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- PDB-9m26: Crystal structure of Enterobacter cloacae YcdY, a member of the r... -

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Basic information

Entry
Database: PDB / ID: 9m26
TitleCrystal structure of Enterobacter cloacae YcdY, a member of the redox enzyme maturation protein family
ComponentsCytoplasmic chaperone TorD family protein
KeywordsCHAPERONE / YcdY / redox enzyme maturation protein
Function / homologyTat proofreading chaperone DmsD-type / : / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Cytoplasmic chaperone TorD family protein
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChoi, H.J. / Lee, S.J. / Kim, J.H. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structural analysis of YcdY, a member of the redox-enzyme maturation protein family.
Authors: Choi, H.J. / Lee, S.J. / Kim, J.H. / You, Y.B. / Yoon, S.I.
History
DepositionFeb 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic chaperone TorD family protein
B: Cytoplasmic chaperone TorD family protein
C: Cytoplasmic chaperone TorD family protein
D: Cytoplasmic chaperone TorD family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,74117
Polymers86,2204
Non-polymers52113
Water2,486138
1
A: Cytoplasmic chaperone TorD family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7556
Polymers21,5551
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-14 kcal/mol
Surface area9140 Å2
MethodPISA
2
B: Cytoplasmic chaperone TorD family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7155
Polymers21,5551
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-15 kcal/mol
Surface area9210 Å2
MethodPISA
3
C: Cytoplasmic chaperone TorD family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6353
Polymers21,5551
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area8620 Å2
MethodPISA
4
D: Cytoplasmic chaperone TorD family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6353
Polymers21,5551
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-14 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.257, 88.690, 82.250
Angle α, β, γ (deg.)90.000, 103.685, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNHISHIS(chain 'A' and (resid 2 or (resid 3 and (name...AA2 - 1237 - 128
12GLUGLUGLUGLU(chain 'A' and (resid 2 or (resid 3 and (name...AA128 - 181133 - 186
23ASNASNHISHIS(chain 'B' and (resid 2 or (resid 3 and (name...BB2 - 1237 - 128
24GLUGLUGLUGLU(chain 'B' and (resid 2 or (resid 3 and (name...BB128 - 181133 - 186
35ASNASNHISHIS(chain 'C' and (resid 2 through 16 or (resid 17...CC2 - 1237 - 128
36GLUGLUGLUGLU(chain 'C' and (resid 2 through 16 or (resid 17...CC128 - 181133 - 186
47ASNASNHISHIS(chain 'D' and (resid 2 through 8 or (resid 9...DD2 - 1237 - 128
48GLUGLUGLUGLU(chain 'D' and (resid 2 through 8 or (resid 9...DD128 - 181133 - 186

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Components

#1: Protein
Cytoplasmic chaperone TorD family protein / CrdA / Molecular chaperone


Mass: 21555.107 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria)
Gene: ycdY, N5E88_20745, N7383_25595, NCTC10005_05540, P3S46_26535
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M7F7K2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 600, calcium acetate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 31272 / % possible obs: 98 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.36 Å2 / CC1/2: 0.945 / Net I/σ(I): 12.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1530 / CC1/2: 0.548 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.85 Å / SU ML: 0.3216 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2663 1473 4.76 %
Rwork0.2133 29475 -
obs0.2158 30948 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.74 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5734 0 13 138 5885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00575878
X-RAY DIFFRACTIONf_angle_d0.83188029
X-RAY DIFFRACTIONf_chiral_restr0.0479901
X-RAY DIFFRACTIONf_plane_restr0.00581038
X-RAY DIFFRACTIONf_dihedral_angle_d20.29993489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.34751250.26292664X-RAY DIFFRACTION97.72
2.58-2.670.29091240.24582663X-RAY DIFFRACTION97.96
2.67-2.780.30811320.23582666X-RAY DIFFRACTION97.87
2.78-2.910.31381380.2462676X-RAY DIFFRACTION97.95
2.91-3.060.29461560.24982663X-RAY DIFFRACTION98.39
3.06-3.250.2721320.22812692X-RAY DIFFRACTION98.23
