PDB Short entry for 1ZE9 HEADER METAL BINDING PROTEIN 18-APR-05 1ZE9 TITLE ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE TITLE 2 COMPLEXED WITH A ZINC (II) CATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 16-MER FROM ALZHEIMER'S DISEASE AMYLOID PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALZHEIMER'S DISEASE AMYLOID A4 PROTEIN, AMYLOID BETA A4 COMPND 5 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. KEYWDS PEPTIDE-ZINC COMPLEX, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.ZIRAH,S.A.KOZIN,A.K.MAZUR,A.BLOND,M.CHEMINANT,I.SEGALAS-MILAZZO, AUTHOR 2 P.DEBEY,S.REBUFFAT REVDAT 3 09-OCT-13 1ZE9 1 JRNL VERSN REVDAT 2 24-FEB-09 1ZE9 1 VERSN REVDAT 1 03-MAY-05 1ZE9 0 JRNL AUTH S.ZIRAH,S.A.KOZIN,A.K.MAZUR,A.BLOND,M.CHEMINANT, JRNL AUTH 2 I.SEGALAS-MILAZZO,P.DEBEY,S.REBUFFAT JRNL TITL STRUCTURAL CHANGES OF REGION 1-16 OF THE ALZHEIMER DISEASE JRNL TITL 2 AMYLOID BETA-PEPTIDE UPON ZINC BINDING AND IN VITRO AGING. JRNL REF J.BIOL.CHEM. V. 281 2151 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16301322 JRNL DOI 10.1074/JBC.M504454200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ICMD 2.7 REMARK 3 AUTHORS : ALEXEY K.MAZUR REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 305 RESTRAINTS, 282 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 6 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, AND 17 ZINC TETRAHEDRAL COORDINATION REMARK 3 CONSTRAINTS. REMARK 4 REMARK 4 1ZE9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-APR-05. REMARK 100 THE RCSB ID CODE IS RCSB032622. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.8MM IN 50MM SODIUM PHOSPHATE REMARK 210 BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D TOCSY; 2D NOESY; REMARK 210 HSQC; HMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.1, AURELIA 1.6, ICMD REMARK 210 2.7 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 2 SER A 8 41.58 -85.94 REMARK 500 3 ALA A 2 -163.04 -100.03 REMARK 500 3 GLU A 11 -166.57 -129.49 REMARK 500 4 PHE A 4 47.12 -95.52 REMARK 500 5 PHE A 4 43.41 -142.33 REMARK 500 6 PHE A 4 50.06 -144.32 REMARK 500 6 SER A 8 42.90 -84.36 REMARK 500 8 SER A 8 34.70 -85.62 REMARK 500 12 SER A 8 31.82 -87.39 REMARK 500 14 PHE A 4 49.97 -85.81 REMARK 500 15 PHE A 4 39.00 -145.93 REMARK 500 15 SER A 8 32.05 -85.42 REMARK 500 16 PHE A 4 41.66 -148.90 REMARK 500 16 HIS A 6 58.61 -119.52 REMARK 500 16 SER A 8 39.67 -85.01 REMARK 500 17 SER A 8 30.82 -85.90 REMARK 500 18 SER A 8 36.47 -83.09 REMARK 500 19 HIS A 6 46.56 -97.05 REMARK 500 19 SER A 8 30.07 -87.52 REMARK 500 20 PHE A 4 81.37 -155.00 REMARK 500 20 SER A 8 37.05 -88.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 19 ARG A 5 0.12 SIDE CHAIN 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 6 ND1 REMARK 620 2 GLU A 11 OE1 123.0 REMARK 620 3 GLU A 11 OE2 88.3 63.8 REMARK 620 4 HIS A 13 NE2 120.7 103.6 81.0 REMARK 620 5 HIS A 14 ND1 103.8 88.2 151.5 112.8 REMARK 620 N 1 2 3 4 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: 2BP4 RELATED DB: PDB REMARK 900 THE SAME PEPTIDE IN TFE/WATER 80/20 SOLUTION REMARK 900 RELATED ID: 1ZE7 RELATED DB: PDB REMARK 900 THE SAME PEPTIDE IN WATER SOLUTION AT PH 6.5 DBREF 1ZE9 A 1 16 UNP P05067 A4_HUMAN 672 687 SEQADV 1ZE9 ACE A 0 UNP P05067 ACETYLATION SEQADV 1ZE9 NH2 A 17 UNP P05067 AMIDATION SEQRES 1 A 18 ACE ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL SEQRES 2 A 18 HIS HIS GLN LYS NH2 HET ACE A 0 6 HET NH2 A 17 3 HET ZN A 18 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N FORMUL 2 ZN ZN 2+ HELIX 1 1 GLU A 11 GLN A 15 5 5 LINK ZN ZN A 18 ND1 HIS A 6 1555 1555 2.11 LINK ZN ZN A 18 OE1 GLU A 11 1555 1555 2.11 LINK ZN ZN A 18 OE2 GLU A 11 1555 1555 2.11 LINK ZN ZN A 18 NE2 HIS A 13 1555 1555 2.15 LINK ZN ZN A 18 ND1 HIS A 14 1555 1555 2.29 LINK C ACE A 0 N ASP A 1 1555 1555 1.33 LINK C LYS A 16 N NH2 A 17 1555 1555 1.33 SITE 1 AC1 4 HIS A 6 GLU A 11 HIS A 13 HIS A 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