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- PDB-5kn0: Native bovine skeletal calsequestrin, low-Ca2+ form -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5kn0
TitleNative bovine skeletal calsequestrin, low-Ca2+ form
ComponentsCalsequestrin
KeywordsMETAL BINDING PROTEIN / calsequestrin / polymer / calcium / glycosylation
Function / homology
Function and homology information


regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / regulation of store-operated calcium entry / Stimuli-sensing channels / Ion homeostasis / sarcoplasmic reticulum lumen / endoplasmic reticulum organization / sarcomere organization / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol ...regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / regulation of store-operated calcium entry / Stimuli-sensing channels / Ion homeostasis / sarcoplasmic reticulum lumen / endoplasmic reticulum organization / sarcomere organization / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol / Z disc / response to heat / mitochondrial matrix / calcium ion binding / identical protein binding
Similarity search - Function
Calsequestrin / Calsequestrin, conserved site / Calsequestrin, middle TRX-fold domain / Calsequestrin, N-terminal TRX-fold domain / Calsequestrin, C-terminal TRX-fold domain / Calsequestrin / Calsequestrin signature 1. / Calsequestrin signature 2. / Glutaredoxin / Glutaredoxin ...Calsequestrin / Calsequestrin, conserved site / Calsequestrin, middle TRX-fold domain / Calsequestrin, N-terminal TRX-fold domain / Calsequestrin, C-terminal TRX-fold domain / Calsequestrin / Calsequestrin signature 1. / Calsequestrin signature 2. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.729 Å
AuthorsLewis, K.M. / Byrd, S. / Kang, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM11125401 United States
M.J. Murdock Charitable Trust United States
CitationJournal: Int J Mol Sci / Year: 2016
Title: Characterization of Post-Translational Modifications to Calsequestrins of Cardiac and Skeletal Muscle.
Authors: Lewis, K.M. / Munske, G.R. / Byrd, S.S. / Kang, J. / Cho, H.J. / Rios, E. / Kang, C.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Calsequestrin
B: Calsequestrin
C: Calsequestrin
D: Calsequestrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,61437
Polymers166,2174
Non-polymers3,39733
Water59433
1
A: Calsequestrin
B: Calsequestrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,74619
Polymers83,1092
Non-polymers1,63717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-185 kcal/mol
Surface area33110 Å2
MethodPISA
2
C: Calsequestrin
D: Calsequestrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,86818
Polymers83,1092
Non-polymers1,75916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-171 kcal/mol
Surface area33650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.342, 92.994, 101.849
Angle α, β, γ (deg.)71.12, 84.57, 73.48
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Calsequestrin /


Mass: 41554.277 Da / Num. of mol.: 4 / Fragment: UNP residues 35-395 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q05JF3

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Sugars , 3 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 62 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, 27.5 % 2-methyl-2,4-pentanediol, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.729→49.664 Å / Num. obs: 52550 / % possible obs: 98 % / Redundancy: 2 % / Rmerge(I) obs: 0.0318 / Net I/σ(I): 14.84
Reflection shellResolution: 2.729→2.827 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3289 / Mean I/σ(I) obs: 2.55 / Num. measured obs: 5026 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000v712data reduction
HKL-2000v712data scaling
PHENIX1.10_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3trp

