HEADER PROTEIN BINDING 09-APR-02 1LE3 TITLE NMR STRUCTURE OF TRYPTOPHAN ZIPPER 4: A STABLE BETA-HAIRPIN PEPTIDE TITLE 2 BASED ON THE C-TERMINAL HAIRPIN OF THE B1 DOMAIN OF PROTEIN G COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPTOPHAN ZIPPER 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL HAIRPIN OF THE B1 DOMAIN OF PROTEIN G; COMPND 5 SYNONYM: IMMUNOGLOBULIN G BINDING PROTEIN G; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS DERIVED FROM RESIDUES 41-56 OF THE SOURCE 4 B1 DOMAIN OF PROTEIN G WITH THREE SUBSTITUTIONS FROM THE NATURAL SOURCE 5 SEQUENCE, Y45W/F52W/V54W. THE PEPTIDE WAS SYNTHESIZED CHEMICALLY. KEYWDS BETA-HAIRPIN, TYPE I BETA-TURN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.G.COCHRAN,N.J.SKELTON,M.A.STAROVASNIK REVDAT 4 10-NOV-21 1LE3 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1LE3 1 VERSN REVDAT 2 20-NOV-02 1LE3 1 REMARK REVDAT 1 24-APR-02 1LE3 0 SPRSDE 24-APR-02 1LE3 1HS0 JRNL AUTH A.G.COCHRAN,N.J.SKELTON,M.A.STAROVASNIK JRNL TITL TRYPTOPHAN ZIPPERS: STABLE, MONOMERIC BETA -HAIRPINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 5578 2001 JRNL REFN ISSN 0027-8424 JRNL PMID 11331745 JRNL DOI 10.1073/PNAS.091100898 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.J.SKELTON,A.G.COCHRAN,M.A.STAROVASNIK REMARK 1 TITL CHEMICAL-SHIFT-BASED METHODS FOR STRUCTURE VALIDATION AND REMARK 1 TITL 2 REFINEMENT: APPLICATION TO TRYPTOPHAN ZIPPER BETA-HAIRPIN REMARK 1 TITL 3 PEPTIDES REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.5, AMBER 6.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), CASE AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL OF 130 REMARK 3 (INCLUDING 29 INTRA-RESIDUE, 30 SEQUENTIAL, 20 MEDIUM-RANGE, AND REMARK 3 51 LONG-RANGE) NOE-DERIVED DISTANCE RESTRAINTS, 22 DIHEDRAL REMARK 3 ANGLE RESTRAINTS, AND 1H CHEMICAL SHIFT RESTRAINTS FOR 46 CARBON- REMARK 3 BOUND 1H RESONANCES; (CHEMICAL SHIFT RESTRAINTS WERE NOT IMPOSED REMARK 3 FOR THE TERMINAL RESIDUES, OR FOR SIDE CHAINS EXHIBITING REMARK 3 EVIDENCE OF ROTATIONAL AVERAGING). THE ENSEMBLE AGREES WELL WITH REMARK 3 THE EXPERIMENTAL RESTRAINTS WITH NO DISTANCE OR DIHEDRAL ANGLE REMARK 3 VIOLATIONS GREATER THAN 0.10 ANGSTROM OR 5 DEG, RESPECTIVELY, REMARK 3 AND AN AVERAGE RMSD OF ONLY 0.106 PPM BETWEEN OBSERVED AND REMARK 3 CALCULATED CHEMICAL SHIFTS. REMARK 4 REMARK 4 1LE3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-APR-02. REMARK 100 THE DEPOSITION ID IS D_1000015869. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM TRPZIP4 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D-ROESY; 2D REMARK 210 -TOCSY; COSY-35 REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98.0, DGII 98.0 REMARK 210 METHOD USED : HYBRID DISTANCE REMARK 210 GEOMETRY/SIMULATED ANNEALING REMARK 210 USING THE PROGRAM DGII, FOLLOWED REMARK 210 BY MOLECULAR DYNAMICS USING THE REMARK 210 PROGRAM AMBER, IN CONJUNCTION REMARK 210 NOT ONLY WITH DISTANCE AND REMARK 210 DIHEDRAL ANGLE RESTRAINTS, BUT REMARK 210 ALSO 1H CHEMICAL SHIFT-BASED REMARK 210 RESTRAINTS. