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- PDB-2bgr: Crystal structure of HIV-1 Tat derived nonapeptides Tat(1-9) boun... -

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Basic information

Entry
Database: PDB / ID: 2bgr
TitleCrystal structure of HIV-1 Tat derived nonapeptides Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)
Components
  • DIPEPTIDYL PEPTIDASE IV
  • HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE
KeywordsHYDROLASE / HYDROLASE-COMPLEX / DPPIV / ALPHA/BETA-HYDROLASE FOLD / BETA-PROPELLER FOLD
Function / homology
Function and homology information


viral gene expression / trans-activation response element binding / regulatory region RNA binding / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / glucagon processing / modulation by virus of host chromatin organization / negative regulation of neutrophil chemotaxis / symbiont-mediated suppression of host translation initiation / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) ...viral gene expression / trans-activation response element binding / regulatory region RNA binding / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / glucagon processing / modulation by virus of host chromatin organization / negative regulation of neutrophil chemotaxis / symbiont-mediated suppression of host translation initiation / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / host cell nucleolus / chemorepellent activity / actinin binding / dipeptidyl-peptidase activity / peptide hormone processing / negative regulation of peptidyl-threonine phosphorylation / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / RNA-binding transcription regulator activity / behavioral fear response / aminopeptidase activity / T cell costimulation / T cell activation / serine-type peptidase activity / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / virus receptor activity / lamellipodium / protease binding / host cell cytoplasm / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / response to hypoxia / cell adhesion / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / protein domain specific binding / signaling receptor binding / serine-type endopeptidase activity / focal adhesion / DNA-templated transcription / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / 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 ...Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / 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
Protein Tat / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWeihofen, W.A. / Liu, J. / Reutter, W. / Saenger, W. / Fan, H.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structures of HIV-1 Tat-Derived Nonapeptides Tat-(1-9) and Trp2-Tat-(1-9) Bound to the Active Site of Dipeptidyl-Peptidase Iv (Cd26)
Authors: Weihofen, W.A. / Liu, J. / Reutter, W. / Saenger, W. / Fan, H.
History
DepositionJan 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_validate_chiral / struct_asym / struct_conn / 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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
Y: HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE
Z: HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,50618
Polymers172,9634
Non-polymers5,54214
Water31,4541746
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint66.3 kcal/mol
Surface area61100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.299, 127.043, 137.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA41 - 27813 - 250
21LYSLYSBB41 - 27813 - 250
12GLYGLYAA296 - 764268 - 736
22GLYGLYBB296 - 764268 - 736

NCS oper: (Code: given
Matrix: (-0.946, 0.152, -0.287), (0.185, -0.473, -0.861), (-0.266, -0.868, 0.42)
Vector: 35.34585, 112.96806, 75.642)

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Components

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Protein / Protein/peptide / Non-polymers , 3 types, 1750 molecules ABYZ

#1: Protein DIPEPTIDYL PEPTIDASE IV / / DPP IV / T-CELL ACTIVATION ANTIGEN CD26 / TP103 / ADENOSINE DEAMINASE COMPLEXING PROTEIN-2 / ADABP


Mass: 85452.570 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 29-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: KIDNEY / Plasmid: PFASTBACHTC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 CELLS / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Protein/peptide HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE / TRANSACTIVATING REGULATORY PROTEIN


Mass: 1029.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / References: UniProt: P12506
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1746 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 14 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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
#5: 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.: 2
Source method: isolated from a genetically manipulated 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
#6: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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.: 4
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

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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: 2.61 Å3/Da / Density % sol: 52.56 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 127470 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.1 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.1.1999refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N1M

1n1m


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.392 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.147 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 29 - 37 ARE DISORDERED AND WERE NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1297 1 %RANDOM
Rwork0.16 ---
obs0.16 127470 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2--
2---0.11 Å2-
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11990 0 364 1746 14100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02112735
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210841
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.95517354
X-RAY DIFFRACTIONr_angle_other_deg0.858325156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38451458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01224620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58152004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8871560
X-RAY DIFFRACTIONr_chiral_restr0.150.21887
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022678
X-RAY DIFFRACTIONr_nbd_refined0.2070.32144
X-RAY DIFFRACTIONr_nbd_other0.1890.310711
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.57131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.52041
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.338
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.540
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0411.59432
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.2031.52960
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06636650
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0484.55522
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 10908 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.485
loose thermal1.0510
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 90
Rwork0.202 8872
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)
11.3739-0.04990.06540.2899-0.08610.63310.02640.02190.07880.0125-0.0197-0.0581-0.05340.0494-0.0067-0.1848-0.00370.0129-0.29030.0109-0.299545.28254.8939.505
21.0067-0.11190.14440.3226-0.24250.53850.0038-0.0716-0.1091-0.01710.00950.06520.0689-0.1017-0.0133-0.1855-0.00840.0232-0.24850.0091-0.2452-10.5260.30531.977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 85
2X-RAY DIFFRACTION1A86 - 200
3X-RAY DIFFRACTION1A301 - 497
4X-RAY DIFFRACTION1A498 - 600
5X-RAY DIFFRACTION1A601 - 766
6X-RAY DIFFRACTION1A201 - 300
7X-RAY DIFFRACTION2B38 - 85
8X-RAY DIFFRACTION2B86 - 200
9X-RAY DIFFRACTION2B301 - 497
10X-RAY DIFFRACTION2B498 - 600
11X-RAY DIFFRACTION2B601 - 766
12X-RAY DIFFRACTION2B201 - 300

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