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- PDB-1r9m: Crystal Structure of Human Dipeptidyl Peptidase IV at 2.1 Ang. Re... -

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Basic information

Entry
Database: PDB / ID: 1r9m
TitleCrystal Structure of Human Dipeptidyl Peptidase IV at 2.1 Ang. Resolution.
ComponentsDipeptidyl peptidase IV
KeywordsHYDROLASE / aminopeptidase / serine protease / glycoprotein
Function / homology
Function and homology information


glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / T cell activation / serine-type peptidase activity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / cell adhesion / response to hypoxia / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / serine-type endopeptidase activity / focal adhesion / signaling receptor binding / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain ...Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsAertgeerts, K. / Ye, S. / Tennant, M.G. / Collins, B. / Rogers, J. / Sang, B.C. / Skene, R.J. / Webb, D.R. / Prasad, G.S.
CitationJournal: Protein Sci. / Year: 2004
Title: Crystal structure of human dipeptidyl peptidase IV in complex with a decapeptide reveals details on substrate specificity and tetrahedral intermediate formation.
Authors: Aertgeerts, K. / Ye, S. / Tennant, M.G. / Kraus, M.L. / Rogers, J. / Sang, B.C. / Skene, R.J. / Webb, D.R. / Prasad, G.S.
History
DepositionOct 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase IV
B: Dipeptidyl peptidase IV
C: Dipeptidyl peptidase IV
D: Dipeptidyl peptidase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)349,30534
Polymers340,6134
Non-polymers8,69130
Water30,2291678
1
A: Dipeptidyl peptidase IV
B: Dipeptidyl peptidase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,39119
Polymers170,3072
Non-polymers5,08517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint59 kcal/mol
Surface area60620 Å2
MethodPISA
2
C: Dipeptidyl peptidase IV
D: Dipeptidyl peptidase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,91315
Polymers170,3072
Non-polymers3,60613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint38 kcal/mol
Surface area59710 Å2
MethodPISA
3
A: Dipeptidyl peptidase IV
B: Dipeptidyl peptidase IV
hetero molecules

C: Dipeptidyl peptidase IV
D: Dipeptidyl peptidase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)349,30534
Polymers340,6134
Non-polymers8,69130
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area20000 Å2
ΔGint96 kcal/mol
Surface area119840 Å2
MethodPISA
4
A: Dipeptidyl peptidase IV
B: Dipeptidyl peptidase IV
hetero molecules

C: Dipeptidyl peptidase IV
D: Dipeptidyl peptidase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)349,30534
Polymers340,6134
Non-polymers8,69130
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area19740 Å2
ΔGint96 kcal/mol
Surface area120090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.823, 124.056, 144.491
Angle α, β, γ (deg.)90.00, 114.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: PRO / Refine code: 1 / Auth seq-ID: 40 - 766 / Label seq-ID: 7 - 733

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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Protein / Non-polymers , 2 types, 1682 molecules ABCD

#1: Protein
Dipeptidyl peptidase IV / DPP IV / T-cell activation antigen CD26 / TP103 / Adenosine deaminase complexing protein-2 / ADABP


