HEADER DE NOVO PROTEIN 11-SEP-01 1JY4 TITLE B4DIMER: A DE NOVO DESIGNED EIGHT-STRANDED BETA-SHEET ASSEMBLED USING TITLE 2 A DISULFIDE BOND COMPND MOL_ID: 1; COMPND 2 MOLECULE: B4DIMER; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS EIGHT-STRANDED BETA-SHEET, DISULFIDE BOND, DE NOVO PROTEIN DESIGN, DE KEYWDS 2 NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.VENKATRAMAN,G.A.NAGANA GOWDA,P.BALARAM REVDAT 3 23-FEB-22 1JY4 1 REMARK LINK REVDAT 2 24-FEB-09 1JY4 1 VERSN REVDAT 1 12-JUN-02 1JY4 0 JRNL AUTH J.VENKATRAMAN,G.A.NAGANA GOWDA,P.BALARAM JRNL TITL DESIGN AND CONSTRUCTION OF AN OPEN MULTISTRANDED BETA-SHEET JRNL TITL 2 POLYPEPTIDE STABILIZED BY A DISULFIDE BRIDGE. JRNL REF J.AM.CHEM.SOC. V. 124 4987 2002 JRNL REFN ISSN 0002-7863 JRNL PMID 11982362 JRNL DOI 10.1021/JA0174276 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, DYANA 1.5 REMARK 3 AUTHORS : GUENTERT (DYANA), GUENTERT (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE TEN STRUCTURES WERE DETERMINED BY NMR AND TORSION ANGLE REMARK 3 DYNAMICS/SIMULATED ANNEALING METHODS. THE PEPTIDE DIMER WAS REMARK 3 TREATED AS A SINGLE ENTITY AND SYMMETRY ELEMENTS WERE NOT UTILIZED REMARK 3 DURING STRUCTURE CALCULATIONS. THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 446 RESTRAINTS, 398 ARE NOE-DERIVED DISTANCE CONSTRAINTS,48 REMARK 3 DISTANCE RESTRAINTS ARE FROM HYDROGEN BONDS. THE LIST OF REMARK 3 CONSTRAINTS IS AVAILABLE IN THE FILE DYANA_UPPERCONST.TXT. REMARK 3 STRUCTURE CALCULATIONS WERE PERFORMED WITH THE PROGRAM DYANA-1.5 REMARK 3 (P. GUENTERT, C. MUMENTHALER, K. WUTHRICH, J. MOL. BIOL.(1997) REMARK 3 VOL.273, 283-298). NO VIOLATION OF DISTANCE CONSTRAINTS FROM NOES REMARK 3 EXCEEDED 0.3ANGSTROMS. REMARK 3 THE ENSEMBLE OF STRUCTURES IS SUPERIMPOSED OVER THE BEST- REMARK 3 STRUCTURED REGION ENCOMPASING RESIDUES E11-L34. THE AVERAGE RMSDS REMARK 3 BETWEEN THE SUPERPOSED STRUCTURES AND THE AVERAGE STRUCTURE ARE AS REMARK 3 FOLLOWS: REMARK 3 0.75(CHAIN A, RESIDUES 11-34, BACKBONE ATOMS) REMARK 3 0.72(CHAIN B, RESIDUES 11-34, BACKBONE ATOMS. REMARK 4 REMARK 4 1JY4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014320. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : UNBUFFERED REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM B4DIMER, CD3OH REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS/ REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 8 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: 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 2 GLU A 3 35.09 -154.44 REMARK 500 2 LYS A 5 -140.11 -111.15 REMARK 500 2 VAL A 25 79.25 -116.65 REMARK 500 2 LEU A 34 67.22 -117.78 REMARK 500 3 GLU B 3 