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- PDB-5zqd: Crystal Structure of Penicillin-Binding Protein D2 from Listeria ... -

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Basic information

Entry
Database: PDB / ID: 5zqd
TitleCrystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the Cefotaxime bound form
ComponentsLmo2812 protein
KeywordsANTIBIOTIC / antibiotics / beta-lactams / DD-carboxypeptidase / LmPBPD2
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
CEFOTAXIME, C3' cleaved, open, bound form / Lmo2812 protein
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.888 Å
AuthorsJeong, J.H. / Kim, Y.G.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: Crystal Structures of Penicillin-Binding Protein D2 from Listeria monocytogenes and Structural Basis for Antibiotic Specificity
Authors: Jeong, J.H. / Cha, H.J. / Kim, Y.G.
History
DepositionApr 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 12, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.0Sep 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo2812 protein
B: Lmo2812 protein
C: Lmo2812 protein
D: Lmo2812 protein
E: Lmo2812 protein
F: Lmo2812 protein
G: Lmo2812 protein
H: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,51531
Polymers240,7338
Non-polymers5,78223
Water17,601977
1
A: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5813
Polymers30,0921
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-3 kcal/mol
Surface area10880 Å2
MethodPISA
2
B: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7655
Polymers30,0921
Non-polymers6744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-5 kcal/mol
Surface area10870 Å2
MethodPISA
3
C: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9794
Polymers30,0921
Non-polymers8873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-3 kcal/mol
Surface area10860 Å2
MethodPISA
4
D: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9794
Polymers30,0921
Non-polymers8873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5 kcal/mol
Surface area10670 Å2
MethodPISA
5
E: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6734
Polymers30,0921
Non-polymers5823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-3 kcal/mol
Surface area10670 Å2
MethodPISA
6
F: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5813
Polymers30,0921
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-4 kcal/mol
Surface area10640 Å2
MethodPISA
7
G: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9794
Polymers30,0921
Non-polymers8873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-3 kcal/mol
Surface area10940 Å2
MethodPISA
8
H: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9794
Polymers30,0921
Non-polymers8873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.858, 98.719, 154.576
Angle α, β, γ (deg.)90.00, 103.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lmo2812 protein


Mass: 30091.605 Da / Num. of mol.: 8 / Fragment: UNP residues 21-272
Source method: isolated from a genetically manipulated source
Details: it contains covalently bound Cefotaxime molecules
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Strain: EGD-e / Gene: lmo2812 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y3M3
#2: Chemical
ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 977 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris-HCl (pH 8.0), 25%(wt/vol) PEG 3350, 0.2M sodium chloride

