HEADER DE NOVO PROTEIN 11-SEP-01 1JY6 TITLE B4DIMERA: A DE NOVO DESIGNED FOUR-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 IS CHEMICALLY SYNTHESIZED. KEYWDS FOUR-STRANDED BETA-SHEET, DISULFIDE BOND, DE NOVO PROTEIN DESIGN, DE KEYWDS 2 NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR J.VENKATRAMAN,G.A.NAGANA GOWDA,P.BALARAM REVDAT 3 23-FEB-22 1JY6 1 REMARK LINK REVDAT 2 24-FEB-09 1JY6 1 VERSN REVDAT 1 12-JUN-02 1JY6 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: THE NINETEEN STRUCTURES WERE DETERMINED REMARK 3 BY NMR AND TORSION ANGLE DYNAMICS/SIMULATED ANNEALING METHODS. REMARK 3 THE PEPTIDE DIMER WAS TREATED AS A SINGLE ENTITY AND SYMMETRY REMARK 3 ELEMENTS WERE NOT UTILIZED DURING STRUCTURE CALCULATIONS. THE REMARK 3 STRUCTURES ARE BASED ON A TOTAL OF 276 NOE-DERIVED RESTRAINTS. REMARK 3 THE LIST OF CONSTRAINTS IS AVAILABLE IN THE FILE WATER_ REMARK 3 UPPERCONS.TXT. STRUCTURE CALCULATIONS WERE PERFORMED WITH THE REMARK 3 PROGRAM DYANA-1.5 (P. GUENTERT, C. MUMENTHALER, K. WUTHRICH, J. REMARK 3 MOL. BIOL.(1997)VOL.273, 283-298). NO VIOLATION OF DISTANCE REMARK 3 CONSTRAINTS FROM NOES EXCEEDED 0.3ANGSTROMS. THE ENSEMBLE OF REMARK 3 STRUCTURES IS SUPERIMPOSED OVER THE BEST-STRUCTURED REGION REMARK 3 ENCOMPASING RESIDUES V19-L34. RESIDUES 1-11 WERE UNSTRUCTURED REMARK 3 AND THEIR CO-ORDINATES ARE NOT GIVEN. THE AVERAGE RMSDS BETWEEN REMARK 3 THE SUPERPOSED STRUCTURES AND THE AVERAGE STRUCTURE ARE AS REMARK 3 FOLLOWS: 1.04(CHAIN A, RESIDUES 20-34, BACKBONE ATOMS) REMARK 3 0.91(CHAIN B, RESIDUES 20-34, BACKBONE ATOMS). REMARK 4 REMARK 4 1JY6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014322. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 323 REMARK 210 PH : 3.5 REMARK 210 IONIC STRENGTH : UNBUFFERED REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM B4DIMER, REMARK 210 TRIMETHYLSILYLPROPIONATE, 90% REMARK 210 H2O, 10% D2O 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 : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19 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 : 2 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-19 REMARK 465 RES C SSSEQI REMARK 465 ARG A 1 REMARK 465 GLY A 2 REMARK 465 GLU A 3 REMARK 465 CYS A 4 REMARK 465 LYS A 5 REMARK 465 PHE A 6 REMARK 465 THR A 7 REMARK 465 VAL A 8 REMARK 465 DPR A 9 REMARK 465 GLY A 10 REMARK 465 ARG A 11 REMARK 465 ARG B 1 REMARK 465 GLY B 2 REMARK 465 GLU B 3 REMARK 465 CYS B 4 REMARK 465 LYS B 5 REMARK 465 PHE B 6 REMARK 465 THR B 7 REMARK 465 VAL B 8 REMARK 465 DPR B 9 REMARK 465 GLY B 10 REMARK 465 ARG B 11 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-19 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLU A 32 CD 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 ASN A 15 93.05 -50.31 REMARK 500 1 ALA A 18 -125.84 -61.66 REMARK 500 1 LEU