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- PDB-4bkm: Crystal structure of the murine AUM (phosphoglycolate phosphatase... -

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Basic information

Entry
Database: PDB / ID: 4bkm
TitleCrystal structure of the murine AUM (phosphoglycolate phosphatase) capping domain as a fusion protein with the catalytic core domain of murine chronophin (pyridoxal phosphate phosphatase)
ComponentsPYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
KeywordsHYDROLASE / HAD FAMILY
Function / homology
Function and homology information


glycerol-1-phosphatase / glycerol-1-phosphatase activity / pyridoxal phosphatase / pyridoxal phosphate catabolic process / glycerol-3-phosphatase activity / actin rod assembly / pyridoxal phosphatase activity / phosphoglycolate phosphatase activity / contractile ring / glycerophospholipid metabolic process ...glycerol-1-phosphatase / glycerol-1-phosphatase activity / pyridoxal phosphatase / pyridoxal phosphate catabolic process / glycerol-3-phosphatase activity / actin rod assembly / pyridoxal phosphatase activity / phosphoglycolate phosphatase activity / contractile ring / glycerophospholipid metabolic process / ADP phosphatase activity / glycerol biosynthetic process / positive regulation of actin filament depolymerization / cellular response to ATP / regulation of mitotic nuclear division / myosin phosphatase activity / protein-serine/threonine phosphatase / growth factor binding / phosphoprotein phosphatase activity / cleavage furrow / lamellipodium membrane / negative regulation of gluconeogenesis / dephosphorylation / heat shock protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / regulation of cytokinesis / protein tyrosine phosphatase activity / ruffle membrane / cell-cell junction / actin cytoskeleton / midbody / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
2-phosphoglycolate phosphatase, eukaryotic / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Chronophin / Glycerol-3-phosphate phosphatase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKnobloch, G. / Seifried, A. / Gohla, A. / Schindelin, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Evolutionary and Structural Analyses of the Mammalian Haloacid Dehalogenase-Type Phosphatases Aum and Chronophin Provide Insight Into the Basis of Their Different Substrate Specificities.
Authors: Seifried, A. / Knobloch, G. / Duraphe, P.S. / Segerer, G. / Manhard, J. / Schindelin, H. / Schultz, J. / Gohla, A.
History
DepositionApr 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 2.0Jun 28, 2017Group: Atomic model / Data collection / Category: atom_site / diffrn_source
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 / _diffrn_source.type
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
B: PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
C: PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
D: PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,07110
Polymers133,8504
Non-polymers2216
Water3,639202
1
C: PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
D: PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9734
Polymers66,9252
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-40.3 kcal/mol
Surface area25230 Å2
MethodPISA
2
A: PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
B: PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0976
Polymers66,9252
Non-polymers1734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-37.1 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.500, 91.960, 105.920
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE / CAC - CHRONOPHIN AUM HYBRID PHOSPHATASE / PLP PHOSPHATASE / CHRONOPHIN / PGP / PGPASE


Mass: 33462.426 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-100,114-233,208-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P60487, UniProt: Q8CHP8, phosphoserine phosphatase, pyridoxal phosphatase, phosphoglycolate phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHYBRID SEQUENCE FROM ENTRIES P60487 AND Q8CHP8

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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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growpH: 7.4
Details: MOTHER LIQUOR: 15% PEG 3350, 0.2 M MG(NO3)2. PROTEIN BUFFER: 10 MM TRIETHANOLAMINE PH 7.4, 0.1 M NACL, 1 MM MGCL2 PROTEIN CONCENTRATION: 10 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 14, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→41.74 Å / Num. obs: 36245 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 49.97 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.6
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.4 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OYC

