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- PDB-6okc: Crosslinked Crystal Structure of Type II Fatty Acid Synthase Keto... -

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Basic information

Entry
Database: PDB / ID: 6okc
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C12-crypto Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 1
  • Acyl carrier protein
KeywordsTRANSFERASE/LIPID TRANSPORT / Thiolase / ketosynthase / KS / AcpP / TRANSFERASE-LIPID TRANSPORT complex
Function / homology
Function and homology information


monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / response to xenobiotic stimulus ...monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / membrane / cytoplasm / cytosol
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Acyl carrier protein (ACP) / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MRJ / Acyl carrier protein / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsMindrebo, J.T. / Kim, W.E. / Bartholow, T.G. / Chen, A. / Davis, T.D. / La Clair, J. / Burkart, M.D. / Noel, J.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM095970-06 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2020
Title: Gating mechanism of elongating beta-ketoacyl-ACP synthases.
Authors: Mindrebo, J.T. / Patel, A. / Kim, W.E. / Davis, T.D. / Chen, A. / Bartholow, T.G. / La Clair, J.J. / McCammon, J.A. / Noel, J.P. / Burkart, M.D.
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 1
B: 3-oxoacyl-[acyl-carrier-protein] synthase 1
C: Acyl carrier protein
D: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6516
Polymers102,6034
Non-polymers1,0472
Water15,151841
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-56 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.070, 112.170, 140.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 1 / 3-oxoacyl-[acyl-carrier-protein] synthase I / Beta-ketoacyl-ACP synthase I / KAS I


Mass: 42656.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fabB, fabC, b2323, JW2320 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A953, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 8645.460 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: acpP, b1094, JW1080 / Plasmid: pMAL / Details (production host): native expression / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6A8
#3: Chemical ChemComp-MRJ / N-[2-(dodecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 523.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H46N3O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 841 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.84 % / Description: Square plates
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8K, 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→87.7 Å / Num. obs: 135639 / % possible obs: 99.6 % / Redundancy: 11.8 % / Biso Wilson estimate: 13.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.033 / Rrim(I) all: 0.115 / Net I/σ(I): 14.2 / Num. measured all: 1594036 / Scaling rejects: 844
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.5811.20.9947269864910.8820.3061.0413.398
8.48-87.711.90.048115339660.9980.0140.05130.9100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G5X (FabB search model), 2FAC (AcpP search model)

