HEADER CELL ADHESION 25-AUG-11 2LI9 TITLE METAL BINDING DOMAIN OF RAT BETA-AMYLOID COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 672-687; COMPND 5 SYNONYM: ABPP, APP, ALZHEIMER DISEASE AMYLOID A4 PROTEIN HOMOLOG, COMPND 6 AMYLOIDOGENIC GLYCOPROTEIN, AG; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 4 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 5 ORGANISM_TAXID: 10116 KEYWDS ALZHEIMER'S DISEASE, DIMER FORMATION, ZINC BINDING, CELL ADHESION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR V.POLSHAKOV,A.ISTRATE,S.KOZIN,A.MAKAROV REVDAT 2 21-MAR-12 2LI9 1 JRNL REVDAT 1 18-JAN-12 2LI9 0 JRNL AUTH A.N.ISTRATE,P.O.TSVETKOV,A.B.MANTSYZOV,A.A.KULIKOVA, JRNL AUTH 2 S.A.KOZIN,A.A.MAKAROV,V.I.POLSHAKOV JRNL TITL NMR SOLUTION STRUCTURE OF RAT ABETA(1-16): TOWARD JRNL TITL 2 UNDERSTANDING THE MECHANISM OF RATS' RESISTANCE TO JRNL TITL 3 ALZHEIMER'S DISEASE. JRNL REF BIOPHYS.J. V. 102 136 2012 JRNL REFN ISSN 0006-3495 JRNL PMID 22225807 JRNL DOI 10.1016/J.BPJ.2011.11.4006 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.N.ISTRATE,A.B.MANTSYZOV,S.A.KOZIN,V.I.POL'SHAKOV REMARK 1 TITL OPTIMIZATION OF THE METHODS FOR SMALL PEPTIDE SOLUTION REMARK 1 TITL 2 STRUCTURE DETERMINATION BY NMR SPECTROSCOPY. REMARK 1 REF MOL.BIOL.(MOSCOW) V. 44 1075 2010 REMARK 1 REFN ISSN 0026-8984 REMARK 1 PMID 21290829 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS, GROMACS/CPMD REMARK 3 AUTHORS : VAN DER SPOEL ET AL. (GROMACS), BISWAS & GOGONEA REMARK 3 (GROMACS/CPMD) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATION IN EXPLICIT WATER ENVIRONMENT REMARK 4 REMARK 4 2LI9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-11. REMARK 100 THE RCSB ID CODE IS RCSB102417. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.1 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5 MM PROTEIN_1, 8 MM ZINC REMARK 210 CLORIDE, 20 MM [U-100% 2H] TRIS, REMARK 210 0.1 % SODIUM AZIDE, 90% H2O/10% REMARK 210 D2O; 5 MM PROTEIN_1, 8 MM ZINC REMARK 210 CLORIDE, 20 MM [U-100% 2H] TRIS, REMARK 210 0.1 % SODIUM AZIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D DQF-COSY; 2D REMARK 210 1H-1H NOESY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, SPARKY, REMARK 210 ANGLESEARCH, GROMACS 3.3.1, REMARK 210 GROMACS/CPMD, PROCHECKNMR, REMARK 210 INSIGHTII REMARK 210 METHOD USED : SIMULATED ANNEALING, QM/MM REMARK 210 GEOMETRY OPTIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ALA A 2 -19.78 -163.12 REMARK 500 1 ASP A 7 -62.71 -101.09 REMARK 500 1 SER A 8 -128.52 -147.48 