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- PDB-4rhu: Crystal structures of Mycobacterium tuberculosis 6-oxopurine phos... -

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Basic information

Entry
Database: PDB / ID: 4rhu
TitleCrystal structures of Mycobacterium tuberculosis 6-oxopurine phosphoribosyltransferase which is a potential target for drug development against this disease
ComponentsHypoxanthine-guanine phosphoribosyltransferase Hpt
Keywordstransferase/transferase inhibitor / 6-oxopurine phosphoribosyltransferase / purine salvage pathway / hypoxanthine-guanine phosphoribosyltransferase / acyclic nucleoside phosphonate inhibitor / transferase-transferase inhibitor complex
Function / homology
Function and homology information


IMP biosynthetic process / guanine salvage / purine-containing compound salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / GMP biosynthetic process ...IMP biosynthetic process / guanine salvage / purine-containing compound salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / GMP biosynthetic process / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3QE / Chem-45T / : / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.573 Å
AuthorsEng, W.S. / Hockova, D. / Spacek, P. / West, N.P. / Woods, K. / Naesens, L.M.J. / Keough, D.T. / Guddat, L.W.
CitationJournal: J.Med.Chem. / Year: 2015
Title: First Crystal Structures of Mycobacterium tuberculosis 6-Oxopurine Phosphoribosyltransferase: Complexes with GMP and Pyrophosphate and with Acyclic Nucleoside Phosphonates Whose Prodrugs Have ...Title: First Crystal Structures of Mycobacterium tuberculosis 6-Oxopurine Phosphoribosyltransferase: Complexes with GMP and Pyrophosphate and with Acyclic Nucleoside Phosphonates Whose Prodrugs Have Antituberculosis Activity.
Authors: Eng, W.S. / Hockova, D. / Spacek, P. / Janeba, Z. / West, N.P. / Woods, K. / Naesens, L.M. / Keough, D.T. / Guddat, L.W.
History
DepositionOct 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase Hpt
B: Hypoxanthine-guanine phosphoribosyltransferase Hpt
C: Hypoxanthine-guanine phosphoribosyltransferase Hpt
D: Hypoxanthine-guanine phosphoribosyltransferase Hpt
E: Hypoxanthine-guanine phosphoribosyltransferase Hpt
F: Hypoxanthine-guanine phosphoribosyltransferase Hpt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,68820
Polymers132,8466
Non-polymers2,84214
Water1,51384
1
A: Hypoxanthine-guanine phosphoribosyltransferase Hpt
B: Hypoxanthine-guanine phosphoribosyltransferase Hpt
C: Hypoxanthine-guanine phosphoribosyltransferase Hpt
D: Hypoxanthine-guanine phosphoribosyltransferase Hpt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,45013
Polymers88,5644
Non-polymers1,8879
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Hypoxanthine-guanine phosphoribosyltransferase Hpt
F: Hypoxanthine-guanine phosphoribosyltransferase Hpt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2377
Polymers44,2822
Non-polymers9555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-38 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.691, 94.691, 335.519
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Hypoxanthine-guanine phosphoribosyltransferase Hpt


Mass: 22140.918 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: P425_03767, RVBD_3624c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: I6YCM5, UniProt: P9WHQ9*PLUS
#2: Chemical ChemComp-3QE / {[(2R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)


Mass: 441.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21N5O9P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-45T / {[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)


