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- PDB-6nly: Fragment of human mitochondrial Alanyl-tRNA Synthetase C-Ala domain -

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Basic information

Entry
Database: PDB / ID: 6nly
TitleFragment of human mitochondrial Alanyl-tRNA Synthetase C-Ala domain
ComponentsAlanine--tRNA ligase, mitochondrial
KeywordsLIGASE / Alanyl-tRNA synthetase / mitochondria / C-terminal domain / alpha-beta domain
Function / homology
Function and homology information


mitochondrial alanyl-tRNA aminoacylation / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / mitochondrion / zinc ion binding / ATP binding
Similarity search - Function
Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain ...Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
Alanine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.307 Å
AuthorsKuhle, B. / Schimmel, P.
CitationJournal: Nat Commun / Year: 2020
Title: Relaxed sequence constraints favor mutational freedom in idiosyncratic metazoan mitochondrial tRNAs.
Authors: Kuhle, B. / Chihade, J. / Schimmel, P.
History
DepositionJan 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _struct.title
Revision 1.2Oct 11, 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
B: Alanine--tRNA ligase, mitochondrial
A: Alanine--tRNA ligase, mitochondrial
C: Alanine--tRNA ligase, mitochondrial
D: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)83,2734
Polymers83,2734
Non-polymers00
Water37821
1
B: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,8181
Polymers20,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,8181
Polymers20,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,8181
Polymers20,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,8181
Polymers20,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.220, 317.230, 54.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 814:815 or resseq 817:818 or resseq...
21(chain B and (resseq 814:815 or resseq 817:818 or resseq...
31(chain C and (resseq 814:815 or resseq 817:818 or resseq...
41(chain D and (resseq 814:815 or resseq 817:818 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 814:815 or resseq 817:818 or resseq...A814 - 815
121(chain A and (resseq 814:815 or resseq 817:818 or resseq...A817 - 818
131(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
141(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
151(chain A and (resseq 814:815 or resseq 817:818 or resseq...A831
161(chain A and (resseq 814:815 or resseq 817:818 or resseq...A844 - 8
171(chain A and (resseq 814:815 or resseq 817:818 or resseq...A71
181(chain A and (resseq 814:815 or resseq 817:818 or resseq...A873 - 87
191(chain A and (resseq 814:815 or resseq 817:818 or resseq...A9
1101(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1111(chain A and (resseq 814:815 or resseq 817:818 or resseq...A892 - 919
1121(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1131(chain A and (resseq 814:815 or resseq 817:818 or resseq...A920
1141(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1151(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1161(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1171(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1181(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
211(chain B and (resseq 814:815 or resseq 817:818 or resseq...B814 - 815
221(chain B and (resseq 814:815 or resseq 817:818 or resseq...B817 - 818
231(chain B and (resseq 814:815 or resseq 817:818 or resseq...B820 - 821
241(chain B and (resseq 814:815 or resseq 817:818 or resseq...B823 - 825
251(chain B and (resseq 814:815 or resseq 817:818 or resseq...B844 - 851
261(chain B and (resseq 814:815 or resseq 817:818 or resseq...B861 - 869
271(chain B and (resseq 814:815 or resseq 817:818 or resseq...B873 - 878
281(chain B and (resseq 814:815 or resseq 817:818 or resseq...B870 - 871
291(chain B and (resseq 814:815 or resseq 817:818 or resseq...B881 - 899
2101(chain B and (resseq 814:815 or resseq 817:818 or resseq...B892 - 910
2111(chain B and (resseq 814:815 or resseq 817:818 or resseq...B920
2121(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
2131(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
2141(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
2151(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
2161(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
2171(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
311(chain C and (resseq 814:815 or resseq 817:818 or resseq...C814 - 815
321(chain C and (resseq 814:815 or resseq 817:818 or resseq...C817 - 818
331(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
341(chain C and (resseq 814:815 or resseq 817:818 or resseq...C827 - 828825
351(chain C and (resseq 814:815 or resseq 817:818 or resseq...C827 - 82841
361(chain C and (resseq 814:815 or resseq 817:818 or resseq...C844 - 859
371(chain C and (resseq 814:815 or resseq 817:818 or resseq...C86159
381(chain C and (resseq 814:815 or resseq 817:818 or resseq...C861 - 868
391(chain C and (resseq 814:815 or resseq 817:818 or resseq...C870 - 871
3101(chain C and (resseq 814:815 or resseq 817:818 or resseq...C881 - 890
3111(chain C and (resseq 814:815 or resseq 817:818 or resseq...C892 - 91
3121(chain C and (resseq 814:815 or resseq 817:818 or resseq...C920
3131(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
3141(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
3151(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
3161(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
3171(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
3181(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
411(chain D and (resseq 814:815 or resseq 817:818 or resseq...D814 - 815
421(chain D and (resseq 814:815 or resseq 817:818 or resseq...D817 - 818
431(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
441(chain D and (resseq 814:815 or resseq 817:818 or resseq...D827 - 828825
451(chain D and (resseq 814:815 or resseq 817:818 or resseq...D827 - 82841
461(chain D and (resseq 814:815 or resseq 817:818 or resseq...D844 - 859
471(chain D and (resseq 814:815 or resseq 817:818 or resseq...D86159
481(chain D and (resseq 814:815 or resseq 817:818 or resseq...D861 - 868
491(chain D and (resseq 814:815 or resseq 817:818 or resseq...D870 - 871
4101(chain D and (resseq 814:815 or resseq 817:818 or resseq...D881 - 890
4111(chain D and (resseq 814:815 or resseq 817:818 or resseq...D892 - 91
4121(chain D and (resseq 814:815 or resseq 817:818 or resseq...D920
4131(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
4141(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
4151(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
4161(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
4171(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
4181(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993