REMARK 500 1 GLU A 11 -54.71 -159.08 REMARK 500 1 HIS A 14 127.97 -36.79 REMARK 500 1 ALA B 2 -7.44 -145.65 REMARK 500 1 SER B 8 -134.22 -177.94 REMARK 500 1 GLU B 11 -54.25 -162.01 REMARK 500 2 ALA A 2 -21.72 -164.54 REMARK 500 2 SER A 8 -146.94 -167.12 REMARK 500 2 GLU A 11 -53.12 -172.08 REMARK 500 2 SER B 8 -93.06 -159.75 REMARK 500 2 PHE B 10 -124.36 -69.11 REMARK 500 3 ALA A 2 -25.57 -167.34 REMARK 500 3 GLU A 11 -50.12 -161.52 REMARK 500 3 ARG A 13 -176.33 -66.65 REMARK 500 3 ALA B 2 -2.62 -143.74 REMARK 500 3 SER B 8 -126.83 -167.86 REMARK 500 3 GLU B 11 -35.59 -147.45 REMARK 500 4 ALA A 2 -27.62 -164.13 REMARK 500 4 SER A 8 -84.85 -160.05 REMARK 500 4 GLU A 11 -48.58 -154.03 REMARK 500 4 ALA B 2 -19.13 -150.79 REMARK 500 4 ASP B 7 -71.72 -76.87 REMARK 500 4 SER B 8 -81.58 -163.50 REMARK 500 5 ALA A 2 -18.23 -162.04 REMARK 500 5 SER A 8 -144.29 -168.23 REMARK 500 5 GLU A 11 -44.22 -155.57 REMARK 500 5 ALA B 2 -15.19 -157.16 REMARK 500 5 SER B 8 -141.34 -174.86 REMARK 500 5 ARG B 13 -158.65 -79.46 REMARK 500 6 ALA A 2 -14.70 80.64 REMARK 500 6 SER A 8 -130.42 -158.87 REMARK 500 6 GLU A 11 -38.01 -131.28 REMARK 500 6 ALA B 2 -34.77 -146.34 REMARK 500 6 SER B 8 -130.23 -174.21 REMARK 500 6 GLU B 11 -62.48 -153.40 REMARK 500 7 ALA A 2 -14.63 -159.68 REMARK 500 7 SER A 8 -158.70 -175.91 REMARK 500 7 GLU A 11 -60.67 -170.48 REMARK 500 7 ALA B 2 -8.56 -150.07 REMARK 500 7 SER B 8 -122.75 -157.07 REMARK 500 7 PHE B 10 -88.23 -95.00 REMARK 500 7 GLN B 15 -17.56 -170.54 REMARK 500 8 ALA A 2 -27.48 -158.38 REMARK 500 8 SER A 8 -138.65 54.77 REMARK 500 8 GLU A 11 -51.44 -163.34 REMARK 500 8 ALA B 2 -18.94 -152.62 REMARK 500 8 SER B 8 -124.93 -167.71 REMARK 500 8 GLU B 11 -34.89 -156.75 REMARK 500 REMARK 500 THIS ENTRY HAS 128 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 11 VAL A 12 1 145.38 REMARK 500 GLU B 11 VAL B 12 1 147.08 REMARK 500 GLU A 11 VAL A 12 2 135.76 REMARK 500 HIS A 6 ASP A 7 3 146.74 REMARK 500 GLU A 11 VAL A 12 3 145.65 REMARK 500 GLU B 11 VAL B 12 3 142.93 REMARK 500 GLU A 11 VAL A 12 4 145.48 REMARK 500 GLU A 11 VAL A 12 5 147.68 REMARK 500 GLU A 11 VAL A 12 6 147.59 REMARK 500 GLU B 11 VAL B 12 6 147.51 REMARK 500 GLU A 11 VAL A 12 7 149.64 REMARK 500 HIS A 6 ASP A 7 8 149.77 REMARK 500 GLU A 11 VAL A 12 8 147.55 REMARK 500 GLU B 11 VAL B 12 8 145.42 REMARK 500 GLU A 11 VAL A 12 9 143.97 REMARK 500 HIS B 6 ASP B 7 9 128.52 REMARK 500 GLU B 11 VAL B 12 9 148.22 REMARK 500 HIS A 6 ASP A 7 10 143.92 REMARK 500 GLU A 11 VAL A 12 10 149.20 REMARK 500 HIS