Mass: 441.271 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H21N5O9P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M potassium sodium tartrate, 0.1 M imidazole pH 8.0, 0.7 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 25, 2014
RadiationMonochromator: None / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.57→47.35 Å / Num. all: 53699 / Num. obs: 53590 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.57→2.65 Å / Redundancy: 4 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.421 / % possible all: 98.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RHX
Resolution: 2.573→47.346 Å / SU ML: 0.39 / σ(F): 1.38 / Phase error: 31.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2983 1978 3.69 %
Rwork0.2304 --
obs0.2329 53576 99.78 %
all-53576 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.573→47.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8198 0 176 84 8458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038527
X-RAY DIFFRACTIONf_angle_d0.60711571
X-RAY DIFFRACTIONf_dihedral_angle_d12.813173
X-RAY DIFFRACTIONf_chiral_restr0.0231350
X-RAY DIFFRACTIONf_plane_restr0.0031461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5733-2.63770.31861420.25763657X-RAY DIFFRACTION98
2.6377-2.7090.38541370.27543689X-RAY DIFFRACTION100
2.709-2.78870.36931420.27813695X-RAY DIFFRACTION100
2.7887-2.87870.35771430.28553662X-RAY DIFFRACTION100
2.8787-2.98160.35511410.26513679X-RAY DIFFRACTION100
2.9816-3.10090.33451460.25223673X-RAY DIFFRACTION100
3.1009-3.2420.31461430.23983694X-RAY DIFFRACTION100
3.242-3.41290.3051350.22983686X-RAY DIFFRACTION100
3.4129-3.62670.31191420.23533707X-RAY DIFFRACTION100
3.6267-3.90650.27551420.21663680X-RAY DIFFRACTION100
3.9065-4.29940.27851380.2053720X-RAY DIFFRACTION100
4.2994-4.9210.26041390.19153679X-RAY DIFFRACTION100
4.921-6.19780.27021490.22663671X-RAY DIFFRACTION100
6.1978-47.35350.30161390.24453706X-RAY DIFFRACTION99
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)
17.1048-3.14950.81414.52810.0913.2376-0.6283-0.86010.0741.06550.3130.01430.0543-0.69950.34450.78-0.10150.00770.62630.06990.35836.35155.55799.5456
20.839-0.96841.52652.8601-0.29657.7981-0.0651-0.15920.11450.2107-0.1074-0.3028-0.2913-0.33140.07080.5365-0.12390.07250.4790.09050.492549.2895.5149-7.1627
38.79482.612-3.85884.5189-2.33327.39440.21770.6977-0.2252-0.4721-0.0254-0.22330.8317-0.5318-0.14980.65680.02360.06660.45890.03090.43843.4726-4.7057-7.1095
47.1042-2.5816-1.44445.17550.26020.81440.00730.35720.00810.2244-0.04030.54770.527-0.69110.04830.6269-0.07580.0770.70820.04190.345127.66896.07481.3169
53.94110.4486-0.78662.4047-0.57952.805-0.3585-1.8738-0.32710.32320.3641-0.031-0.41870.28620.12840.8095-0.00280.16950.74030.04040.438850.756321.85319.6066
66.67481.5445-3.03673.4888-2.9254.23040.21330.1235-0.10530.3434-0.11390.2048-0.4669-0.2798-0.10490.63150.06760.08430.48760.04260.365436.476521.5692-1.7607
72.1640.78350.46391.43140.72241.97210.21750.31970.3969-0.08330.0192-0.0441-0.61140.0795-0.05330.69860.02860.1090.50640.10330.453942.282729.0637-8.2761
89.4166-5.08010.33616.2632-0.0760.8190.18180.15940.0527-0.2296-0.0406-0.363-0.3106-0.0685-0.05710.5719-0.04620.08090.53370.04130.345861.067219.7640.8992