65.89 -116.09 REMARK 500 3 LYS B 5 -141.47 -119.48 REMARK 500 4 DPR A 9 -27.40 74.95 REMARK 500 4 LEU A 34 56.85 -115.94 REMARK 500 4 ALA B 18 17.60 91.54 REMARK 500 5 GLU A 3 73.72 -116.26 REMARK 500 5 CYS A 4 42.57 -150.03 REMARK 500 5 CYS B 4 63.93 -119.64 REMARK 500 5 DPR B 9 -23.08 74.85 REMARK 500 6 DPR A 9 -30.42 75.06 REMARK 500 6 ALA A 18 27.55 -160.65 REMARK 500 6 LEU A 26 89.34 -150.60 REMARK 500 6 CYS B 4 75.64 -115.70 REMARK 500 6 DPR B 17 -31.96 74.97 REMARK 500 6 ALA B 18 -27.97 162.30 REMARK 500 7 ALA A 18 21.68 91.14 REMARK 500 7 LEU A 34 53.96 -109.99 REMARK 500 7 LEU B 34 67.92 -114.41 REMARK 500 8 GLU A 3 67.94 -117.50 REMARK 500 9 THR A 7 65.88 -118.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JY6 RELATED DB: PDB REMARK 900 B4DIMERA: A DE NOVO DESIGNED FOUR-STRANDED BETA-SHEET ASSEMBLED REMARK 900 USING A DISULFIDE BOND DBREF 1JY4 A 1 35 PDB 1JY4 1JY4 1 35 DBREF 1JY4 B 1 35 PDB 1JY4 1JY4 1 35 SEQRES 1 A 35 ARG GLY GLU CYS LYS PHE THR VAL DPR GLY ARG THR ALA SEQRES 2 A 35 LEU ASN THR DPR ALA VAL GLN LYS TRP HIS PHE VAL LEU SEQRES 3 A 35 DPR GLY TYR LYS CYS GLU ILE LEU ALA SEQRES 1 B 35 ARG GLY GLU CYS LYS PHE THR VAL DPR GLY ARG THR ALA SEQRES 2 B 35 LEU ASN THR DPR ALA VAL GLN LYS TRP HIS PHE VAL LEU SEQRES 3 B 35 DPR GLY TYR LYS CYS GLU ILE LEU ALA MODRES 1JY4 DPR A 9 PRO D-PROLINE MODRES 1JY4 DPR A 17 PRO D-PROLINE MODRES 1JY4 DPR A 27 PRO D-PROLINE MODRES 1JY4 DPR B 9 PRO D-PROLINE MODRES 1JY4 DPR B 17 PRO D-PROLINE MODRES 1JY4 DPR B 27 PRO D-PROLINE HET DPR A 9 14 HET DPR A 17 14 HET DPR A 27 14 HET DPR B 9 14 HET DPR B 17 14 HET DPR B 27 14 HETNAM DPR D-PROLINE FORMUL 1 DPR 6(C5 H9 N O2) SHEET 1 A 8 LYS A 5 VAL A 8 0 SHEET 2 A 8 ARG A 11 THR A 16 -1 O ALA A 13 N PHE A 6 SHEET 3 A 8 VAL A 19 LEU A 26 -1 O VAL A 19 N THR A 16 SHEET 4 A 8 TYR A 29 ALA A 35 -1 O CYS A 31 N PHE A 24 SHEET 5 A 8 TYR B 29 ALA B 35 -1 O GLU B 32 N LYS A 30 SHEET 6 A 8 VAL B 19 LEU B 26 -1 N GLN B 20 O ALA B 35 SHEET 7 A 8 ARG B 11 THR B 16 -1 N THR B 12 O HIS B 23 SHEET 8 A 8 LYS B 5 VAL B 8 -1 N VAL B 8 O ARG B 11 SSBOND 1 CYS A 31 CYS B 31 1555 1555 2.00 LINK C VAL A 8 N DPR A 9 1555 1555 1.36 LINK C DPR A 9 N GLY A 10 1555 1555 1.32 LINK C THR A 16 N DPR A 17 1555 1555 1.36 LINK C DPR A 17 N ALA A 18 1555 1555 1.33 LINK C LEU A 26 N DPR A 27 1555 1555 1.36 LINK C DPR A 27 N GLY A 28 1555 1555 1.33 LINK C VAL B 8 N DPR B 9 1555 1555 1.36 LINK C DPR B 9 N GLY B 10 1555 1555 1.32 LINK C THR B 16 N DPR B 17 1555 1555 1.36 LINK C DPR B 17 N ALA B 18 1555 1555 1.32 LINK C LEU B 26 N DPR B 27 1555 1555 1.36 LINK C DPR B 27 N GLY B 28 1555 1555 1.32 CRYST1 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