A 6 ASP A 7 11 139.46 REMARK 500 GLU A 11 VAL A 12 11 144.64 REMARK 500 GLU A 11 VAL A 12 12 147.69 REMARK 500 GLU B 11 VAL B 12 12 144.94 REMARK 500 GLU A 11 VAL A 12 13 145.82 REMARK 500 GLU A 11 VAL A 12 14 143.87 REMARK 500 GLU B 11 VAL B 12 14 149.44 REMARK 500 GLU A 11 VAL A 12 15 147.71 REMARK 500 GLU B 11 VAL B 12 15 140.21 REMARK 500 ASP A 7 SER A 8 16 -145.69 REMARK 500 GLU A 11 VAL A 12 16 144.99 REMARK 500 GLU B 11 VAL B 12 16 146.88 REMARK 500 HIS A 6 ASP A 7 17 -147.60 REMARK 500 GLU B 11 VAL B 12 17 146.09 REMARK 500 GLU A 11 VAL A 12 18 146.83 REMARK 500 GLU B 11 VAL B 12 18 146.50 REMARK 500 GLU A 11 VAL A 12 19 148.33 REMARK 500 HIS B 6 ASP B 7 19 147.82 REMARK 500 GLU A 11 VAL A 12 20 143.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 18 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 14 NE2 REMARK 620 2 HIS B 14 NE2 106.4 REMARK 620 3 HIS A 6 ND1 115.0 106.8 REMARK 620 4 HIS B 6 ND1 109.0 113.4 106.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 18 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZE7 RELATED DB: PDB REMARK 900 RELATED ID: 17884 RELATED DB: BMRB DBREF 2LI9 A 1 16 UNP P08592 A4_RAT 672 687 DBREF 2LI9 B 1 16 UNP P08592 A4_RAT 672 687 SEQADV 2LI9 ACE A 0 UNP P08592 ACETYLATION SEQADV 2LI9 NH2 A 17 UNP P08592 AMIDATION SEQADV 2LI9 ACE B 0 UNP P08592 ACETYLATION SEQADV 2LI9 NH2 B 17 UNP P08592 AMIDATION SEQRES 1 A 18 ACE ASP ALA GLU PHE GLY HIS ASP SER GLY PHE GLU VAL SEQRES 2 A 18 ARG HIS GLN LYS NH2 SEQRES 1 B 18 ACE ASP ALA GLU PHE GLY HIS ASP SER GLY PHE GLU VAL SEQRES 2 B 18 ARG HIS GLN LYS NH2 HET ACE A 0 6 HET NH2 A 17 3 HET ACE B 0 6 HET NH2 B 17 3 HET ZN A 18 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 NH2 2(H2 N) FORMUL 3 ZN ZN 2+ LINK C ACE A 0 N ASP A 1 1555 1555 1.34 LINK C LYS A 16 N NH2 A 17 1555 1555 1.33 LINK C ACE B 0 N ASP B 1 1555 1555 1.34 LINK C LYS B 16 N NH2 B 17 1555 1555 1.34 LINK NE2 HIS A 14 ZN ZN A 18 1555 1555 2.08 LINK NE2 HIS B 14 ZN ZN A 18 1555 1555 2.08 LINK ND1 HIS A 6 ZN ZN A 18 1555 1555 2.13 LINK ND1 HIS B 6 ZN ZN A 18 1555 1555 2.13 SITE 1 AC1 6 HIS A 6 SER A 8 HIS A 14 HIS B 6 SITE 2 AC1 6 SER B 8 HIS B 14 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 HETATM 1 C ACE A 0 32.247 14.458 21.636 1.00 0.00 C HETATM 2 O ACE A 0 32.264 13.490 20.877 1.00 0.00 O HETATM 3 CH3 ACE A 0 33.524 15.267 21.825 1.00 0.00 C HETATM 4 H1 ACE A 0 33.301 16.244 22.243 1.00 0.00 H HETATM 5 H2 ACE A 0 34.195 14.735 22.499 1.00 0.00 H HETATM 6 H3 ACE A 0 34.007 15.406 20.859 1.00 0.00 H