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- PDB-8axi: Sialidases and Fucosidases of Akkermansia muciniphila are key for... -

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Basic information

Entry
Database: PDB / ID: 8axi
TitleSialidases and Fucosidases of Akkermansia muciniphila are key for rapid growth on colonic mucin and nutrient sharing amongst mucin-associated human gut microbiota
ComponentsSialidase domain-containing protein
KeywordsHYDROLASE / Sialidase / Neuraminidase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / metal ion binding / membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / beta-D-galactopyranose / exo-alpha-sialidase
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSakanaka, H. / Nielsen, T.S. / Pichler, M.J. / Nordberg Karlsson, E. / Abou Hachem, M. / Morth, J.P.
Funding support Denmark, Iraq, 2items
OrganizationGrant numberCountry
Danish Council for Independent Research1026-00386B Denmark
Other governmentIraq
CitationJournal: Nat Commun / Year: 2023
Title: Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria.
Authors: Shuoker, B. / Pichler, M.J. / Jin, C. / Sakanaka, H. / Wu, H. / Gascuena, A.M. / Liu, J. / Nielsen, T.S. / Holgersson, J. / Nordberg Karlsson, E. / Juge, N. / Meier, S. / Morth, J.P. / ...Authors: Shuoker, B. / Pichler, M.J. / Jin, C. / Sakanaka, H. / Wu, H. / Gascuena, A.M. / Liu, J. / Nielsen, T.S. / Holgersson, J. / Nordberg Karlsson, E. / Juge, N. / Meier, S. / Morth, J.P. / Karlsson, N.G. / Abou Hachem, M.
History
DepositionAug 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 2.0Oct 18, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / pdbx_branch_scheme / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / struct_asym / struct_conn / struct_mon_prot_cis
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.title / _citation.year / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_branch_scheme.pdb_asym_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _struct_conn.pdbx_dist_value / _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 / _struct_mon_prot_cis.pdbx_omega_angle
Description: Chirality error
Details: it is a link between GAL and NGA so there should not be a problem
Provider: author / Type: Coordinate replacement
Revision 2.1Apr 3, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialidase domain-containing protein
B: Sialidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,73217
Polymers128,6412
Non-polymers2,09115
Water27,6891537
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.920, 51.510, 118.470
Angle α, β, γ (deg.)90.000, 93.150, 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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sialidase domain-containing protein


Mass: 64320.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (bacteria)
Strain: ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc
Gene: Amuc_1547 / Production host: Escherichia coli (E. coli) / References: UniProt: B2ULI1

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Sugars , 3 types, 6 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-gulopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGulpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2212h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GulpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO8 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1546 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1537 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: MgCl2, BIS-TRIS pH 5.5, Polyethylene glycol 3350 / PH range: 5 - 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.25→51.51 Å / Num. obs: 323513 / % possible obs: 93.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 14.13 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.054 / Net I/σ(I): 16.27
Reflection shellResolution: 1.25→1.28 Å / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.51 / Num. unique obs: 17780 / CC1/2: 0.85 / Rrim(I) all: 0.713 / % possible all: 69.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold model

