10 20 30 40 50 60 70 80 1JY6 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DE NOVO PROTEIN 11-SEP-01 1JY6
TITLE B4DIMERA: A DE NOVO DESIGNED FOUR-STRANDED BETA-SHEET TITLE 2 ASSEMBLED USING 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 KEYWDS 2 DESIGN
EXPDTA SOLUTION NMR
NUMMDL 19
AUTHOR J.VENKATRAMAN,G.A.NAGANA GOWDA,P.BALARAM
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 JRNL TITL 2 BETA-SHEET POLYPEPTIDE STABILIZED BY A DISULFIDE JRNL TITL 3 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : GUENTERT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE NINETEEN STRUCTURES WERE REMARK 3 DETERMINED BY NMR AND TORSION ANGLE DYNAMICS/SIMULATED REMARK 3 ANNEALING METHODS. THE PEPTIDE DIMER WAS TREATED AS A SINGLE REMARK 3 ENTITY AND SYMMETRY ELEMENTS WERE NOT UTILIZED DURING REMARK 3 STRUCTURE CALCULATIONS. THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 276 NOE-DERIVED RESTRAINTS. THE LIST OF CONSTRAINTS IS REMARK 3 AVAILABLE IN THE FILE WATER_UPPERCONS.TXT. STRUCTURE REMARK 3 CALCULATIONS WERE PERFORMED WITH THE PROGRAM DYANA-1.5 (P. REMARK 3 GUENTERT, C. MUMENTHALER, K. WUTHRICH, J. MOL. BIOL.(1997) REMARK 3 VOL.273, 283-298). NO VIOLATION OF DISTANCE CONSTRAINTS FROM REMARK 3 NOES EXCEEDED 0.3ANGSTROMS. THE ENSEMBLE OF STRUCTURES IS REMARK 3 SUPERIMPOSED OVER THE BEST-STRUCTURED REGION ENCOMPASING REMARK 3 RESIDUES V19-L34. RESIDUES 1-11 WERE UNSTRUCTURED AND THEIR CO REMARK 3 -ORDINATES ARE NOT GIVEN. THE AVERAGE RMSDS BETWEEN THE REMARK 3 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 RCSB ID CODE IS RCSB014322.
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 : DYANA 1.5 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, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 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 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(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 9 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 LEU B 34 66.45 -118.35 REMARK 500 3 ALA A 13 146.70 -172.87 REMARK 500 4 LEU A 34 76.09 -116.39 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 13 LYS A 21 76.12 -113.56 REMARK 500 14 LYS B 21 74.68 -111.36 REMARK 500 15 ALA A 13 123.45 179.60 REMARK 500 15 PHE A 24 73.66 -165.21 REMARK 500 16 ALA A 13 68.97 73.27 REMARK 500 16 TYR A 29 168.59 167.71 REMARK 500 17 ALA A 13 70.49 -109.31 REMARK 500 17 LEU A 14 65.92 -109.07 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 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 REMARK 900 ASSEMBLED 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
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 1.000 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