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Components

#1: Protein
Alanine--tRNA ligase, mitochondrial / Alanyl-tRNA synthetase / AlaRS


Mass: 20818.125 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 802-985)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AARS2, AARSL, KIAA1270 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5JTZ9, alanine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5 / Details: 0.1 M Tris-HCl, 40% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97938 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.31→38.019 Å / Num. obs: 40004 / % possible obs: 99.3 % / Redundancy: 7.291 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Χ2: 1.075 / Net I/σ(I): 23.99 / Num. measured all: 291673 / Scaling rejects: 96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.31-2.377.4930.7323.5721617293528850.9440.78598.3
2.37-2.437.6170.5324.7921799286728620.9730.5799.8
2.43-2.57.5020.4295.6320841278327780.9850.46199.8
2.5-2.587.3650.356.7919907271327030.9850.37699.6
2.58-2.666.9940.2369.1418072261525840.9910.25598.8
2.66-2.767.1230.20510.4417879253625100.9920.22199
2.76-2.867.6830.17212.618831246124510.9960.18599.6
2.86-2.987.5920.12616.0717916236623600.9970.13599.7
2.98-3.117.4880.10218.6216922226522600.9980.10999.8
3.11-3.267.3830.07624.0616161219521890.9980.08299.7
3.26-3.447.060.05728.7814692209120810.9990.06199.5
3.44-3.656.9410.04435.4513486196319430.9990.04899
3.65-3.97.4840.03544.5613891186118560.9990.03799.7
3.9-4.217.3380.0350.3712607172417180.9990.03299.7
4.21-4.617.1560.02756.7611406159815940.9990.02999.7
4.61-5.166.5950.02554.7294831464143810.02798.2
5.16-5.967.160.02752.5392581301129310.02999.4
5.96-7.37.1450.02457.6280021123112010.02699.7
7.3-10.326.3650.01962.93548087886110.0298.1
10.32-38.0196.6080.01966.53342353751810.02196.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.31 Å38.45 Å
Translation2.31 Å38.45 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NLQ