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 64 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE OF TRPZIP4 WAS ORIGINALLY DETERMINED USING REMARK 210 STANDARD 2D HOMONUCLEAR TECHNIQUES (COCHRAN ET AL., 2001, PROC. REMARK 210 NATL. ACAD. SCI. USA, 98, 5578-5583). DISTANCE AND DIHEDRAL REMARK 210 ANGLE RESTRAINTS WERE DERIVED FROM ANALYSIS OF NOESY, ROESY, DQF- REMARK 210 COSY, AND COSY-35 DATA. CHI-1 ROTAMERS AND STEREOSPECIFIC REMARK 210 ASSIGNMENTS FOR BETA-METHYLENE GROUPS WERE BASED ON COMBINED REMARK 210 ANALYSIS OF 3JHAHB AND LOCAL ROES, SUGGESTING THAT ALL FOUR TRP REMARK 210 RESIDUES ADOPT A CHI1 OF -60 DEG. QUANTITATIVE ANALYSIS OF THE REMARK 210 1H CHEMICAL SHIFTS, HOWEVER, REVEALED THAT THE FREQUENCIES OF REMARK 210 THE HB AND HE3 RESONANCES OF TRP5 AND TRP14 WERE INCONSISTENT REMARK 210 WITH A -60 DEG CHI1 VALUE, AND INDICATED THAT THE SIDE CHAINS REMARK 210 FOR THESE TRYPTOPHANS ACTUALLY RESIDE PRIMARILY IN THE 180 DEG REMARK 210 CHI1 ROTAMER (SKELTON ET AL., MANUSCRIPT IN PREPARATION). THE REMARK 210 CURRENT COORDINATES RESULT FROM REFINEMENT WITH THE SANDER REMARK 210 MODULE OF AMBER (V6.0), AND INCLUDED NOT ONLY NOE-DERIVED REMARK 210 DISTANCE RESTRAINTS AND DIHEDRAL ANGLE RESTRAINTS, BUT ALSO 1H REMARK 210 CHEMICAL SHIFT-BASED RESTRAINTS. THUS, THE RESULTING UPDATED REMARK 210 COORDINATES DIFFER FROM THE PREVIOUS ONES IN THE SIDE CHAIN REMARK 210 ORIENTATIONS OF TRP5 AND TRP14. HOWEVER, THE REST OF THE REMARK 210 STRUCTURE IS SIMILAR WITH A BACKBONE RMSD BETWEEN THE AVERAGE REMARK 210 COORDINATES OF THE TWO ENSEMBLES OF 0.72 ANGSTROM(RES.43-54). REMARK 210 THE TWO STRANDS ARE HIGHLY TWISTED, AS DESCRIBED PREVIOUSLY, REMARK 210 HOWEVER THERE IS A SLIGHT DIFFERENCE IN THE RELATIVE POSITION OF REMARK 210 THE TURN WITH RESPECT TO THE STRANDS. THE KEY DIFFERENCE, REMARK 210 HOWEVER, IS THAT EACH PAIR OF CROSS-STRAND TRYPTOPHAN RINGS NOW REMARK 210 SHOWS EDGE-TO-FACE PACKING AGAINST ONE ANOTHER. THIS SORT OF REMARK 210 PACKING IS OBSERVED FOR ALL TRYPTOPHAN ZIPPER PEPTIDES, REMARK 210 REGARDLESS OF TURN TYPE. 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 3 LYS A 50 44.56 33.83 REMARK 500 5 LYS A 50 66.62 37.64 REMARK 500 6 LYS A 50 44.92 34.79 REMARK 500 10 LYS A 50 48.30 31.75 REMARK 500 13 THR A 49 -18.21 -140.67 REMARK 500 15 ALA A 48 0.94 -69.91 REMARK 500 19 LYS A 50 47.87 34.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 57 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LE0 RELATED DB: PDB REMARK 900 1LE0 CONTAINS TRYPTOPHAN ZIPPER 1 REMARK 900 RELATED ID: 1LE1 RELATED DB: PDB REMARK 900 1LE1 CONTAINS TRYPTOPHAN ZIPPER 2 DBREF 1LE3 A 41 56 UNP P06654 SPG1_STRSG 267 282 SEQADV 1LE3 TRP A 45 UNP P06654 TYR 271 ENGINEERED MUTATION SEQADV 1LE3 TRP A 52 UNP P06654 PHE 278 ENGINEERED MUTATION SEQADV 1LE3 TRP A 54 UNP P06654 VAL 280 ENGINEERED MUTATION SEQRES 1 A 17 GLY GLU TRP THR TRP ASP ASP ALA THR LYS THR TRP THR SEQRES 2 A 17 TRP THR GLU NH2 HET NH2 A 57 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N SHEET 1 A 2 GLU A 42 TRP A 45 0 SHEET 2 A 2 TRP A 52 THR A 55 -1 O THR A 53 N THR A 44 LINK C GLU A 56 N NH2 A 57 1555 1555 1.33 SITE 1 AC1 1 GLU A 56 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 MODEL 1