Resolution: 1.25→50.21 Å / SU ML: 0.111 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.176 16212 5.02 %
Rwork0.1608 306997 -
obs0.1616 323209 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.92 Å2
Refinement stepCycle: LAST / Resolution: 1.25→50.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9002 0 131 1537 10670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719465
X-RAY DIFFRACTIONf_angle_d1.050512859
X-RAY DIFFRACTIONf_chiral_restr0.09391382
X-RAY DIFFRACTIONf_plane_restr0.01131677
X-RAY DIFFRACTIONf_dihedral_angle_d7.73981317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.2753870.24447201X-RAY DIFFRACTION66.18
1.26-1.280.28044090.24597791X-RAY DIFFRACTION71.96
1.28-1.290.26684300.25058819X-RAY DIFFRACTION80.57
1.29-1.310.27975350.254910036X-RAY DIFFRACTION92.44
1.31-1.330.26015350.242710190X-RAY DIFFRACTION93.25
1.33-1.350.27495540.235110171X-RAY DIFFRACTION93.3
1.35-1.370.23245540.219810152X-RAY DIFFRACTION93.64
1.37-1.390.24715590.215810188X-RAY DIFFRACTION93.92
1.39-1.410.21525190.200610309X-RAY DIFFRACTION94.16
1.41-1.430.21325330.19210361X-RAY DIFFRACTION94.42
1.43-1.460.21275060.188110223X-RAY DIFFRACTION94.3
1.46-1.480.21845750.181210297X-RAY DIFFRACTION94.6
1.48-1.510.18165640.166610378X-RAY DIFFRACTION94.88
1.51-1.540.19575770.171310280X-RAY DIFFRACTION95
1.54-1.570.18865620.167610402X-RAY DIFFRACTION95.11
1.57-1.610.18165580.155210421X-RAY DIFFRACTION95.55
1.61-1.650.18245290.154310446X-RAY DIFFRACTION95.77
1.65-1.70.16495550.153910454X-RAY DIFFRACTION96
1.7-1.750.16845620.152210559X-RAY DIFFRACTION96.24
1.75-1.80.16736130.153910435X-RAY DIFFRACTION96.35
1.8-1.870.18185860.156510577X-RAY DIFFRACTION96.67
1.87-1.940.17475360.158510607X-RAY DIFFRACTION96.77
1.94-2.030.1735800.1510600X-RAY DIFFRACTION96.95
2.03-2.140.15865870.146810661X-RAY DIFFRACTION97.34
2.14-2.270.16195040.151110777X-RAY DIFFRACTION97.54
2.27-2.450.17495780.158510778X-RAY DIFFRACTION97.96
2.45-2.690.1745840.16210806X-RAY DIFFRACTION98.07
2.69-3.080.17714990.162510900X-RAY DIFFRACTION98.29
3.08-3.880.16125760.151110933X-RAY DIFFRACTION98.45
3.88-50.210.15145660.14311245X-RAY DIFFRACTION98.73
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)
11.57609066410.01172010404210.4096359559190.7981404617480.1923130079740.904060006751-0.00251230451447-0.00529795766471-0.1513111659550.01886863632580.01135659931760.03637063857460.09049678990970.0153535685867-0.01097959117010.119768580350.01051590828950.01057016066790.09681003317490.003391091830780.14597142901932.6029958554-6.1979700764862.4154468294
21.4435703305-0.4454810881560.9867046895291.38982780446-0.9263469146212.60170889819-0.0758882698796-0.2028698244880.05349608403550.2267033527770.0106415671697-0.07510853344180.002038784392690.05432986137560.05408886452290.1624271365960.01444430054729.78185828804E-50.171234541753-0.01442032822890.13579943626640.7400966343.1973679308776.1470865389
31.829837363460.01882726225350.2028229490430.306987645327-0.02395688865320.268760162935-0.03511393117750.001254568071540.2590571654330.008813579178440.006054551262520.00719163389456-0.04797920243590.01900056712070.0298367625080.112403630439-0.007984032458150.001593939048430.09544755671440.01066361822650.17132940560631.251768223317.367439397456.7980621309
41.58588661918-0.08809143210880.08935819093720.449520673529-0.1232841378480.370193252341-0.0003628718026510.155259567221-0.069967693099-0.0495105556863-0.004731167689510.07132938297840.02296518148870.00185784795712-0.00344942545350.110535524596-0.00322687879279-0.006321467115890.109385153191-0.006762402608570.1375153128413.73873831794.1460310150249.2385330225