3.25-3.50.27351400.20772657X-RAY DIFFRACTION98.42
3.5-3.850.25661270.19412720X-RAY DIFFRACTION97.84
3.85-4.410.22181540.17452627X-RAY DIFFRACTION96.83
4.41-5.550.2231290.18932687X-RAY DIFFRACTION97.71
5.55-29.850.25821160.21272760X-RAY DIFFRACTION97.62
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)
11.745615571460.7493694971321.849967646540.3749660601460.9865532594844.060668489930.0455673763820.23813275457-0.4647588219890.09399795822660.148766535369-0.0721671107140.3847597678430.221278572316-0.1768413383390.0713917855576-0.00058751341249-0.003121280958890.1462925012040.01236368037480.26152604417826.12394591914.4010124127149.0938785786
23.47871160859-0.8763547355750.7925510910911.02460186547-0.2334446925680.3058962234840.03262632445380.2702511770780.252042199343-0.116770268731-0.0583903054837-0.1406631117740.06714298464640.4163459208860.09792509993240.1016273496210.0651239446043-0.03250495129460.2304135501980.01319949534630.36802167189136.263432580212.664994855152.5294621827
34.472553278111.09186732685-0.4038534729482.46054046343-0.1218481773095.14393474924-0.09384572263050.1089979783170.382638662955-0.09655274102250.10638225182-0.175278471647-0.3757203994730.5531267120020.02050297434380.0807502168838-0.002300883887450.001006221202540.1581956930210.003777401842820.23056830351332.873893892119.959195050558.9845055917
42.86961679678-0.585404632706-0.04288459827625.422683307481.699064493062.744407658980.205467299416-0.6910373071990.07692005982370.263157564621-0.07252881627180.1069442963770.0841259414871-0.288225167918-0.08993414287390.04919518003390.03824904094630.02831584331980.2851015622320.07459608089360.30910991445319.42274894457.8317032549270.4312373857
54.655743307530.1188864071710.6307773726646.369915266251.004097642784.344717638370.350273386699-0.315739853269-0.4787476759370.1748520593940.05527187140860.05849809105980.499741175934-0.0715735372651-0.3103367533070.218203132884-0.0385076646146-0.07556537876640.2189215291250.1358410410130.33912817736519.7422037115-6.8803503992163.740630857
62.96527309248-0.3006547780620.2063866783396.750430964512.651557812173.707155486620.306765737992-0.0998285833865-0.4645728307870.003023280140270.275933468232-0.4928912675330.4436849262680.203708361275-0.5020016612940.2344415286060.0150549307665-0.03063681802190.209469881036-0.000928642569540.41993138406725.7910211425-4.0244484033863.3824976838
73.983004935320.3850348041021.770147933870.267535346467-0.1187147391721.779379560810.1394429902290.0826215958161-0.5408632863020.01060297951270.0616433421575-0.06044325908740.2372934233990.185901220932-0.1614757162780.0721783407779-0.012455191448-0.07847534581770.1225362573750.0231260208550.33191847554825.6315473264-0.70998504766655.0516534247
83.0283373862-0.503472451741.037555736041.918838335860.05329780519312.39471451630.2617586243230.0581871664424-0.755287826142-0.1053598844360.05600111434460.01753954989410.3135970431480.00557235593413-0.2264847299930.1360384443520.0191885689994-0.116414489880.1484326199970.09100941297980.50474906457216.7119175975-3.0100641419652.5170459647
90.9271730834890.1257512094160.2966835579720.3225696299830.2156058404790.421513490023-0.0928778568262-0.01044028135280.0463754594938-0.0509429948342-0.00530508926462-0.0197587877091-0.0801926318989-0.01580784494070.05175480562250.1010240343690.0449997678669-0.01926391374040.1362560709250.01048502539230.27327194889118.955356636412.549018559954.8979340393
101.18444839253-0.01140992355070.6778664214510.510159895651-0.4367092758971.91109982778-0.01335303731810.2659305080.1818407971120.08343215318950.161737817649-0.0212910547535-0.1350367904320.05120204470620.07750863686850.06973350962820.0610515480592-0.07857999403350.1390957091730.0231191948340.35862842368852.34771385391.7690917598349.0010119956
111.900217763-1.21012194782-1.398681328741.681367257040.6884620743911.655656274520.122045119670.0578900918727-0.165421181221-0.211659649829-0.09713025113370.166447930795-0.0245476835781-0.3322985309460.05734897143820.0786650583660.08412640724910.01959892533140.240531834746-0.05637488884570.28558999318242.0084741913-6.7000926429952.5835115025
121.76801230067-0.349115750432-0.4959995370161.6274395201-0.3084130351161.75609113232-0.0422447619436-0.261784087616-0.1284247736620.1490642672580.0557773327020.101967913876-0.01121943421870.0185101379154-0.02857034063790.1076033831990.0483722750593-0.07347240043980.1350511754660.004177933073290.34802314862452.4455046413-4.8773811500863.8069938411