94.28032.54482.25034.95011.28173.1867-0.29690.6994-0.0158-0.62370.3984-0.1042-0.1579-0.0071-0.1110.65680.22390.05420.79420.09490.360932.74321.7004-50.5291
107.8268-1.01586.87599.53394.30079.2719-0.58320.76230.71910.31640.4381-1.8498-1.54232.81660.02570.7392-0.25940.06580.99380.120.87654.235935.1857-41.4323
110.3078-0.272-0.97333.47950.25196.7003-0.17240.1757-0.22250.04170.0831-0.32020.4044-0.22450.06930.42020.10420.04270.5370.04210.429243.386922.6174-33.9486
125.19281.26563.09172.34831.24072.6239-0.0816-0.28570.02930.09080.1152-0.076-0.3239-0.3063-0.00110.59390.1080.01630.50230.06420.385834.856331.0939-34.5541
135.61910.22280.70639.0852-1.65396.0612-0.0463-0.1578-0.15490.3590.22860.46250.2612-1.066-0.22130.52990.02180.04560.6850.07560.363925.472414.6881-42.5716
143.48143.1206-3.09128.9031-1.62265.7894-0.49161.3392-0.3008-0.93910.6613-0.2983-0.004-0.10030.1020.98760.06870.21440.6148-0.04680.522350.11497.696-52.8787
151.97553.1895-3.39431.9914-2.4127.01740.4583-0.8049-0.8464-1.56640.34422.1487-0.0723-2.30380.27270.3732-0.1514-0.08391.22550.03011.109731.1213-4.9433-42.929
162.7933-1.29912.79312.27110.54075.6506-0.02080.0506-0.0623-0.1215-0.04570.0505-0.00230.15580.11830.60050.09180.04970.48050.08090.399541.96896.7565-35.0684
174.1074-3.22342.8332.8803-0.79636.99451.14630.00540.3356-0.2046-0.9767-0.28510.44410.8458-0.09280.76380.08220.00430.62310.16590.467950.331.721-38.8311
187.11595.1369-7.17883.7283-5.29827.4030.5782-0.435-1.60250.7657-0.5449-0.48030.36110.3084-0.07211.10910.2062-0.01080.5190.08290.603549.4055-1.5923-29.3571
197.07694.2041-5.78316.7564-3.69677.3139-0.2783-0.2063-1.3098-0.1812-0.3108-1.28430.65910.57270.47250.61440.14750.16150.54750.07580.768451.5951-2.6357-40.9549
206.31271.8639-2.06252.94331.4745.16750.2812-0.0561-0.309-0.4045-0.0546-0.8623-0.01421.1772-0.06830.68280.11220.1160.76590.03860.491557.800511.0429-44.5777
215.8797-1.3174-0.05123.5337-2.96166.65630.12080.64430.8402-0.0547-0.3608-0.3232-0.35620.24210.42450.6306-0.11160.06180.46630.0120.4039-1.225728.7845-30.2539
225.3675-3.6406-1.26558.17010.45067.0293-0.3509-0.1344-0.17420.87770.21780.11330.9022-0.30910.18490.6588-0.12060.12970.54980.01050.3498-13.530717.9058-24.1226
235.4399-0.48050.35963.6998-0.19014.7883-0.0520.2349-0.3353-0.3069-0.02950.02971.053-0.81260.15570.75-0.23340.02260.7010.03360.3929-13.616215.2892-35.6552
245.0442-2.34631.28494.7918-1.45698.39420.03990.03360.0672-0.19910.0241-0.47170.8611.60220.01240.6047-0.01660.1280.81610.06790.51228.147418.5154-30.559
253.06614.07074.7638.61144.67058.35110.56190.63031.1702-0.4142-0.0595-0.3107-0.0658-0.5903-0.32390.7450.01960.29080.56770.07590.7673-20.46233.3585-10.9583
265.3387-4.50642.25864.1131-1.41027.26180.14590.18871.34121.2882-0.1392-0.8220.27591.11520.29740.8341-0.23040.05230.7172-0.0730.62182.023729.6786-7.6339
278.36191.28474.9775.471-2.12188.60940.8010.61330.2024-0.3316-0.8505-0.44250.61980.82780.00440.70580.01860.08360.82830.02720.41823.017115.4949-12.5106
287.05984.0296-1.82038.4121-0.68598.11480.0603-0.3031-0.0246-0.0383-0.43910.07010.76981.25110.33360.5576-0.00120.04670.81760.10120.3932-0.52218.4158-15.0868
