1JY4 - Header Asymmetric Unit

HEADER DE NOVO PROTEIN 11-SEP-01 1JY4

TITLE B4DIMER: A DE NOVO DESIGNED EIGHT-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 WAS CHEMICALLY SYNTHESIZED.

KEYWDS EIGHT-STRANDED BETA-SHEET, DISULFIDE BOND, DE NOVO PROTEIN KEYWDS 2 DESIGN

EXPDTA SOLUTION NMR

NUMMDL 10

AUTHOR J.VENKATRAMAN,G.A.NAGANA GOWDA,P.BALARAM

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 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 TEN 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 446 RESTRAINTS, 398 ARE NOE REMARK 3 -DERIVED DISTANCE CONSTRAINTS,48 DISTANCE RESTRAINTS ARE FROM REMARK 3 HYDROGEN BONDS. THE LIST OF CONSTRAINTS IS AVAILABLE IN THE REMARK 3 FILE DYANA_UPPERCONST.TXT. STRUCTURE CALCULATIONS WERE REMARK 3 PERFORMED WITH THE PROGRAM DYANA-1.5 (P. GUENTERT, C. REMARK 3 MUMENTHALER, K. WUTHRICH, J. MOL. BIOL.(1997)VOL.273, 283-298) REMARK 3 . NO VIOLATION OF DISTANCE CONSTRAINTS FROM NOES EXCEEDED REMARK 3 0.3ANGSTROMS. THE ENSEMBLE OF STRUCTURES IS SUPERIMPOSED OVER REMARK 3 THE BEST-STRUCTURED REGION ENCOMPASING RESIDUES E11-L34. THE REMARK 3 AVERAGE RMSDS BETWEEN THE SUPERPOSED STRUCTURES AND THE REMARK 3 AVERAGE STRUCTURE ARE AS FOLLOWS: 0.75(CHAIN A, RESIDUES 11- REMARK 3 34, BACKBONE ATOMS) 0.72(CHAIN B, RESIDUES 11-34, BACKBONE REMARK 3 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 RCSB ID CODE IS RCSB014320.

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 : DYANA 1.5 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, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 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 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 LEU A 34 56.85 -115.94 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 6 CYS B 4 75.64 -115.70 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 REMARK 900 ASSEMBLED 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

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 1.000 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