2oyc


Resolution: 2.65→41.737 Å / SU ML: 0.36 / σ(F): 1.33 / Phase error: 30.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1830 5.1 %
Rwork0.1976 --
obs0.2006 36013 95.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→41.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9236 0 12 202 9450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049414
X-RAY DIFFRACTIONf_angle_d0.83312766
X-RAY DIFFRACTIONf_dihedral_angle_d13.5393492
X-RAY DIFFRACTIONf_chiral_restr0.0431452
X-RAY DIFFRACTIONf_plane_restr0.0041694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-2.72170.3291430.28782583X-RAY DIFFRACTION94
2.7217-2.80180.32451560.26172553X-RAY DIFFRACTION94
2.8018-2.89220.34041440.24532578X-RAY DIFFRACTION95
2.8922-2.99550.27021250.23252626X-RAY DIFFRACTION95
2.9955-3.11540.35491670.2352572X-RAY DIFFRACTION95
3.1154-3.25710.29981370.22592637X-RAY DIFFRACTION96
3.2571-3.42880.28611180.21082633X-RAY DIFFRACTION95
3.4288-3.64350.25541220.19232653X-RAY DIFFRACTION96
3.6435-3.92460.27031470.19232650X-RAY DIFFRACTION96
3.9246-4.31920.24121430.16932655X-RAY DIFFRACTION96
4.3192-4.94340.21511450.15842656X-RAY DIFFRACTION97
4.9434-6.22480.22971520.19072705X-RAY DIFFRACTION97
6.2248-41.74180.20341310.18812682X-RAY DIFFRACTION94
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)
12.9819-3.6285-3.86398.90623.22356.45051.00121.04920.8926-0.5254-0.04550.0551-2.07580.4358-0.84130.90780.04910.271.01990.08020.7-2.021419.8481-46.7373
23.2651-2.4035-1.5094.6348-0.35822.18960.42580.9201-0.2496-0.7361-0.47910.54880.35980.32530.13770.68590.1718-0.07240.9493-0.20680.6349-1.98311.8791-44.6619
37.6507-1.10065.4026.46280.48216.31140.14450.161-0.3902-0.9161-0.81530.64721.2818-0.05460.6710.84860.42460.1361.2034-0.47470.71911.2708-6.4035-43.5722
41.4575-0.0936-0.1821.8727-2.52426.36630.2130.0599-0.0265-0.0225-0.0869-0.11750.10441.0673-0.11270.46780.03540.04110.7373-0.18110.47030.83522.5456-25.0743
59.84394.7487-0.1656.86663.67676.04570.0136-0.36180.807-0.11550.013-0.0531-1.52310.4486-0.09060.9743-0.1451-0.00321.002-0.06730.7089-12.477318.164220.2821
64.3066-0.8585-1.68487.32674.28898.1009-0.258-0.8539-0.44691.09230.2286-0.37831.47180.19860.04610.8787-0.1012-0.051.08450.22060.5665-16.1585-2.062617.7124
70.62771.40880.69683.02621.70328.87120.0807-1.12250.2820.6402-0.22010.508-0.42-2.2639-0.21490.6599-0.0170.09371.2617-0.0720.5903-26.97030.01994.3789
84.5216-0.2485-0.08573.08240.91127.00970.2812-0.1306-0.501-0.1612-0.06890.52970.9177-1.1606-0.11250.5935-0.1604-0.06680.67680.06560.5207-21.3459-8.1483-12.5799
98.5637-0.9787.48975.81091.19158.3795-0.1727-0.6731-0.14980.40240.6236-0.40250.19270.4569-0.41050.39150.0810.05490.7564-0.02620.4355-6.8974-0.8256-4.2232
106.0695-0.4242-2.90356.13015.79797.92890.3863-0.67810.2991-0.1156-0.32310.7652-0.959-1.5341-0.20480.56120.06420.0170.87730.0550.5818-21.55257.163-2.5236
118.2491-2.53351.16395.9511.91412.16850.4089-0.62190.2284-0.2304-0.4488-0.0489-0.4531-0.07050.12550.686-0.08320.10960.92310.05510.4258-17.688711.97279.414
122.59780.5357-3.54038.852-0.3235.17650.4021-1.27690.16420.05060.1324-1.1281-0.81381.4685-0.44030.5931-0.2505-0.06351.2041-0.06780.7191-5.879514.150113.1629
137.78641.50112.12448.9418-0.82149.07770.5845-0.9044-0.48150.6028-0.28560.6556-0.0544-1.0251-0.29050.4706-0.07070.03660.92860.05210.5749-21.377632.0248-6.2789
145.3046-0.99362.9438.91-7.3616.9578-0.0293-0.16680.25240.06030.06790.155-0.1697-0.38930.02760.6659-0.06170.01230.8947-0.05980.4839-15.129940.9596-14.2631
153.70650.2431-3.32532.81191.53584.1858-0.5362-0.36960.90890.9783-0.2630.2524-1.7774-0.64590.70341.24960.0142-0.04770.9844-0.07670.7025-16.097349.4774-9.5486
164.1428-1.71051.12496.0736-1.97398.03340.16360.3924-0.05550.0023-0.0557-0.5571-0.39741.8439-0.02130.6035-0.12220.03421.0545-0.08110.5188-6.320947.1853-27.7157
174.10133.22780.18273.4337-1.44467.95480.03150.93180.2875-0.16220.0238-0.1919-1.45331.2116-0.02290.7788-0.06260.13360.9222-0.00960.4707-16.132654.3873-42.6055
184.7810.98442.10474.763-1.85356.30580.03160.11050.1386-0.11850.4729-0.0002-0.150.4529-0.47120.4642-0.01510.08450.7612-0.01020.4443-20.106444.5454-36.1479