51.17241629137-0.0728943174858-0.1178272011930.6610481840920.1369319082451.28176578595-0.008178630089210.3013586835850.0781924514264-0.0756546415044-0.003451245289170.198341570088-0.0355107020932-0.1403649722330.01602041312310.1262484477010.00712203879698-0.04095638768320.1845867303950.03019337418240.207190688627-1.1539789628912.81327966842.1003237925
60.252620319222-0.09679899553290.4376452263230.566242240021-0.07636543653480.867685811703-0.04621876237940.4177759228140.175797354675-0.1776890300150.01318376517670.146792246115-0.106409216322-0.03076707581940.03154845313490.184853972641-0.00576075041871-0.05306651952540.3301143032420.07867597998780.2217888635063.4967897179815.96832489433.1017556762
71.918048631870.0701096566862-0.7158164356370.788541137999-0.1823870666250.8566959204330.0109424055017-0.1339377795740.2129796593670.01550050457470.0138552188480.0961406828017-0.0990406015449-0.059186675965-0.03219382431750.1153666139470.0267739791663-0.00186491943840.128590331592-0.02325630737060.1809893330439.85510149127-2.63749534742121.307233488
81.84313056296-0.641961978175-1.12660811311.836818887010.8273552940012.33550404165-0.134047622849-0.560022992889-0.02360777785640.3480137681810.07454806191320.2142119532460.00467619294440.06853327997150.04268844381560.1903080680710.04186657403160.05092895891430.348368516580.005223459831940.2066619555481.68554725923-11.6225796933135.251079925
92.09449741259-0.172923033965-0.1416011156450.3286685851490.02745007556090.396375593274-0.0578677597414-0.0534609484089-0.2555804031230.01718594215930.03242401523340.1743567034270.0428144852627-0.09311912477110.02541395745760.124394188644-0.008888172953540.009286112501320.1311767787660.0135884353210.24240362204910.6905918371-26.2629339065116.189252239
101.11588323407-0.0581236622459-0.09107329297420.4911585243730.02218503392780.432368211405-0.007982588245490.03815044203160.0343101589278-0.02584717931630.0003311715473340.0537926377004-0.0225877107852-0.05562386811950.002684170202510.113298335720.00209512917211-0.007610888695560.0990022793880.001107020699350.11568032565128.7172600755-13.4497504772108.298414685
110.9027318454760.0396809113129-0.1479311225190.607896746061-0.1157556222250.96779388294-0.01366453006270.189085238726-0.142296176012-0.0958034313436-0.020587971825-0.06062994233880.09559353959280.05770092551210.0320396598020.1381391324150.01347652898160.0146219405060.127306553683-0.03085299561310.13409159388242.4500431044-25.092811373798.2421618924
121.30005097410.142065061148-0.518192281170.7288416802380.07049962661870.93661267996-0.02581283552070.354129230093-0.182313064007-0.1726040371620.00348813825060.009576654342110.101874487801-0.07834071311630.01156583624970.1890992519840.00625016834332-0.006623639868020.195530020491-0.04341477444460.13455906457835.4674359629-24.245573978890.8736478329
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 127 )AA25 - 1271 - 103
22chain 'A' and (resid 128 through 157 )AA128 - 157104 - 133
33chain 'A' and (resid 158 through 271 )AA158 - 271134 - 247
44chain 'A' and (resid 272 through 436 )AA272 - 436248 - 412
55chain 'A' and (resid 437 through 492 )AA437 - 492413 - 468
66chain 'A' and (resid 493 through 595 )AA493 - 595469 - 571
77chain 'B' and (resid 25 through 127 )BG25 - 1271 - 103
88chain 'B' and (resid 128 through 157 )BG128 - 157104 - 133
99chain 'B' and (resid 158 through 271 )BG158 - 271134 - 247
1010chain 'B' and (resid 272 through 436 )BG272 - 436248 - 412
1111chain 'B' and (resid 437 through 535 )BG437 - 535413 - 511
1212chain 'B' and (resid 536 through 596 )BG536 - 596512 - 572

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