298.95124.46524.55568.14681.04525.33410.2914-0.0321-0.3054-0.2675-0.3025-0.04981.27220.72510.01530.97390.16250.11380.50310.11140.6267-3.45633.7239-12.1617
303.0078-2.74464.26473.345-4.24466.28930.81490.73580.0317-0.4766-0.9189-0.12780.22561.3154-0.05850.83320.02820.14140.7183-0.05610.6124-4.295915.9048-4.6712
316.1112-4.2434-5.66788.80666.45696.7561-1.0368-0.2119-2.0014-0.44740.25610.25681.73361.02650.68721.16680.05820.03790.77050.13340.6167-3.21225.6031-3.3047
324.9399-0.59-3.81543.20943.2745.68150.0519-1.5496-0.465-0.13450.09620.4189-0.19271.5-0.05630.5514-0.01780.05510.88540.07180.3949-1.072816.48-1.439
337.0797-2.1524-2.221.873-2.58929.451-1.0661-0.8703-0.59911.5506-0.2685-0.5806-0.37311.30951.21381.229-0.06390.0850.85470.12450.4758-2.165117.7223.8344
345.2244-2.0935-0.22925.2736-3.07642.29490.4514-1.59430.39620.94070.8325-0.32270.14790.4252-1.05310.8217-0.26170.14020.6539-0.21620.636-14.181225.98050.0795
356.6621-1.1064-2.54714.6742-1.99846.10520.39890.3240.1043-0.0365-0.09690.3905-0.1877-0.2164-0.27310.5282-0.05770.02560.3456-0.00340.375-21.301225.7279-10.9179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 168 )
4X-RAY DIFFRACTION4chain 'A' and (resid 169 through 202 )
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 47 )
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 92 )
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 169 )
8X-RAY DIFFRACTION8chain 'B' and (resid 170 through 202 )
9X-RAY DIFFRACTION9chain 'C' and (resid 18 through 47 )
10X-RAY DIFFRACTION10chain 'C' and (resid 48 through 58 )
11X-RAY DIFFRACTION11chain 'C' and (resid 59 through 116 )
12X-RAY DIFFRACTION12chain 'C' and (resid 117 through 169 )
13X-RAY DIFFRACTION13chain 'C' and (resid 170 through 199 )
14X-RAY DIFFRACTION14chain 'D' and (resid 21 through 47 )
15X-RAY DIFFRACTION15chain 'D' and (resid 48 through 58 )
16X-RAY DIFFRACTION16chain 'D' and (resid 59 through 116 )
17X-RAY DIFFRACTION17chain 'D' and (resid 117 through 128 )
18X-RAY DIFFRACTION18chain 'D' and (resid 129 through 141 )
19X-RAY DIFFRACTION19chain 'D' and (resid 142 through 159 )
20X-RAY DIFFRACTION20chain 'D' and (resid 160 through 199 )
21X-RAY DIFFRACTION21chain 'E' and (resid 17 through 48 )
22X-RAY DIFFRACTION22chain 'E' and (resid 49 through 110 )
23X-RAY DIFFRACTION23chain 'E' and (resid 111 through 168 )
24X-RAY DIFFRACTION24chain 'E' and (resid 169 through 202 )
25X-RAY DIFFRACTION25chain 'F' and (resid 17 through 29 )
26X-RAY DIFFRACTION26chain 'F' and (resid 30 through 47 )
27X-RAY DIFFRACTION27chain 'F' and (resid 48 through 68 )
28X-RAY DIFFRACTION28chain 'F' and (resid 69 through 91 )
29X-RAY DIFFRACTION29chain 'F' and (resid 92 through 116 )
30X-RAY DIFFRACTION30chain 'F' and (resid 117 through 128 )
31X-RAY DIFFRACTION31chain 'F' and (resid 129 through 141 )
32X-RAY DIFFRACTION32chain 'F' and (resid 142 through 157 )
33X-RAY DIFFRACTION33chain 'F' and (resid 158 through 168 )
34X-RAY DIFFRACTION34chain 'F' and (resid 169 through 176 )
35X-RAY DIFFRACTION35chain 'F' and (resid 177 through 202 )

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