6nlq


Resolution: 2.307→38.019 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1997 5 %
Rwork0.2094 37919 -
obs0.2118 39916 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.85 Å2 / Biso mean: 77.1161 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.307→38.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5407 0 0 21 5428
Biso mean---45.96 -
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115484
X-RAY DIFFRACTIONf_angle_d1.4157418
X-RAY DIFFRACTIONf_chiral_restr0.084902
X-RAY DIFFRACTIONf_plane_restr0.011935
X-RAY DIFFRACTIONf_dihedral_angle_d20.2443407
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2502X-RAY DIFFRACTION14.106TORSIONAL
12B2502X-RAY DIFFRACTION14.106TORSIONAL
13C2502X-RAY DIFFRACTION14.106TORSIONAL
14D2502X-RAY DIFFRACTION14.106TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3072-2.36480.41651390.33992638277798
2.3648-2.42880.3041410.285626872828100
2.4288-2.50020.29091410.25982668280999
2.5002-2.58090.30541410.24632672281399
2.5809-2.67310.3021390.22572631277099
2.6731-2.78010.30981420.23672712285499
2.7801-2.90660.25511420.2422676281899
2.9066-3.05980.29351420.237927062848100
3.0598-3.25140.31711440.243327182862100
3.2514-3.50230.29781400.22312686282699
3.5023-3.85440.26741440.204827262870100
3.8544-4.41140.221440.175627512895100
4.4114-5.55520.22471460.18362764291099
5.5552-38.02440.21251520.19042884303699
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)
11.680.9988-0.44488.1116-3.55621.110.07580.15660.2240.03820.039-0.6489-0.39360.2084-0.18690.6534-0.04910.13750.55270.00040.7169-48.8737-79.5517.8378
27.92521.4184-1.29774.844-0.37576.21620.5955-0.762-0.22150.7441-0.67830.73070.1496-0.1371-0.11330.6018-0.18450.08910.59590.09610.9349-41.3453-57.1069-3.1987
31.0257-0.4782-0.40576.73452.11530.74820.5184-1.1571-1.29141.5858-0.7031-0.44751.12690.1426-0.37620.8173-0.2563-0.24820.92660.49361.2843-31.3589-63.27250.8065
47.59461.0794-2.16857.4745-0.23975.58580.3973-0.1337-0.65990.5573-0.3039-0.29710.36750.1384-0.06140.3964-0.0656-0.05210.48210.08180.8562-31.452-56.9906-11.0049
51.66461.0621.55373.06283.41491.98040.3746-0.1671-0.16880.6843-0.2144-0.3170.4422-0.1345-0.11780.5624-0.0317-0.01820.59210.01250.7085-3.2411-5.73977.8523
66.06510.28733.01496.94943.19255.83290.1705-0.2428-0.13950.3525-0.32820.26820.0995-0.43770.14510.3031-0.02840.04920.3988-0.01330.51-17.732-24.5802-7.6583
71.12490.69080.04560.40230.01851.6909-0.3949-0.07690.1549-0.42310.77031.072-0.4267-0.3369-0.26310.68810.12310.10990.76780.04531.1893-6.2948-75.7665-38.3355
83.2388-2.3658-2.17723.86353.40111.78910.0941-0.17040.2507-0.0430.2656-0.7501-0.20660.1544-0.24650.56710.04120.03340.6211-0.00070.7075-0.5794-66.3997-33.2811
96.3861-0.5549-2.27316.1886-0.0413.83990.31690.4283-0.2213-0.5947-0.2163-0.07870.0748-0.0106-0.07590.31680.0392-0.05660.3687-0.02020.5864-18.1477-51.0107-21.6102
104.6261-3.861-1.9824.95473.14782.9945-0.1167-0.1279-0.0619-1.05150.2867-0.67530.68310.3805-0.3370.66050.0936-0.08860.4926-0.00760.7929-45.42432.2811-38.2734
113.6531-2.76351.38723.4789-2.56820.66140.2283-0.0923-0.31010.54-0.12121.13430.1701-0.04140.01790.5287-0.01450.0030.54610.02110.4336-51.9122-7.6251-33.5481
126.84410.54262.0336.471-0.38556.32510.24810.51360.03-0.24120.01560.4707-0.0775-0.001-0.18540.28970.07480.02220.3778-0.00370.5017-37.26-25.3808-23.2321
132.87531.466-1.92617.437-1.37462.76490.05740.1891-0.0313-0.40930.1994-0.0414-0.11951.0037-0.05130.3970.0811-0.00870.6904-0.00650.6655-31.6578-21.6436-22.7512
143.9962.00090.15783.7138-3.5468.66770.1898-0.3552-0.4777-0.0633-0.52840.47931.05940.26910.27050.51660.03020.10880.5161-0.04880.8404-31.6054-36.4786-15.5703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 811 through 877 )B811 - 877
2X-RAY DIFFRACTION2chain 'B' and (resid 878 through 917 )B878 - 917
3X-RAY DIFFRACTION3chain 'B' and (resid 918 through 928 )B918 - 928
4X-RAY DIFFRACTION4chain 'B' and (resid 929 through 988 )B929 - 988
5X-RAY DIFFRACTION5chain 'A' and (resid 808 through 877 )A808 - 877
6X-RAY DIFFRACTION6chain 'A' and (resid 878 through 988 )A878 - 988
7X-RAY DIFFRACTION7chain 'C' and (resid 812 through 837 )C812 - 837
8X-RAY DIFFRACTION8chain 'C' and (resid 838 through 877 )C838 - 877
9X-RAY DIFFRACTION9chain 'C' and (resid 878 through 987 )C878 - 987
10X-RAY DIFFRACTION10chain 'D' and (resid 812 through 837 )D812 - 837
11X-RAY DIFFRACTION11chain 'D' and (resid 838 through 877 )D838 - 877
12X-RAY DIFFRACTION12chain 'D' and (resid 878 through 956 )D878 - 956
13X-RAY DIFFRACTION13chain 'D' and (resid 957 through 969 )D957 - 969
14X-RAY DIFFRACTION14chain 'D' and (resid 970 through 993 )D970 - 993

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