Mass: 85153.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P27487, dipeptidyl-peptidase IV
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1678 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 30 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.: 6
Source method: isolated from a genetically manipulated 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 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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 genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated 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
#6: Sugar ChemComp-FUC / alpha-L-fucopyranose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.01 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 218087 / Num. obs: 218087 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rsym value: 0.062 / Net I/σ(I): 19.9
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.3 / % possible all: 76.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.549 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24883 4355 2 %RANDOM
Rwork0.21845 ---
obs0.21906 213577 100 %-
all-218087 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.914 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å2-1.35 Å2
2--1.73 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23872 0 561 1678 26111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02125187
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.94834215
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.24532910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.986154156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1580.23719
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219225
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.311804
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.52492
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.340
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5131.514514
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.714223546
X-RAY DIFFRACTIONr_scbond_it1.268310673
X-RAY DIFFRACTIONr_scangle_it1.5884.510669
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5946 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.430.05
2Btight positional0.390.05
3Ctight positional0.430.05
4Dtight positional0.40.05
1Atight thermal0.220.5
2Btight thermal0.210.5
3Ctight thermal0.190.5
4Dtight thermal0.210.5
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 203
Rwork0.276 11728
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)
11.58080.2230.39650.79880.01191.0837-0.09110.10130.1825-0.11640.0540.09330.0074-0.06240.03720.0780.01240.00540.0025-0.00510.071723.2989-0.50366.5209
21.51440.03570.48230.8871-0.2831.4508-0.0737-0.38710.26240.2622-0.00920.2694-0.0336-0.32930.08290.20210.00780.09470.2474-0.08050.22123.0531-6.166529.493
31.34310.2144-0.04820.7286-0.10370.7982-0.07370.03640.3101-0.00620.0562-0.0897-0.13150.1110.01750.09480.0212-0.02280.053-0.04230.163254.543113.433713.1463
41.13390.1284-0.07710.8766-0.48611.0406-0.0925-0.0809-0.03570.01320.0608-0.27170.18160.20560.03160.17310.0807-0.05280.2261-0.0990.220976.2286-4.425627.1128
51.79430.4609-0.02761.31140.29830.97350.0938-0.133-0.32770.0539-0.11240.19360.2197-0.21280.01860.1686-0.0307-0.00310.1230.00080.1903-19.493747.089839.2473
61.43080.15120.10491.47410.46321.08820.0165-0.09330.05960.0362-0.14210.4031-0.1514-0.47880.12560.23220.06580.04830.4324-0.06340.2782-36.464769.64252.5143
71.99920.1193-0.32030.89160.20541.13570.05610.1264-0.2741-0.111-0.0318-0.05420.11410.1184-0.02430.12120.0505-0.0130.0343-0.03110.097510.483555.008223.3617
82.0657-0.228-0.57660.80120.58141.3310.0475-0.6599-0.10860.18490.0084-0.17880.10660.4932-0.05590.1923-0.0155-0.02570.47240.01320.178535.754762.074640.3431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA40 - 557 - 22
2X-RAY DIFFRACTION1AA232 - 262199 - 229
3X-RAY DIFFRACTION1AA500 - 766467 - 733
4X-RAY DIFFRACTION1AK - L5201 - 68511
5X-RAY DIFFRACTION2AA56 - 23123 - 198
6X-RAY DIFFRACTION2AA263 - 499230 - 466
7X-RAY DIFFRACTION2AE - J851 - 32121 - 2
8X-RAY DIFFRACTION3BB34 - 551 - 22
9X-RAY DIFFRACTION3BB232 - 262199 - 229
10X-RAY DIFFRACTION3BB500 - 766467 - 733
11X-RAY DIFFRACTION3BT - U5201 - 68511
12X-RAY DIFFRACTION4BB56 - 23123 - 198
13X-RAY DIFFRACTION4BB263 - 499230 - 466
14X-RAY DIFFRACTION4BM - S851 - 32111 - 2
15X-RAY DIFFRACTION5CC40 - 557 - 22
16X-RAY DIFFRACTION5CC232 - 262199 - 229
17X-RAY DIFFRACTION5CC500 - 766467 - 733
18X-RAY DIFFRACTION5CAA52011
19X-RAY DIFFRACTION6CC56 - 23123 - 198
20X-RAY DIFFRACTION6CC263 - 499230 - 466
21X-RAY DIFFRACTION6CV - Z1501 - 32111
22X-RAY DIFFRACTION7DD40 - 557 - 22
23X-RAY DIFFRACTION7DD232 - 262199 - 229
24X-RAY DIFFRACTION7DD500 - 766467 - 733
25X-RAY DIFFRACTION7DGA - HA5201 - 68511
26X-RAY DIFFRACTION8DD56 - 23123 - 198
27X-RAY DIFFRACTION8DD263 - 499230 - 466
28X-RAY DIFFRACTION8DBA - FA1501 - 32111

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