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2016
RadiationMonochromator: Double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.888→29.87 Å / Num. obs: 170527 / % possible obs: 97.42 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 10.88 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1814 / Rpim(I) all: 0.0751 / Rrim(I) all: 0.1967 / Net I/σ(I): 5.45
Reflection shellResolution: 1.888→1.956 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 15963 / CC1/2: 0.929 / Rpim(I) all: 0.2402 / Rrim(I) all: 0.6332 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZQA
Resolution: 1.888→29.867 Å / Cross valid method: NONE / σ(F): 223.48 / Phase error: 35.24
RfactorNum. reflection% reflection
Rfree0.2424 2011 1.18 %
Rwork0.1951 --
obs0.1961 170476 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.888→29.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14957 0 378 977 16312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615540
X-RAY DIFFRACTIONf_angle_d0.84320973
X-RAY DIFFRACTIONf_dihedral_angle_d4.9139363
X-RAY DIFFRACTIONf_chiral_restr0.0452456
X-RAY DIFFRACTIONf_plane_restr0.0042669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8906-1.93790.24811390.231411520X-RAY DIFFRACTION93
1.9379-1.99030.25491390.218911847X-RAY DIFFRACTION96
1.9903-2.04880.23271450.210111899X-RAY DIFFRACTION96
2.0488-2.1150.25921420.20811931X-RAY DIFFRACTION96
2.115-2.19050.26441420.196611971X-RAY DIFFRACTION96
2.1905-2.27820.2091420.193411982X-RAY DIFFRACTION97
2.2782-2.38180.2551450.194712019X-RAY DIFFRACTION97
2.3818-2.50740.26841420.198711995X-RAY DIFFRACTION97
2.5074-2.66430.24081440.203112092X-RAY DIFFRACTION97
2.6643-2.86990.27651450.198412114X-RAY DIFFRACTION97
2.8699-3.15840.2641430.200512156X-RAY DIFFRACTION98
3.1584-3.61470.22881450.186712167X-RAY DIFFRACTION98
3.6147-4.55140.20621430.166912279X-RAY DIFFRACTION98
4.5514-29.26490.24531450.197812378X-RAY DIFFRACTION98
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)
16.3966-2.33680.04321.5949-1.16761.78950.01520.3277-1.125-0.01030.0718-0.1320.23790.033-0.03550.09930.03860.00990.2226-0.05230.20174.8474-44.587228.6369
21.8356-1.7506-0.29313.17320.43680.7-0.0658-0.1-0.1351-0.00560.02820.06930.0553-0.00280.04190.0529-0.0283-0.00660.17660.02150.0696-9.9147-29.176233.9203
34.22243.1974-2.11023.28010.30916.7998-0.0225-0.21910.00560.3630.1218-0.9450.21680.79830.16480.129-0.0024-0.10760.4102-0.05530.35630.1444-8.771534.3059
41.0485-0.4394-0.10781.16030.21210.4633-0.01970.0193-0.04740.02010.0271-0.00850.00740.0269-0.00420.0506-0.0187-0.0140.17210.00110.0874-4.8488-28.122930.5408
51.61940.45260.15260.93050.14290.5199-0.07110.1917-0.2078-0.02940.1117-0.02550.05880.0895-0.04220.05650.0249-0.01680.2672-0.00390.064825.338416.636142.3402
64.3157-1.8332-0.5725.6611-1.83235.8764-0.13890.43340.2913-0.2365-0.0251.10330.0087-1.03590.17010.15430.0204-0.04950.3135-0.00540.31318.772640.446840.556
70.86890.450.55011.32970.05580.7357-0.04620.1230.0356-0.06110.05210.03470.00020.00070.00170.04460.007-0.0080.26920.01980.092526.717524.725542.027
82.9437-0.2070.19213.2605-0.2660.9145-0.10060.1358-0.1210.16860.0769-0.02310.0070.00590.02270.0534-0.00320.00340.2452-0.01660.067117.457114.060949.6514
96.9906-1.46430.94120.85470.68861.5729-0.19070.42890.9803-0.1205-0.01420.1731-0.3084-0.16920.08670.090.0486-0.04760.1737-0.01070.2101-23.469531.308750.7721
102.831-1.9323-0.25173.25850.12470.99350.0146-0.25760.1137-0.0149-0.017-0.10190.03770.0190.00750.0619-0.0108-0.02120.1363-0.0170.0409-8.689315.975555.77
113.7277-0.23220.96273.9235-0.37483.8189-0.1305-0.2963-0.28730.321-0.01230.47810.2696-0.39320.10940.1547-0.04290.03160.17090.02140.1577-14.5992-1.254152.5019
120.855-0.2668-0.09121.54570.08640.9445-0.0071-0.0844-0.00090.0609-0.04530.0060.0158-0.03810.0520.03790.0004-0.01640.1550.00280.0771-11.013412.950255.541
133.46230.55070.3162.5058-0.21510.61930.0106-0.00380.0164-0.0131-0.0213-0.0014-0.0394-0.0269-0.00330.03280.0121-0.01380.2029-0.03510.05-19.96122.324647.292
145.5279-0.05570.36772.0528-0.60711.4159-0.17420.12590.6380.14680.1441-0.1212-0.2270.12050.020.10150.0161-0.04930.23750.02050.158838.8455-18.963321.4336
152.26490.43410.09111.63670.31281.6967-0.09780.08260.03040.0050.00060.18910.0864-0.08310.09810.07930.0025-0.00730.2626-0.01210.051622.1541-42.310119.3614
166.2984-0.79091.49023.4082.34165.4032-0.13180.1824-0.4596-0.70640.0893-1.0030.49381.29280.07550.29330.06570.10650.31230.00940.30937.7027-53.80720.4272
170.58170.5594-0.06741.3117-0.15110.7388-0.05650.0569-0.0461-0.04760.0395-0.01360.02960.05430.01080.05490.0025-0.01170.24640.00310.091429.6857-37.979820.3443