3trp


Resolution: 2.729→49.664 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.95
RfactorNum. reflection% reflection
Rfree0.2405 2000 3.81 %
Rwork0.1963 --
obs0.198 52529 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.729→49.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11267 0 99 33 11399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511604
X-RAY DIFFRACTIONf_angle_d0.70615797
X-RAY DIFFRACTIONf_dihedral_angle_d13.8076937
X-RAY DIFFRACTIONf_chiral_restr0.0471729
X-RAY DIFFRACTIONf_plane_restr0.0042085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7287-2.79690.40421330.35493351X-RAY DIFFRACTION92
2.7969-2.87250.35141430.32823645X-RAY DIFFRACTION98
2.8725-2.95710.3921420.31043571X-RAY DIFFRACTION98
2.9571-3.05250.34321440.29523633X-RAY DIFFRACTION99
3.0525-3.16160.3061440.28533648X-RAY DIFFRACTION99
3.1616-3.28810.30811430.25373609X-RAY DIFFRACTION99
3.2881-3.43770.29861440.22823648X-RAY DIFFRACTION99
3.4377-3.61890.26211430.21683602X-RAY DIFFRACTION99
3.6189-3.84560.23631440.19553625X-RAY DIFFRACTION99
3.8456-4.14240.22341440.1683651X-RAY DIFFRACTION99
4.1424-4.5590.18711440.1433644X-RAY DIFFRACTION99
4.559-5.21810.17661440.14083638X-RAY DIFFRACTION99
5.2181-6.57180.22141440.17743642X-RAY DIFFRACTION99
6.5718-49.67180.20831440.16943622X-RAY DIFFRACTION98
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)
10.5679-0.6097-0.32140.7714-0.05391.29820.06260.02670.09820.0872-0.16270.0698-1.1640.1220.00020.88980.0824-0.03020.5916-0.02340.5766-69.5257-87.690739.1665
20.96690.0953-0.86451.14910.39360.96980.2594-0.13310.00610.4437-0.1534-0.2295-0.56530.24990.00020.94960.0268-0.08360.5785-0.04970.5324-63.7042-90.87241.8177
30.05480.0608-0.11330.0575-0.17661.44960.19480.11250.2352-0.1491-0.1574-0.0755-0.0823-0.36080.00010.62060.0472-0.06970.7204-0.04560.535-75.0966-105.532232.2316
40.5002-0.35660.49741.4552-1.21411.10140.20410.0862-0.1804-0.656-0.15910.15890.0101-0.40570.00030.5820.003-0.15910.7976-0.12620.7458-84.6703-118.089432.1545
50.1292-0.1730.14480.5566-0.52280.49150.1329-0.5485-0.8007-0.3487-0.3285-0.16790.0138-0.16570.00020.5671-0.1471-0.04310.6989-0.00160.6713-78.0687-122.367139.123
61.49650.7725-0.3850.7855-0.32860.1553-0.1148-0.0368-0.2063-0.52980.17290.24590.0285-0.1275-0.00030.6293-0.0404-0.08910.49390.06150.6545-59.1752-116.698829.5464
70.3780.1387-0.13330.0495-0.04910.0462-0.5946-0.1894-0.9178-0.5514-0.0873-0.3188-0.3396-1.05130.00360.8644-0.13160.13390.67430.04320.7811-64.4044-129.676429.718
80.77620.3562-0.54660.39850.22421.3401-0.0494-0.0467-0.22850.2035-0.0794-0.33530.1004-0.02120.00010.58630.0034-0.04380.54480.06890.7396-50.4042-116.224227.9412
90.2193-0.08220.10830.0277-0.04080.0535-0.13950.2814-0.82210.64030.3122-0.7611-1.1482-0.0876-0.0011.13210.19110.28320.64550.02351.026-51.8031-131.740124.9583
100.42920.02150.09220.7703-0.56390.43410.0306-0.1342-0.1410.4387-0.0764-0.2364-0.50440.088800.6559-0.0626-0.13020.55440.03670.6059-42.813-88.883925.4947
111.66970.9343-0.01470.6224-0.14881.02540.0626-0.0340.18950.4001-0.1043-0.014-0.7830.10410.00020.6811-0.0577-0.09050.58830.06740.6673-48.3208-84.716222.3143
121.0469-0.6552-0.34221.06790.24911.9493-0.0322-0.0279-0.19830.0013-0.0853-0.33570.07410.1142-00.4547-0.01880.03980.50620.05510.6113-47.4088-107.35084.8879
130.3510.1586-0.40420.7846-0.54851.28380.52720.44370.1244-0.5353-0.4819-0.0065-0.1382-0.142100.71560.05590.02820.59950.00130.6223-52.1501-105.3117-7.1989