131.95035719097-0.53330784047-0.3029836362572.10282443432-2.042452654366.081022289890.00680239024628-0.05222153346260.5612266190270.1689879681510.08196131631660.0585381786981-0.63193245786-0.300020303135-0.10701760640.1082586451160.0650884031169-0.0207741558440.166423446271-0.07081721440790.4686906391552.53384904618.4701738875359.4195103442
142.731152738490.586458920146-1.064850515380.4153574549770.3124990917071.429348153460.0373577100148-0.1199534947340.287689295747-0.007937231916890.136255771538-0.0655330769556-0.2256369680260.134455335215-0.0643668101744-0.01585752581030.0641371239672-0.02781218457410.205870351279-0.07145578549180.27230979255660.41941778980.26736059627857.6122888835
151.566060668391.4357060718-0.7618560497691.83912246898-1.275286257841.07189956235-0.121183094030.210719890090.0714420526427-0.08581762402350.00961840177624-0.13633821223-0.01433592403610.0826542650960.03760993778080.04544000585580.03102461683530.005419135285260.0648631918263-0.01707981947910.26535290756359.6518682032-4.9782607116750.5882775539
162.592486141940.9121194710270.180010452922.19744798744-0.9591169005851.873561485010.0599591541438-0.0837999438039-0.349042026226-0.0531943062160.0152301634421-0.01817016094970.224886744767-0.0784410036779-0.05904197848530.0786626959079-0.0678819169993-0.03049385759010.1131783376060.02254682554980.30154814747351.26832485662.674098057326.9493845334
175.528177215931.65465572414-0.8119858368522.210067654071.413859953876.73612940384-0.1553307279260.5088828247090.2193785575580.0607920084022-0.08863918059170.425351932864-0.0711220644118-0.5029228030230.0979710647860.1292331628490.02448333123860.05175835128860.2924177080290.1231362699080.27715533583840.13125467811.934474669323.0944012461
183.57130031315-0.822237117130.6930850931293.36754857963-1.93642373044.312567532390.061685438182-0.3769084138340.2330111766730.402915775097-0.07076693725890.0471609136294-0.549305395175-0.155779959426-0.01438359163420.158957269399-0.02783266495120.004677738942170.127365759373-0.05856731547420.29539903744450.571771044715.751123602132.3309510429
194.35601250008-2.42894447854-0.8833798075254.548453818131.633093124642.89790776707-0.02313778965160.5256704728020.31204106252-0.25659397860.05373685774560.04698683432690.119233679044-0.1813881171-0.004222359943470.0873781131189-0.1195201800640.0259069346690.247275609088-0.004868377828030.21099518016252.126634664710.767483153710.2953796059
200.1687677475470.206201696971-0.6045948637923.47608001278-0.03615906713174.806790998740.1590579997930.187509695092-0.459869253813-0.2041352351830.1671092675670.07400738700780.558453029037-0.331335537105-0.2165114560940.18846932038-0.0538955319233-0.03761884501860.214976499076-0.07468583088990.38346853288651.4795584792-5.8637868507317.0646977574
211.58148146968-0.943210948245-0.1396592911162.53141856556-0.6409630693852.499471774030.00289814505604-0.136909332989-0.3425856519150.01805652012750.175429270806-0.2695633492430.4360042417010.0525406215099-0.06246772133810.21676817228-0.0127412424891-0.1062465334340.143466309140.04405748019570.53659078931459.5018730544-7.5655669541923.136484093
220.204863150261-0.1675693559930.1007460188780.519413763469-0.05458891791210.07818568307420.04591495473340.0876147747320.0881068404585-0.004401786690380.007486572844820.00307080275151-0.0110717711312-0.004809181303850.0900930026247-0.0328903210842-0.07538005626430.04325745222860.198599121483-0.03193083490870.2734839881959.652642693312.086682562115.3898341952
230.429121082888-0.05623924576790.052312126460.494508398111-0.1644265741630.153750263470.0244977281163-0.1753767700870.04704848749580.0145226216207-0.04326339130250.00553980170959-0.02261035088060.0647527473149-0.01909424565140.0398924256907-0.0491903891687-0.09850327093310.15147552423-0.00338737475410.39380580205659.91602343737.781178855226.3485233559
242.274586775470.795585165497-0.8393438331761.671465126990.606132871281.825623365230.0439575655839-0.08038452041810.3719170527230.001558525218010.08943104771490.0709977220202-0.2298959039040.1191656987130.01058736545130.111678001522-0.103843697584-0.0449277438120.170111794994-0.03656340340730.31454292897827.53801377763.5327753173426.869862431