1g5x

2fac


Resolution: 1.55→87.7 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 14.78
RfactorNum. reflection% reflectionSelection details
Rfree0.1638 6845 5.05 %Random selection
Rwork0.1472 ---
obs0.148 135501 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.51 Å2 / Biso mean: 22.5945 Å2 / Biso min: 5.71 Å2
Refinement stepCycle: final / Resolution: 1.55→87.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7120 0 102 842 8064
Biso mean--29.21 33.06 -
Num. residues----962
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.549-1.56660.24732110.20344161437298
1.5666-1.5850.19132230.19194186440999
1.585-1.60440.19222410.18764214445599
1.6044-1.62470.22992230.184212443599
1.6247-1.64610.20992280.17444220444899
1.6461-1.66860.18322110.16394202441399
1.6686-1.69250.19692060.16394283448999
1.6925-1.71770.20662250.16374214443999
1.7177-1.74460.21072270.15944224445199
1.7446-1.77320.17122350.15214242447799
1.7732-1.80370.17432250.15094246447199
1.8037-1.83650.16382140.145343184532100
1.8365-1.87190.16332170.14714251446899
1.8719-1.91010.16762150.15074280449599
1.9101-1.95160.17772290.154442644493100
1.9516-1.9970.17252360.151342424478100
1.997-2.0470.1692450.147642624507100
2.047-2.10230.15772260.141542964522100
2.1023-2.16420.16432130.14242874500100
2.1642-2.2340.1562500.140942864536100
2.234-2.31390.16582540.143142434497100
2.3139-2.40650.16322440.145542864530100
2.4065-2.51610.15282350.149843404575100
2.5161-2.64870.16112290.14443244553100
2.6487-2.81470.17272260.148443724598100
2.8147-3.0320.16582670.148442994566100
3.032-3.33720.16072290.144443724601100
3.3372-3.82010.12772140.131244214635100
3.8201-4.81290.14122020.124844734675100
4.8129-87.84450.15712450.153946364881100
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)
11.1634-0.31730.26611.6931-0.29231.41860.01470.0053-0.13060.05840.00430.06630.0408-0.1113-0.0320.0502-0.018-0.00260.0682-0.00190.0679-27.4203-16.288536.0369
20.55440.13130.76554.8721.82642.21580.00580.02060.3558-0.0117-0.06120.368-0.1526-0.09560.03470.1120.0303-0.02570.10410.04720.1089-24.24746.060825.191
31.4879-0.03960.25291.04940.00451.11790.0305-0.16930.08920.053-0.05350.0521-0.0219-0.09450.0180.0696-0.0080.00910.1039-0.00690.0638-21.1883-7.441148.1345
42.47841.1689-0.16732.8538-2.25362.9831-0.0323-0.08810.2654-0.00690.06490.0698-0.2075-0.1718-0.0160.12750.02180.00080.0972-0.00910.1376-11.21713.069345.7627
50.8014-0.04980.3581.0479-0.45522.13580.028-0.04920.0028-0.02960.00640.00790.07050.0578-0.02990.0613-0.0048-0.0020.07950.01150.0745-11.5731-12.827244.35
61.33910.17440.22642.26330.74741.34960.00370.23570.1295-0.1852-0.0220.0142-0.0433-0.03670.01540.11250.0183-0.00630.13510.04190.0793-18.90790.893820.366
71.3467-0.023-0.25730.71770.22581.12010.0037-0.0535-0.24850.11210.0153-0.00350.1796-0.06340.00270.1074-0.0134-0.02950.06910.02850.1136-17.6891-24.291141.6337
81.68020.20090.37210.2687-0.20650.7519-0.00640.205-0.1193-0.0657-0.0161-0.0069-0.0120.03780.01760.14030.0134-0.00760.145-0.04690.1355-9.1662-19.910723.6468
91.8331-0.8-0.56782.67-0.04170.5427-0.01820.3283-0.1692-0.28110.02940.00760.11790.0769-0.01860.1427-0.0059-0.02230.2294-0.04620.0922-15.3183-16.664418.3598
101.33820.29090.07431.3273-0.14151.9036-0.03660.2761-0.1353-0.23770.0451-0.00290.0579-0.07920.01360.09940.0045-0.00720.1247-0.03310.0852-24.1436-18.086721.9491
113.10372.5006-0.01064.3823-0.22830.85920.05720.12190.0486-0.0355-0.01330.20530.00390.0144-0.04790.0888-0.004-0.01240.0988-0.01830.1216-12.8979-19.793928.7223
121.0931-0.5922-0.00012.27390.35560.5006-0.0503-0.06720.2504-0.03710.0701-0.1088-0.0870.0727-0.00760.071-0.0167-0.01320.0814-0.00270.082313.26123.480848.3744
130.9097-0.11780.10030.80670.12171.08790.01210.12630.0873-0.0539-0.0288-0.019-0.10360.04980.01670.081-0.00880.00170.1080.01360.073410.0982-4.898532.5427
142.8044-1.2553-0.53252.98761.2830.61540.01510.10670.2225-0.10850.0518-0.1598-0.14460.0728-0.01610.1381-0.0130.01550.07850.02350.1107-5.906711.258229.0889
150.8435-0.36510.01151.2160.69051.55870.00570.030.03260.0189-0.0172-0.0139-0.0032-0.04310.0090.0501-0.00680.00230.07340.00270.07182.6611-11.378338.0929
161.2033-0.2640.1131.4196-0.731.5064-0.0754-0.15010.28510.15440.0037-0.0447-0.1150.03740.05940.137-0.0109-0.01280.0954-0.05350.13733.886910.549457.0401
171.3602-0.2777-0.45650.68870.00630.6989-0.0622-0.0651-0.149-0.01980.0087-0.06590.09660.05790.05960.0858-0.005-0.01240.08660.00470.100512.185-19.277643.9596
182.2605-0.1410.54080.36810.40280.8751-0.0431-0.2248-0.01650.06910.03180.0412-0.009-0.01370.0140.1436-0.0026-0.0080.16820.01450.10181.4639-12.131260.1517
192.31990.7162-0.9192.6017-0.90341.53120.0183-0.51330.00190.268-0.0550.00850.0665-0.03120.02920.1438-0.0182-0.02330.2485-0.0230.08036.0679-6.223563.9183