B 34 66.45 -118.35 REMARK 500 2 ALA A 18 -49.23 -146.32 REMARK 500 2 ALA B 18 -149.51 -60.69 REMARK 500 3 ALA A 13 146.70 -172.87 REMARK 500 3 ALA A 18 -158.32 -58.12 REMARK 500 3 ALA B 18 -74.81 -65.92 REMARK 500 4 LEU A 34 76.09 -116.39 REMARK 500 5 ALA B 18 -90.08 -44.13 REMARK 500 6 LEU A 14 82.38 -150.88 REMARK 500 6 TRP A 22 130.79 167.61 REMARK 500 7 ALA A 13 75.86 176.16 REMARK 500 7 LYS A 21 59.88 -115.89 REMARK 500 7 LYS B 21 77.58 -119.13 REMARK 500 7 LYS B 30 75.99 -119.70 REMARK 500 7 LEU B 34 77.71 -119.78 REMARK 500 11 VAL A 25 75.36 -118.44 REMARK 500 11 ASN B 15 70.78 -113.91 REMARK 500 11 GLN B 20 85.13 -159.53 REMARK 500 11 ILE B 33 73.60 -106.47 REMARK 500 12 ALA A 18 30.25 -165.32 REMARK 500 13 LYS A 21 76.12 -113.56 REMARK 500 13 LEU A 26 79.92 -161.23 REMARK 500 13 ALA B 18 35.98 -176.80 REMARK 500 14 ALA A 18 -74.78 -134.60 REMARK 500 14 ALA B 18 -72.68 -43.55 REMARK 500 14 LYS B 21 74.68 -111.36 REMARK 500 15 ALA A 13 123.45 179.60 REMARK 500 15 ALA A 18 -72.68 -51.89 REMARK 500 15 PHE A 24 73.66 -165.21 REMARK 500 16 ALA A 13 68.97 73.27 REMARK 500 16 LEU A 26 51.95 -148.02 REMARK 500 16 DPR A 27 162.66 75.00 REMARK 500 16 TYR A 29 168.59 167.71 REMARK 500 16 THR B 16 77.64 -113.12 REMARK 500 17 ALA A 13 70.49 -109.31 REMARK 500 17 LEU A 14 65.92 -109.07 REMARK 500 17 ALA A 18 -70.60 -41.51 REMARK 500 17 LEU A 26 82.91 -153.04 REMARK 500 17 THR B 16 77.79 -114.38 REMARK 500 17 LEU B 26 73.58 -118.64 REMARK 500 18 ILE B 33 70.66 -107.50 REMARK 500 19 ALA A 13 70.49 -109.31 REMARK 500 19 LEU A 14 65.92 -109.07 REMARK 500 19 ALA A 18 -70.60 -41.51 REMARK 500 19 LEU A 26 82.91 -153.04 REMARK 500 19 THR B 16 77.79 -114.38 REMARK 500 19 LEU B 26 73.58 -118.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JY4 RELATED DB: PDB REMARK 900 B4DIMER: A DE NOVO DESIGNED EIGHT-STRANDED BETA-SHEET ASSEMBLED REMARK 900 USING A DISULFIDE BOND DBREF 1JY6 A 1 35 PDB 1JY6 1JY6 1 35 DBREF 1JY6 B 1 35 PDB 1JY6 1JY6 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 1JY6 DPR A 17 PRO D-PROLINE MODRES 1JY6 DPR A 27 PRO D-PROLINE MODRES 1JY6 DPR B 17 PRO D-PROLINE MODRES 1JY6 DPR B 27 PRO D-PROLINE HET DPR A 17 14 HET DPR A 27 14 HET DPR B 17 14 HET DPR B 27 14 HETNAM DPR D-PROLINE FORMUL 1 DPR 4(C5 H9 N O2) SHEET 1 A 5 HIS A 23 LEU A 26 0 SHEET 2 A 5 TYR A 29 GLU A 32 -1 O TYR A 29 N LEU A 26 SHEET 3 A 5 TYR B 29 ILE B 33 -1 O LYS B 30 N GLU A 32 SHEET 4 A 5 LYS B 21 LEU B 26 -1 N PHE B 24 O CYS B 31 SHEET 5 A 5 ALA B 13 LEU B 14 -1 N LEU B 14 O LYS B 21 SSBOND 1 CYS A 31 CYS B 31 1555 1555 2.04 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 THR B 16 N DPR B 17 1555 1555 1.36 LINK C DPR B 17 N ALA B 18 1555 1555 1.33 LINK C LEU B 26 N DPR B 27 1555 1555 1.36 LINK C DPR B 27 N GLY B 28 1555 1555 1.33 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