184.3715-0.8961-0.26892.71640.52411.1655-0.02980.06660.08110.0865-0.01260.0035-0.04130.06820.03780.0569-0.0141-0.0320.14840.02440.059438.8365-27.124427.7516
196.9671-1.6873-1.59561.1547-0.21010.8365-0.17010.4788-0.7954-0.05280.0865-0.03640.2375-0.03720.06270.10790.01710.02920.1252-0.02150.215813.5089-42.008565.8386
201.7234-1.1791-0.1342.01920.09770.5942-0.02550.0336-0.1948-0.07510.01180.14480.0862-0.12360.0240.0649-0.02720.00530.1522-0.00550.0767-1.0927-27.089772.1376
214.79110.00740.725.72111.14065.61310.0559-0.25960.22190.1962-0.0098-0.75590.1070.69050.06910.1238-0.0252-0.03750.27030.02470.17459.1441-6.853372.9943
221.0074-0.75380.27552.7946-0.49460.9067-0.0518-0.03820.00180.1975-0.01560.05940.01710.1460.0640.073-0.0058-0.01480.1711-0.00960.07071.1284-21.035377.7794
231.9043-0.2677-0.31731.8575-0.13651.16060.00960.239-0.0604-0.0468-0.02770.05910.02430.06520.01540.06250.0106-0.01710.1465-0.02470.0645.8239-28.896262.9
241.93661.0476-0.30731.4968-0.23370.579-0.0562-0.0032-0.2584-0.0403-0.0161-0.08020.02960.00070.06980.06490.0355-0.00790.1595-0.0090.093216.559418.73714.3686
257.0299-1.17750.37333.39831.15118.30110.1410.05180.0493-0.2411-0.01290.66020.2719-0.82570.02230.1440.0072-0.07330.19540.03230.21369.720242.62042.3121
261.00491.56820.72012.70171.22641.7638-0.14910.1024-0.0359-0.15080.1025-0.06980.0410.11350.0430.09040.0222-0.0080.15710.00560.070317.749628.3541-2.7597
271.72010.6912-0.12851.03270.01670.41710.1193-0.1396-0.09950.1731-0.17760.0338-0.09170.14430.0239-0.01080.0228-0.0420.25640.01920.087713.058720.348312.1661
281.3388-0.9990.12351.9497-0.16880.5658-0.05550.05670.19090.084-0.0108-0.0968-0.0635-0.01230.08080.0725-0.0368-0.02550.2167-0.00860.0735-20.730722.725716.2184
295.65251.14991.71974.7323-0.63356.20580.0603-0.3706-0.18250.4140.06140.90310.2064-0.94260.07720.1676-0.01750.04940.2220.00790.2225-27.3615-1.135619.0835
300.817-0.40470.18771.0776-0.26170.4738-0.01320.03260.01310.07950.00120.04350.0006-0.0080.01040.0505-0.0078-0.00350.1777-0.0080.0771-19.271114.747417.1274
313.93090.21510.45971.6621-0.18110.72060.0636-0.01570.0779-0.1219-0.05560.0668-0.0270.1042-0.02160.0234-0.0007-0.03540.2385-0.00670.0795-28.609324.70118.7176
322.19711.11410.24711.87830.31970.7052-0.120.07280.2278-0.05810.06480.0635-0.0925-0.05010.05880.07210.0174-0.03010.13170.00350.067239.6107-26.627558.8473
334.1289-0.12510.5675.2593-0.01953.35890.03730.2964-0.0246-0.47950.0174-1.04140.22840.94420.07680.15850.02530.04460.3686-0.01850.242346.2338-50.521455.9774
340.50750.42310.27941.08740.26720.8917-0.03110.03430.0218-0.0565-0.0065-0.0105-0.05490.0410.03760.04640.0084-0.00670.1449-0.00140.087238.149-34.612957.9038
353.4626-0.5144-0.44552.83560.27211.5383-0.1197-0.06570.083-0.03710.04970.0059-0.13280.07340.05980.0505-0.0105-0.02130.11780.00140.055147.5405-24.678166.2659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 270 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 84 )
6X-RAY DIFFRACTION6chain 'B' and (resid 85 through 103 )
7X-RAY DIFFRACTION7chain 'B' and (resid 104 through 217 )
8X-RAY DIFFRACTION8chain 'B' and (resid 218 through 270 )
9X-RAY DIFFRACTION9chain 'C' and (resid 24 through 38 )
10X-RAY DIFFRACTION10chain 'C' and (resid 39 through 84 )
11X-RAY DIFFRACTION11chain 'C' and (resid 85 through 119 )
12X-RAY DIFFRACTION12chain 'C' and (resid 120 through 217 )
13X-RAY DIFFRACTION13chain 'C' and (resid 218 through 270 )
14X-RAY DIFFRACTION14chain 'D' and (resid 24 through 56 )
15X-RAY DIFFRACTION15chain 'D' and (resid 57 through 84 )
16X-RAY DIFFRACTION16chain 'D' and (resid 85 through 103 )
17X-RAY DIFFRACTION17chain 'D' and (resid 104 through 217 )
18X-RAY DIFFRACTION18chain 'D' and (resid 218 through 270 )
19X-RAY DIFFRACTION19chain 'E' and (resid 24 through 38 )
20X-RAY DIFFRACTION20chain 'E' and (resid 39 through 84 )
21X-RAY DIFFRACTION21chain 'E' and (resid 85 through 103 )
22X-RAY DIFFRACTION22chain 'E' and (resid 104 through 170 )
23X-RAY DIFFRACTION23chain 'E' and (resid 171 through 270 )
24X-RAY DIFFRACTION24chain 'F' and (resid 24 through 84 )
25X-RAY DIFFRACTION25chain 'F' and (resid 85 through 103 )
26X-RAY DIFFRACTION26chain 'F' and (resid 104 through 170 )
27X-RAY DIFFRACTION27chain 'F' and (resid 171 through 270 )
28X-RAY DIFFRACTION28chain 'G' and (resid 24 through 84 )
29X-RAY DIFFRACTION29chain 'G' and (resid 85 through 103 )
30X-RAY DIFFRACTION30chain 'G' and (resid 104 through 217 )
31X-RAY DIFFRACTION31chain 'G' and (resid 218 through 270 )
32X-RAY DIFFRACTION32chain 'H' and (resid 24 through 84 )
33X-RAY DIFFRACTION33chain 'H' and (resid 85 through 103 )
34X-RAY DIFFRACTION34chain 'H' and (resid 104 through 217 )
35X-RAY DIFFRACTION35chain 'H' and (resid 218 through 270 )

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