140.9141-0.1205-1.00921.61450.05462.5431-0.11750.25520.0319-0.2951-0.15440.1477-0.3248-0.63370.00010.58840.1175-0.12620.7226-0.08460.506-71.162-98.03338.2793
150.266-0.1013-0.16440.2825-0.04020.14040.3240.64210.1288-0.2379-0.05370.489-0.356-0.86980.00570.56940.12-0.11631.2408-0.14610.8073-83.8636-102.7672.299
161.10780.8751-0.14450.692-0.03520.6463-0.0574-0.1827-0.24990.23140.08730.39610.7041-1.02780.00030.6029-0.08990.04670.8315-0.06220.6742-81.5022-120.144868.0775
170.2059-0.03130.23720.17420.0080.27970.20290.1628-0.1846-0.3431-0.2092-0.04110.4331-0.3079-0.00010.6436-0.02930.05840.65930.03350.6702-71.2341-124.931267.4868
181.6131-0.12980.02860.221-0.2851.0136-0.26030.0778-0.1399-0.3381-0.09920.2138-0.0901-0.3397-0.00150.626-0.0683-0.00620.62930.01420.5959-73.1082-113.107663.1674
191.4735-0.5421-1.00191.1358-0.67311.7956-0.0175-0.15260.0713-0.1399-0.0183-0.0476-0.4836-0.08260.00020.75090.0934-0.00940.5681-0.02280.5369-71.3769-88.346174.1829
201.2833-0.17750.18131.9116-0.19181.9439-0.20980.1397-0.0076-0.32240.1726-0.1755-0.24350.12880.00010.5739-0.07470.12160.5486-0.01550.5959-50.4209-104.89374.9945
210.5989-0.5497-0.08130.49550.0740.0093-0.2901-0.03010.1385-0.0230.3342-1.1413-0.02720.93370.00190.569-0.11540.15460.8516-0.09060.9087-37.7887-101.116177.2846
220.40660.0599-0.70681.0132-0.17311.1572-0.26610.0297-0.151-0.68920.2201-0.26840.8352-0.04670.00010.82740.04970.07520.5729-0.00740.6693-57.1748-136.763378.6617
230.4161-0.2716-0.49590.3940.23270.6288-0.14210.9988-0.5113-0.25220.25750.02420.4782-0.11670.00050.7721-0.00780.02620.6180.030.6742-63.9003-132.185176.8656
240.7127-0.8863-0.13121.201-0.09690.6439-0.161-0.1902-0.41420.34550.1379-0.04750.3048-0.238-00.72450.01790.14790.53580.05280.6179-60.3914-134.673389.1599
251.73880.0723-0.19511.2055-0.51812.15690.1996-0.07410.04550.0456-0.3022-0.3126-0.0790.06890.00010.5945-0.06790.00810.54130.06340.6873-47.4792-117.7215105.9938
260.8654-0.1660.76590.9691-0.50471.8724-0.0143-0.08150.05980.1696-0.01010.1286-0.1552-0.3316-00.54190.00270.10690.61620.00210.535-72.6024-112.401697.5234
270.4004-0.02140.11870.2147-0.13320.1073-0.0417-0.53550.14880.6566-0.12970.4368-0.1129-0.35510.00080.95070.29030.13150.9307-0.06630.7882-79.4785-101.2266104.4905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:42)
2X-RAY DIFFRACTION2(chain A and resid 43:91)
3X-RAY DIFFRACTION3(chain A and resid 92:142)
4X-RAY DIFFRACTION4(chain A and resid 143:204)
5X-RAY DIFFRACTION5(chain A and resid 205:232)
6X-RAY DIFFRACTION6(chain A and resid 233:266)
7X-RAY DIFFRACTION7(chain A and resid 267:282)
8X-RAY DIFFRACTION8(chain A and resid 283:329)
9X-RAY DIFFRACTION9(chain A and resid 330:348)
10X-RAY DIFFRACTION10(chain B and resid 3:42)
11X-RAY DIFFRACTION11(chain B and resid 43:98)
12X-RAY DIFFRACTION12(chain B and resid 99:190)
13X-RAY DIFFRACTION13(chain B and resid 191:228)
14X-RAY DIFFRACTION14(chain B and resid 229:324)
15X-RAY DIFFRACTION15(chain B and resid 325:348)
16X-RAY DIFFRACTION16(chain C and resid 4:37)
17X-RAY DIFFRACTION17(chain C and resid 38:70)
18X-RAY DIFFRACTION18(chain C and resid 71:123)
19X-RAY DIFFRACTION19(chain C and resid 124:228)
20X-RAY DIFFRACTION20(chain C and resid 229:319)
21X-RAY DIFFRACTION21(chain C and resid 320:348)
22X-RAY DIFFRACTION22(chain D and resid 3:42)
23X-RAY DIFFRACTION23(chain D and resid 43:73)
24X-RAY DIFFRACTION24(chain D and resid 74:123)
25X-RAY DIFFRACTION25(chain D and resid 124:228)
26X-RAY DIFFRACTION26(chain D and resid 229:324)
27X-RAY DIFFRACTION27(chain D and resid 325:348)

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