.0749261054596-0.02800513313491.625024017940.3911180629931.47569190997-64.1001755628.7212938729-34.0269679951
228.95679403461-4.371147921661.785739200167.76252568481-2.453105459998.709231422180.620311440841.29298563064-0.938689696121-0.253848777104-0.3241875576470.8023827580821.26967559784-0.170362334748-0.5951661137151.07098806878-0.104758735576-0.03646845641121.0394356365-0.1411204646171.09641567877-47.3813471514.1635124917-24.926449668
234.79789547785.25073533776-2.516856628118.336515325280.08503002469865.05517420451-0.59379684118-1.6905480618-1.46881376504-0.245804650166-0.149966973078-0.2466529842220.212898763974-0.03144230444180.842497301971.175756340250.10456851292-0.08420030901031.1955605641-0.1973554722791.43732349468-33.586772466610.6988007467-23.6912775347
244.82210958288-0.0416530873441-2.392977839712.40253169582.179222905494.46138698346-0.08806346648240.9213957717570.926931182037-0.601021419695-0.1991957419410.1051376426210.959917303183-0.8564006769960.3457696745211.488518888640.0584894539892-0.1124300942281.01659985462-0.1934387656591.07087919194-39.203971198911.7977205464-35.7246984642
254.562068342114.79382508761-4.637095941495.19068420802-5.245034135485.807224074030.196856074608-1.0643545421-0.116971060864-1.25439398969-1.28398919411-0.5976966493270.1086812668981.788386240711.330366599361.36993445168-0.07799085544160.0937367603111.448499475130.05445616276921.25147051643-26.932229014416.4757552525-30.7162964733
269.32392253871-1.321220243232.54192448759.0159781385-2.256611853183.94180054394-0.2602616993460.4649529795160.527686984127-0.142448401690.115674158262-0.424935472374-0.6432817103311.019026980140.218474840940.650007114434-0.07723550431040.04459608066470.807265876431-0.07479086654690.841844507469-32.090427812722.9368718884-26.3196015456
273.305307814750.396082657501-0.7801027828893.66822963926-2.083486372463.982113566330.04124783730910.0691507031681-0.251216459533-0.5268091547310.1578613761910.198896543310.2707734470851.34368387414-0.1259242274840.920320050117-0.04112153613950.047101771391.32995572318-0.09191840614590.97726830253-39.573822465415.7151547713-19.5255344581
283.74992828794-0.900220821539-0.5001909429264.43379336785-3.082560023283.31508409289-0.7840526428630.1613304185920.7872843133490.1388368219250.702397354747-0.970138879946-0.0883734709995-0.776823584677-0.2632196951.4389413328-0.0552919851817-0.2732056169881.362538673480.2079221920871.05590627703-34.276546484538.912179541-41.9138121525
293.111269544052.21469532469-0.162390976163.62403662782-2.494984150032.89421205911-0.2445115939781.134567784022.355852748591.237719309290.7950360778321.083092249090.368683077371.53193734639-0.495382475970.990714662002-0.08827749619310.0207692195681.108259628520.1048599679251.43304578784-29.763258947418.3297666066-25.9569367864
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 24 )AA2 - 241 - 23
22chain 'A' and (resid 25 through 86 )AA25 - 8624 - 85
33chain 'A' and (resid 87 through 134 )AA87 - 13486 - 133
44chain 'A' and (resid 500 through 500 )AB500
55chain 'B' and (resid 2 through 12 )BC2 - 121 - 11
66chain 'B' and (resid 13 through 41 )BC13 - 4112 - 40
77chain 'B' and (resid 42 through 74 )BC42 - 7441 - 73
88chain 'B' and (resid 75 through 86 )BC75 - 8674 - 85
99chain 'B' and (resid 87 through 104 )BC87 - 10486 - 103
1010chain 'B' and (resid 105 through 119 )BC105 - 119104 - 118
1111chain 'B' and (resid 120 through 134 )BC120 - 134119 - 133
1212chain 'B' and (resid 500 through 500 )BD500
1313chain 'C' and (resid 2 through 12 )CE2 - 121 - 11
1414chain 'C' and (resid 13 through 24 )CE13 - 2412 - 23
1515chain 'C' and (resid 25 through 33 )CE25 - 3324 - 32
1616chain 'C' and (resid 34 through 63 )CE34 - 6333 - 62
1717chain 'C' and (resid 64 through 91 )CE64 - 9163 - 90
1818chain 'C' and (resid 92 through 103 )CE92 - 10391 - 102
1919chain 'C' and (resid 104 through 109 )CE104 - 109103 - 108
2020chain 'C' and (resid 110 through 133 )CE110 - 133109 - 132
2121chain 'C' and (resid 500 through 500 )CF500
2222chain 'D' and (resid 2 through 24 )DG2 - 241 - 23
2323chain 'D' and (resid 25 through 33 )DG25 - 3324 - 32
2424chain 'D' and (resid 34 through 48 )DG34 - 4833 - 47
2525chain 'D' and (resid 49 through 64 )DG49 - 6448 - 63
2626chain 'D' and (resid 65 through 104 )DG65 - 10464 - 103
2727chain 'D' and (resid 105 through 119 )DG105 - 119104 - 118
2828chain 'D' and (resid 120 through 134 )DG120 - 134119 - 133
2929chain 'D' and (resid 500 through 500 )DH500

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