194.018-1.34172.48114.7375-4.21274.36730.56070.6824-0.3291-0.338-0.0767-0.21510.04221.292-0.55660.58450.11160.07230.8789-0.07020.5305-12.144835.3085-28.9105
207.18291.60391.06566.4033-0.46448.20480.5773-0.0422-0.58960.2757-0.1590.63610.5502-1.0292-0.38980.5265-0.0058-0.08960.75570.01050.5664-21.117628.4992-16.7738
213.09551.94245.16266.1261.45489.36960.5023-1.4571-0.97960.29160.07590.45590.506-1.2817-0.71510.6933-0.101-0.0521.28510.10540.9661-24.878525.9074-10.6089
224.505-1.20561.98315.4633.22978.2341-0.03280.5247-0.1476-0.85520.2712-0.2471-0.5361.3092-0.27420.6913-0.05460.02491.07430.05430.5299-30.997234.2567-71.5287
233.3006-0.0442-4.22596.9324-4.45538.4166-0.32530.46780.2702-0.9634-0.3165-0.5659-2.42840.71940.44551.6439-0.1171-0.0431.15070.17360.5804-35.192949.2041-69.7882
241.8680.5859-2.12474.50720.56922.75090.06560.1718-0.8646-0.6771-0.52740.4892-0.6664-1.24480.1590.71190.0578-0.06471.01160.06870.5935-44.06442.2289-57.4411
257.26713.9391.43366.22781.52177.07390.2918-0.73940.852-0.0364-0.30721.2419-0.743-1.8893-0.02540.73530.38380.05991.0440.01890.7421-45.511850.2812-48.0107
260.5864-1.08220.80932.2881-0.2638.2352-0.243-0.42890.8781-0.10270.06680.0896-1.3027-1.15290.35521.01810.2450.12810.9658-0.03860.6744-35.816156.5267-33.0312
273.7775-0.68634.16294.79811.66596.19830.00040.04180.0204-0.03590.23750.0492-0.2045-0.3846-0.24540.41660.03680.0440.60150.03890.4118-31.123445.3145-43.5485
282.19793.41082.28016.65126.5299.17070.4973-0.6678-0.24910.2256-0.10030.42450.8156-0.9907-0.20060.4687-0.06860.0010.8810.21010.6081-39.640134.883-51.378
292.3402-4.165-0.51098.7382-0.65822.1559-0.5492-1.3885-0.81130.0663-0.0821-0.01790.55251.19390.39080.62230.07620.05290.91720.13590.61-33.918229.2267-62.2373
304.4111.47880.07458.84341.34245.3860.0830.050.14920.28280.4603-1.14650.50522.0431-0.39960.72310.23440.01741.8527-0.14490.708-21.626927.1109-62.9138
316.3056-1.492.00026.2283-0.66927.170.02320.061-0.7306-0.11740.7066-0.14650.37022.1204-0.37140.65610.07820.06511.2857-0.05660.6439-25.262526.1007-68.6347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 0 THROUGH 25 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 26 THROUGH 64 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 65 THROUGH 81 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 82 THROUGH 303 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 0 THROUGH 25 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 26 THROUGH 81 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 82 THROUGH 99 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 100 THROUGH 189 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 190 THROUGH 213 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 214 THROUGH 232 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 233 THROUGH 259 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 260 THROUGH 303 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 0 THROUGH 49 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 50 THROUGH 64 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 65 THROUGH 81 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 82 THROUGH 128 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 129 THROUGH 164 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 165 THROUGH 213 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 214 THROUGH 232 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 233 THROUGH 282 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 283 THROUGH 303 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 0 THROUGH 64 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 65 THROUGH 81 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 82 THROUGH 99 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 100 THROUGH 128 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 129 THROUGH 153 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 154 THROUGH 213 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 214 THROUGH 234 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 235 THROUGH 259 )
30X-RAY DIFFRACTION30CHAIN D AND (RESID 260 THROUGH 282 )
31X-RAY DIFFRACTION31CHAIN D AND (RESID 283 THROUGH 303 )

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