201.0752-0.00970.44251.63610.35792.0403-0.0452-0.26040.06080.17990.0863-0.0265-0.04130.0572-0.03410.08410.0007-0.01070.1417-0.00730.065815.1001-5.38160.3544
216.1656-3.02042.28182.8866-1.56381.0098-0.0683-0.2010.17070.08930.0537-0.0568-0.0405-0.02340.01270.09160.007-0.00990.12090.00990.08395.6581-12.94254.7834
226.163-1.177-0.58461.9430.22623.21460.24620.19031.02610.2640.08950.9323-0.9704-1.1894-0.23950.59590.30030.16170.96520.09370.5852-27.711519.354162.9773
234.9831-2.0790.60996.63974.99635.30010.131-0.3151-0.02860.73870.03651.08880.0464-0.7121-0.1270.63170.01750.07661.44420.31160.7862-31.4559.5566.4756
244.6464-0.0547-1.3784.52711.19516.76580.1324-1.13960.12990.9292-0.04380.4411-0.2747-0.4387-0.03680.4444-0.01070.06620.5627-0.01320.2111-21.599310.555470.1954
256.3388-2.3794-1.48177.05110.36535.49360.32910.36650.5319-0.15240.18710.3903-0.9208-0.7773-0.39390.34490.1190.04860.3417-0.01320.2379-17.828116.774158.324
265.4313-3.91453.40283.7109-3.81874.230.28820.34320.9156-0.9972-0.2617-0.1037-0.47120.0484-0.02081.208-0.02240.11760.29220.0030.53-14.20826.168658.3806
275.1460.0841-4.80712.0859-1.33485.24710.0659-0.81820.2857-0.22480.1334-0.2231-0.58030.1833-0.13441.0428-0.3546-0.11980.7674-0.05390.3681-11.795319.239167.5538
282.7551-0.5327-1.55180.56881.2652.87330.4844-0.03550.6727-0.3897-0.22330.0154-1.1502-0.2778-0.32161.3559-0.05090.35770.5739-0.16590.593-20.006426.361967.4121
291.7571.0066-1.11572.8189-3.7545.168-0.0038-0.24950.08630.1522-0.2359-0.4667-0.45331.07040.18070.2732-0.10680.00420.36040.00950.149212.138913.535412.3918
305.47234.4101-5.656.6064-5.02635.9102-0.16090.3464-0.4171-0.5993-0.1138-0.2050.68890.27030.33720.27190.03040.04360.2715-0.02190.11978.11114.22587.1732
312.64342.7838-1.17377.7892-2.50661.71890.1668-0.19660.13720.3544-0.01730.2698-0.6151-0.0688-0.12560.3046-0.00770.02490.21850.01510.11310.681412.473216.0836
322.00852.04912.02462.15592.06412.0479-0.2403-0.55011.40950.6989-0.64741.0282-0.6473-0.77770.8370.51610.103-0.03040.3616-0.01540.4943-4.40120.542212.0708
333.0881-3.7575-4.22045.3144.58286.18240.1240.6477-0.2859-0.3236-0.28991.2929-0.5452-1.55580.1050.2360.0695-0.02270.5420.01770.3591-4.795211.16535.4884
345.14431.22920.11543.9204-0.56853.75630.2290.08640.7036-0.0049-0.18020.2123-1.3287-0.3948-0.34350.44580.0410.06370.37160.03650.12932.986719.51874.0401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )A2 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 50 )A29 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 109 )A51 - 109
4X-RAY DIFFRACTION4chain 'A' and (resid 110 through 137 )A110 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 194 )A138 - 194
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 233 )A195 - 233
7X-RAY DIFFRACTION7chain 'A' and (resid 234 through 264 )A234 - 264
8X-RAY DIFFRACTION8chain 'A' and (resid 265 through 302 )A265 - 302
9X-RAY DIFFRACTION9chain 'A' and (resid 303 through 334 )A303 - 334
10X-RAY DIFFRACTION10chain 'A' and (resid 335 through 383 )A335 - 383
11X-RAY DIFFRACTION11chain 'A' and (resid 384 through 404 )A384 - 404
12X-RAY DIFFRACTION12chain 'B' and (resid 2 through 50 )B2 - 50
13X-RAY DIFFRACTION13chain 'B' and (resid 51 through 109 )B51 - 109
14X-RAY DIFFRACTION14chain 'B' and (resid 110 through 137 )B110 - 137
15X-RAY DIFFRACTION15chain 'B' and (resid 138 through 194 )B138 - 194
16X-RAY DIFFRACTION16chain 'B' and (resid 195 through 233 )B195 - 233
17X-RAY DIFFRACTION17chain 'B' and (resid 234 through 264 )B234 - 264
18X-RAY DIFFRACTION18chain 'B' and (resid 265 through 302 )B265 - 302
19X-RAY DIFFRACTION19chain 'B' and (resid 303 through 334 )B303 - 334
20X-RAY DIFFRACTION20chain 'B' and (resid 335 through 383 )B335 - 383
21X-RAY DIFFRACTION21chain 'B' and (resid 384 through 404 )B384 - 404
22X-RAY DIFFRACTION22chain 'C' and (resid 1 through 15 )C1 - 15
23X-RAY DIFFRACTION23chain 'C' and (resid 16 through 21 )C16 - 21
24X-RAY DIFFRACTION24chain 'C' and (resid 22 through 35 )C22 - 35
25X-RAY DIFFRACTION25chain 'C' and (resid 36 through 50 )C36 - 50
26X-RAY DIFFRACTION26chain 'C' and (resid 51 through 55 )C51 - 55
27X-RAY DIFFRACTION27chain 'C' and (resid 56 through 64 )C56 - 64
28X-RAY DIFFRACTION28chain 'C' and (resid 65 through 77 )C65 - 77
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 20 )D1 - 20
30X-RAY DIFFRACTION30chain 'D' and (resid 21 through 35 )D21 - 35
31X-RAY DIFFRACTION31chain 'D' and (resid 36 through 50 )D36 - 50
32X-RAY DIFFRACTION32chain 'D' and (resid 51 through 55 )D51 - 55
33X-RAY DIFFRACTION33chain 'D' and (resid 56 through 64 )D56 - 64
34X-RAY DIFFRACTION34chain 'D' and (resid 65 through 77 )D65 - 77

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