253.434542259332.34815365286-0.8104872052182.59229937804-2.147486821435.07225302713-0.15028480361-0.0836781226902-0.251029844369-0.0470962534077-0.146964465832-0.261529346579-0.1236066509920.5836793126430.1643593624170.1459170141770.012132480502-0.09359870285540.246933010251-0.09569899854440.38893675189138.4911433806-5.6930224377123.1640312754
261.16693195802-0.381421360887-0.7000248425915.433454488982.725921847092.431801655620.169905660186-0.307055952891-0.4373011914960.3273299884180.0435105940577-0.1329273788710.3119119967440.122471624457-0.04974193959190.235356880509-0.0678465289519-0.1007146954150.1524007503260.1217923526760.37021395786727.9377951395-9.444929709132.4792760863
274.489735041010.3503547303061.11193890572.54469791822-1.148860859995.51963228952-0.008631849163020.111768598484-0.308672630501-0.003687965896450.0999501794779-0.3669331636550.07990218163930.491825633313-0.05376735793120.0655150148893-0.0335794596367-0.0009208057950820.164708571579-0.01960163816240.32704529130532.463824623-11.22377351414.2536329567
283.47012493674-1.295445082030.3496256784733.892536221420.5651770479782.905495384850.2367529257310.579296448718-0.108488300358-0.559302644429-0.05437862595410.320979853054-0.288327766049-0.183626941052-0.04218168581390.1788929338180.0271616591167-0.05448978706280.2290482591950.1077311254770.26763726380221.50891559250.3547531762247.47383261665
291.517601146631.754873650881.485686853263.75298917960.6550459713124.001905856880.04398780044990.1302890258960.845357456058-0.1694262961690.119263756249-0.019701549445-0.5064832920050.469684948141-0.1204911089040.158293770918-0.02461396474080.06214224759340.2494651604510.04704192970130.60022594575527.032586541113.420969015913.3853428419
302.143319543-0.267959063964-0.2023473946533.636973148611.885724189172.673230008810.186909277916-0.08775631389630.6435910737380.189567976387-0.1656951029280.353534185227-0.231310821085-0.1121865662270.02154246679960.178139604291-0.01724697340120.05549896140370.147449716546-0.007205305344380.39846026556822.451566963211.794058659823.2247490969
311.76459240579-0.974264768006-0.06487523723931.5249742680.2335582755590.810182353343-0.0186441674090.219471480283-0.22487412174-0.017837067639-0.01902365878790.01940801911580.0122327882809-0.1905980095110.05478375627590.0547952233017-0.0648896438755-0.09816365187380.2080395357770.0723774323510.34407795628518.6970634666-5.4022892397415.4345936166
320.615599895992-0.32394125612-0.1342422313741.598165019440.8274554275150.7103523377420.06576275431-0.1143850463430.0418319442331-0.0252677859566-0.0137560045350.1841240163420.0333030710261-0.08224951220110.03859016194720.0297656342179-0.0332663747109-0.02747614037490.1836284956070.04038260835010.35003605878518.6128720236-1.8178332368926.4211254891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 87 )
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 97 )
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 109 )
7X-RAY DIFFRACTION7chain 'A' and (resid 110 through 122 )
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 140 )
9X-RAY DIFFRACTION9chain 'A' and (resid 141 through 184 )
10X-RAY DIFFRACTION10chain 'B' and (resid -4 through 16 )
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 44 )
12X-RAY DIFFRACTION12chain 'B' and (resid 45 through 97 )
13X-RAY DIFFRACTION13chain 'B' and (resid 98 through 122 )
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 157 )
15X-RAY DIFFRACTION15chain 'B' and (resid 158 through 184 )
16X-RAY DIFFRACTION16chain 'C' and (resid 0 through 16 )
17X-RAY DIFFRACTION17chain 'C' and (resid 17 through 32 )
18X-RAY DIFFRACTION18chain 'C' and (resid 33 through 56 )
19X-RAY DIFFRACTION19chain 'C' and (resid 57 through 87 )
20X-RAY DIFFRACTION20chain 'C' and (resid 88 through 122 )
21X-RAY DIFFRACTION21chain 'C' and (resid 123 through 140 )
22X-RAY DIFFRACTION22chain 'C' and (resid 141 through 157 )
23X-RAY DIFFRACTION23chain 'C' and (resid 158 through 181 )
24X-RAY DIFFRACTION24chain 'D' and (resid 0 through 16 )
25X-RAY DIFFRACTION25chain 'D' and (resid 17 through 32 )
26X-RAY DIFFRACTION26chain 'D' and (resid 33 through 56 )
27X-RAY DIFFRACTION27chain 'D' and (resid 57 through 68 )
28X-RAY DIFFRACTION28chain 'D' and (resid 69 through 87 )
29X-RAY DIFFRACTION29chain 'D' and (resid 88 through 109 )
30X-RAY DIFFRACTION30chain 'D' and (resid 110 through 139 )
31X-RAY DIFFRACTION31chain 'D' and (resid 140 through 157 )
32X-RAY DIFFRACTION32chain 'D' and (resid 158 through 182 )

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