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- PDB-6fj3: High resolution crystal structure of parathyroid hormone 1 recept... -

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Basic information

Entry
Database: PDB / ID: 6fj3
TitleHigh resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist.
Components
  • Parathyroid hormone
  • Parathyroid hormone/parathyroid hormone-related peptide receptor,Parathyroid hormone/parathyroid hormone-related peptide receptor,GlgA glycogen synthase,Parathyroid hormone/parathyroid hormone-related peptide receptor
KeywordsMEMBRANE PROTEIN / GPCR / cell signalling / 7TM
Function / homology
Function and homology information


parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / positive regulation of cell proliferation in bone marrow / parathyroid hormone receptor activity / magnesium ion homeostasis / positive regulation of signal transduction / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / phosphate ion homeostasis ...parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / positive regulation of cell proliferation in bone marrow / parathyroid hormone receptor activity / magnesium ion homeostasis / positive regulation of signal transduction / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / phosphate ion homeostasis / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / osteoblast development / peptide hormone receptor binding / positive regulation of inositol phosphate biosynthetic process / bone mineralization / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / chondrocyte differentiation / positive regulation of glycogen biosynthetic process / bone resorption / positive regulation of bone mineralization / cell maturation / homeostasis of number of cells within a tissue / skeletal system development / positive regulation of D-glucose import / hormone activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / cell-cell signaling / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / basolateral plasma membrane / in utero embryonic development / transcription by RNA polymerase II / cell surface receptor signaling pathway / cell population proliferation / receptor complex / apical plasma membrane / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of cell population proliferation / nucleolus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Parathyroid hormone / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / GPCR, family 2, parathyroid hormone receptor ...Parathyroid hormone / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / GPCR, family 2, parathyroid hormone receptor / Glycosyl transferases group 1 / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
ACETIC ACID / alpha-D-mannopyranose / OLEIC ACID / Parathyroid hormone/parathyroid hormone-related peptide receptor / Parathyroid hormone / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi (archaea)
Equus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEhrenmann, J. / Schoppe, J. / Klenk, C. / Rappas, M. / Kummer, L. / Dore, A.S. / Pluckthun, A.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: High-resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist.
Authors: Ehrenmann, J. / Schoppe, J. / Klenk, C. / Rappas, M. / Kummer, L. / Dore, A.S. / Pluckthun, A.
History
DepositionJan 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Parathyroid hormone/parathyroid hormone-related peptide receptor,Parathyroid hormone/parathyroid hormone-related peptide receptor,GlgA glycogen synthase,Parathyroid hormone/parathyroid hormone-related peptide receptor
B: Parathyroid hormone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,57720
Polymers72,6662
Non-polymers5,91118
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer of the chimeric receptor bound to a single hormone molecule
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint27 kcal/mol
Surface area33160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.115, 52.864, 111.874
Angle α, β, γ (deg.)80.63, 83.76, 79.16
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Parathyroid hormone/parathyroid hormone-related peptide receptor,Parathyroid hormone/parathyroid hormone-related peptide receptor,GlgA glycogen synthase,Parathyroid hormone/parathyroid hormone-related peptide receptor / PTH/PTHrP type I receptor / PTH/PTHr receptor / Parathyroid hormone 1 receptor / PTH1 receptor / ...PTH/PTHrP type I receptor / PTH/PTHr receptor / Parathyroid hormone 1 receptor / PTH1 receptor / PTH/PTHrP type I receptor / PTH/PTHr receptor / Parathyroid hormone 1 receptor / PTH1 receptor / Glycogen synthase / PTH/PTHrP type I receptor / PTH/PTHr receptor / Parathyroid hormone 1 receptor / PTH1 receptor


Mass: 68389.203 Da / Num. of mol.: 1
Mutation: Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, ...Mutation: Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Gene: PTH1R, PTHR, PTHR1, PAB2292 / Strain: GE5 / Orsay / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q03431, UniProt: Q9V2J8
#2: Protein/peptide Parathyroid hormone / PTH / Parathyrin


Mass: 4277.009 Da / Num. of mol.: 1 / Mutation: N41Q, G43A, H45W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: PTH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q27IM2

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Sugars , 4 types, 6 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 168 molecules

#7: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C18H34O2
#8: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H4O2
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.47 Å3/Da / Density % sol: 64.53 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 0.1 M sodium citrate pH 6.0, 0.3 M sodium acetate, 31% PEG400, 20 uM E-PTH(1-34)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2017
RadiationMonochromator: LN2 cooled fixed exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.39 Å / Num. obs: 33759 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 50.93 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.103 / Net I/σ(I): 5.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.662 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3825 / CC1/2: 0.501 / Rpim(I) all: 1.214 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EE7, 3C4M

5ee7

3c4m


Resolution: 2.5→49.386 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 1657 4.92 %
Rwork0.2092 --
obs0.211 33645 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 348 156 5344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025310
X-RAY DIFFRACTIONf_angle_d0.5067147
X-RAY DIFFRACTIONf_dihedral_angle_d13.8163146
X-RAY DIFFRACTIONf_chiral_restr0.038801
X-RAY DIFFRACTIONf_plane_restr0.003856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.57370.39371450.3572660X-RAY DIFFRACTION99
2.5737-2.65670.35451300.3082660X-RAY DIFFRACTION100
2.6567-2.75170.31871480.28172660X-RAY DIFFRACTION100
2.7517-2.86180.3511360.26682638X-RAY DIFFRACTION100
2.8618-2.99210.31151460.24852669X-RAY DIFFRACTION100
2.9921-3.14980.27331360.23252694X-RAY DIFFRACTION99
3.1498-3.34710.27281340.22342649X-RAY DIFFRACTION100
3.3471-3.60540.24781500.2052663X-RAY DIFFRACTION100
3.6054-3.96810.20091420.17482675X-RAY DIFFRACTION100
3.9681-4.5420.16451200.17282672X-RAY DIFFRACTION100
4.542-5.72110.21351350.18262665X-RAY DIFFRACTION100
5.7211-49.39550.25871350.19552683X-RAY DIFFRACTION100
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)
13.66760.4077-0.25755.95850.40314.33860.05590.3170.3081-0.00370.14290.092-0.44970.4464-0.19650.3642-0.0345-0.02830.32820.08410.423556.5263-116.8187248.7511
20.312-0.3164-1.34350.01070.88014.2341-0.25490.5358-0.125-0.3632-0.38320.20841.8862-0.852-0.32941.51310.13760.01371.07790.1680.642852.2381-126.6211212.3274
31.2328-0.07360.50050.8306-0.61543.8228-0.0276-0.374-0.03860.3459-0.0916-0.01940.33510.57270.10020.57590.05280.03420.516-0.00560.365946.5901-111.2984170.6847
40.524-0.42681.06690.4626-0.90012.13840.27551.2053-0.0911-0.79170.0193-0.22710.8530.2489-0.35751.03580.0746-0.01561.21620.01240.452656.2808-122.4542225.5416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 162 )
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 211 )
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 480 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 34 )

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