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- PDB-1e1r: BOVINE MITOCHONDRIAL F1-ATPASE INHIBITED BY MG2+ADP AND ALUMINIUM... -

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Basic information

Entry
Database: PDB / ID: 1e1r
TitleBOVINE MITOCHONDRIAL F1-ATPASE INHIBITED BY MG2+ADP AND ALUMINIUM FLUORIDE
Components(BOVINE MITOCHONDRIAL F1- ...) x 3
KeywordsATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit ...ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / ATP synthase subunit beta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBraig, K. / Menz, R.I. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
Citation
Journal: Structure / Year: 2000
Title: Structure of Bovine Mitochondrial F1-ATPase Inhibited by Mg2+Adp and Aluminium Fluoride
Authors: Braig, K. / Menz, R.I. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
#1: Journal: Nature / Year: 1994
Title: Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria
Authors: Abrahams, J.P. / Leslie, A.G.W. / Lutter, R. / Walker, J.E.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of F1-ATPase from Bovine Heart Mitochondria
Authors: Lutter, R. / Abrahams, J.P. / Van Raaij, M.J. / Todd, R.J. / Lundqvist, T. / Buchanan, S.K. / Leslie, A.G. / Walker, J.E.
#3: Journal: Embo J. / Year: 1993
Title: Inherent Asymmetry of the Structure of F1-ATPase from Bovine Heart Mitochondria at 6.5 A Resolution
Authors: Abrahams, J.P. / Lutter, R. / Todd, R.J. / Van Raaij, M.J. / Leslie, A.G. / Walker, J.E.
History
DepositionMay 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 6, 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_asym_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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.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: BOVINE MITOCHONDRIAL F1-ATPASE
B: BOVINE MITOCHONDRIAL F1-ATPASE
C: BOVINE MITOCHONDRIAL F1-ATPASE
D: BOVINE MITOCHONDRIAL F1-ATPASE
E: BOVINE MITOCHONDRIAL F1-ATPASE
F: BOVINE MITOCHONDRIAL F1-ATPASE
G: BOVINE MITOCHONDRIAL F1-ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,11519
Polymers351,3637
Non-polymers2,75212
Water15,493860
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35690 Å2
ΔGint-159.8 kcal/mol
Surface area126380 Å2
MethodPQS
Unit cell
Length a, b, c (Å)278.600, 106.700, 137.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE F1-ATPASE MOLECULE HAS THREE COPIES OF THENON-CATALYTIC ALPHA SUBUNIT AND THREE COPIES OF THECATALYTIC BETA SUBUNIT.IN THE PRIMARY REFERENCE, THE BETA SUBUNITS WERE LABELEDACCORDING TO THE BOUND NUCLEOTIDE, AS,BETA(DP) (BINDS ADP ),BETA(E) (NO BOUND NUCLEOTIDE) ANDBETA(TP) ( AMPPNP BOUND).THE ALPHA SUBUNITS (WHICH ALL BIND AMPPNP) CONTRIBUTE TOTHE CATALYTIC SITES OF THE BETA SUBUNITS, AND HAVE BEENLABELED ACCORDINGLY. THUS,ALPHA(DP) CONTRIBUTES TO THE CATALYTIC SITE ON BETA(DP),ALPHA(TP) TO THE SITE ON BETA ( TP) ANDALPHA(E) TO THE SITE ON BETA(E).THE CORRESPONDENCE BETWEEN THE SUBUNIT NAMES AND THE CHAINIDENTIFIERS IS GIVEN BELOW:.CHAIN A: ALPHA(E )CHAIN B: ALPHA(TP)CHAIN C: ALPHA(DP)CHAIN D : BETA(DP)CHAIN E: BETA(E)CHAIN F: BETA(TP) CHAIN G: GAMMA SUBUNIT

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Components

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BOVINE MITOCHONDRIAL F1- ... , 3 types, 7 molecules ABCDEFG

#1: Protein BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE ALPHA CHAIN HEART ISOFORM


Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P19483, EC: 3.6.1.34
#2: Protein BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE BETA CHAIN


Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00829, EC: 3.6.1.34
#3: Protein BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE GAMMA CHAIN


Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P05631, EC: 3.6.1.34

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Non-polymers , 6 types, 872 molecules

#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details1BMF A SWS P19483 1 - 66 NOT IN ATOMS LIST 1BMF B SWS P19483 1 - 66 NOT IN ATOMS LIST 1BMF C SWS ...1BMF A SWS P19483 1 - 66 NOT IN ATOMS LIST 1BMF B SWS P19483 1 - 66 NOT IN ATOMS LIST 1BMF C SWS P19483 1 - 61 NOT IN ATOMS LIST 1BMF D SWS P00829 1 - 58 NOT IN ATOMS LIST 1BMF D SWS P00829 526 - 528 NOT IN ATOMS LIST 1BMF E SWS P00829 1 - 58 NOT IN ATOMS LIST 1BMF E SWS P00829 525 - 528 NOT IN ATOMS LIST 1BMF F SWS P00829 1 - 58 NOT IN ATOMS LIST 1BMF F SWS P00829 525 - 528 NOT IN ATOMS LIST 1BMF G SWS P05631 1 - 25 NOT IN ATOMS LIST 1BMF G SWS P05631 298 - 298 NOT IN ATOMS LIST REFERENCE: 1) FOR THE ALPHA SUBUNIT: J. E. WALKER, S. J. POWELL, O. VINAS AND M. J. RUNSWICK, BIOCHEMISTRY VOL 28, PP 4702-4708, 1989. 2) FOR THE GAMMA SUBUNIT: M. R. DYER, N. J. GAY, S. J. POWELL AND J.E. WALKER, BIOCHEMISTRY VOL 28, PP 3670-3680, 1989. DIFFERENT RESIDUE: GLY A 481, GLY B 481, GLY C 481 THIS RESIDUE WAS IDENTIFIED AS A GLY FROM THE PROTEIN SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS RESIDUE WAS AGC (SER) IN THREE CLONES WHILE IN TWO OTHERS IT WAS GGC (GLY). THE DIFFERENCE WAS THOUGHT TO BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN THIS POSITION. DIFFERENT RESIDUE: ASP G 273 THIS RESIDUE IS NOT PRESENT IN THE BOVINE GAMMA SUBUNIT IN THE MATERIAL USED IN THIS STRUCTURE DETERMINATION. THERE IS NO CODON FOR AN ASP IN THE CDNA SEQUENCE, NO C-TERMINAL ASP WAS FOUND IN THE PROTEIN SEQUENCE FOR THE GAMMA SUBUNIT AS ISOLATED FROM BEEF HEART MITOCHONDRIA.

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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: 2.92 Å3/Da / Density % sol: 54 %
Description: 1BMF STRUCTURE WAS REFINED AGAINST DATA COLLECTED AT 277K, THIS DATA WAS COLLECTED AT 100K
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
pH: 8.2 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
199.9 %deuterium oxide11
2100 mMTris-HCl11
314 %(w/v)PEG600011
4400 mMsodium chloride11
52 mMEDTA11
60.04 %(w/v)sodium azide11
70.02 %(w/v)PMSF11
810 mMdithiothreitol11
98 mMmagnesium chloride11
100.5 mMAMP-PNP11
1110 mMADP11
1299.9 %deutrium oxide12
1350 mMTris-HCl12
149 %(w/v)PEG600012
15200 mMsodium chloride121 mM EDTA, 0.02%(w/v) sidium azide, 5mM 2-mercaptoethanol, 0.001% PMSF, 5mM dithiothreitol, 20mM magnesiumsulphate, 0.25mMAMP-PNP, 0.005mM ADP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 28, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.48→20 Å / Num. obs: 136913 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 2.34 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.5
Reflection shellResolution: 2.48→2.61 Å / Redundancy: 2 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.8 / % possible all: 74.6
Reflection
*PLUS
Num. measured all: 320630
Reflection shell
*PLUS
% possible obs: 74.6 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1E1Q, BOVINE MITOCHONDRIAL F1-ATPASE AT 100K

1e1q

100k


Resolution: 2.5→20 Å / SU B: 10.7 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.46 / ESU R Free: 0.31
Details: INITIAL REFINEMENT CARRIED OUT WITH TNT AND XPLOR RESIDUES B 402 - B 409 INCLUSIVE HAVE BEEN GIVEN ZERO OCCUPANCY AS THERE WAS NO INTERPRETABLE ELECTRON DENSITY IN THIS REGION. THE POSITIONS ...Details: INITIAL REFINEMENT CARRIED OUT WITH TNT AND XPLOR RESIDUES B 402 - B 409 INCLUSIVE HAVE BEEN GIVEN ZERO OCCUPANCY AS THERE WAS NO INTERPRETABLE ELECTRON DENSITY IN THIS REGION. THE POSITIONS OF SIDE CHAIN ATOMS WITH TEMPERATURE FACTORS GREATER THAN 75 IS UNCERTAIN. THE MAIN CHAIN CONFORMATION IS ALSO UNCERTAIN FOR REGIONS WITH TEMPERATURE FACTORS ABOVE 60. SOLVENT MOLECULES HAVE BEEN USED TO MODEL SOME FEATURES IN THE ELECTRON DENSITY THAT ARE PROBABLY DUE TO THE "MISSING" REGIONS OF THE GAMMA SUBUNIT (CHAIN G) THE PEPTIDE BOND BETWEEN ASP 269 AND ASP 270 IN CHAINS A, B, C AND THE PEPTIDE BOND BETWEEN ASP 256 AND ASN 257 IN CHAINS D, E, AND F HAVE BEEN MODELED IN A CIS CONFORMATION. RESIDUAL FEATURES IN THE ELECTRON DENSITY MAP SUGGEST THAT THERE IS SOME CONFORMATIONAL DISORDER IN ASP 270 IN CHAINS A, B, AND C. CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 6163 5 %RANDOM
Rwork0.218 ---
obs-129652 95 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22663 0 165 860 23688
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0230.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.0680.05
X-RAY DIFFRACTIONp_mcbond_it1.72.5
X-RAY DIFFRACTIONp_mcangle_it2.63.5
X-RAY DIFFRACTIONp_scbond_it4.75
X-RAY DIFFRACTIONp_scangle_it66
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.110.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.210.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.190.3
X-RAY DIFFRACTIONp_planar_tor3.17
X-RAY DIFFRACTIONp_staggered_tor16.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.520
X-RAY DIFFRACTIONp_special_tor

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