10 20 30 40 50 60 70 80 1LE3 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN BINDING 09-APR-02 1LE3
TITLE NMR STRUCTURE OF TRYPTOPHAN ZIPPER 4: A STABLE BETA-HAIRPIN TITLE 2 PEPTIDE BASED ON THE C-TERMINAL HAIRPIN OF THE B1 DOMAIN TITLE 3 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- SOURCE 4 56 OF THE B1 DOMAIN OF PROTEIN G WITH THREE SUBSTITUTIONS SOURCE 5 FROM THE NATURAL SEQUENCE, Y45W/F52W/V54W. THE PEPTIDE WAS SOURCE 6 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 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 JRNL TITL 2 -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 REMARK 1 TITL 2 VALIDATION AND REFINEMENT: APPLICATION TO REMARK 1 TITL 3 TRYPTOPHAN ZIPPER BETA-HAIRPIN 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 : AMBER 6.0 REMARK 3 AUTHORS : CASE AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 130 (INCLUDING 29 INTRA-RESIDUE, 30 SEQUENTIAL, 20 MEDIUM- REMARK 3 RANGE, AND 51 LONG-RANGE) NOE-DERIVED DISTANCE RESTRAINTS, 22 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, AND 1H CHEMICAL SHIFT RESTRAINTS REMARK 3 FOR 46 CARBON-BOUND 1H RESONANCES; (CHEMICAL SHIFT RESTRAINTS REMARK 3 WERE NOT IMPOSED FOR THE TERMINAL RESIDUES, OR FOR SIDE CHAINS REMARK 3 EXHIBITING EVIDENCE OF ROTATIONAL AVERAGING). THE ENSEMBLE REMARK 3 AGREES WELL WITH THE EXPERIMENTAL RESTRAINTS WITH NO DISTANCE REMARK 3 OR DIHEDRAL ANGLE VIOLATIONS GREATER THAN 0.10 ANGSTROM OR 5 REMARK 3 DEG, RESPECTIVELY, AND AN AVERAGE RMSD OF ONLY 0.106 PPM REMARK 3 BETWEEN OBSERVED AND 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 RCSB ID CODE IS RCSB015869.
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, REMARK 210 2D-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 : XWINNMR 2.5, FELIX 98.0, DGII REMARK 210 98.0 REMARK 210 METHOD USED : HYBRID DISTANCE GEOMETRY/ REMARK 210 SIMULATED ANNEALING USING THE REMARK 210 PROGRAM DGII, FOLLOWED BY REMARK 210 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 REMARK 210 USING STANDARD 2D HOMONUCLEAR TECHNIQUES (COCHRAN ET AL., REMARK 210 2001, PROC. NATL. ACAD. SCI. USA, 98, 5578-5583). DISTANCE AND REMARK 210 DIHEDRAL ANGLE RESTRAINTS WERE DERIVED FROM ANALYSIS OF NOESY, REMARK 210 ROESY, DQF-COSY, AND COSY-35 DATA. CHI-1 ROTAMERS AND REMARK 210 STEREOSPECIFIC ASSIGNMENTS FOR BETA-METHYLENE GROUPS WERE REMARK 210 BASED ON COMBINED ANALYSIS OF 3JHAHB AND LOCAL ROES, REMARK 210 SUGGESTING THAT ALL FOUR TRP RESIDUES ADOPT A CHI1 OF -60 DEG. REMARK 210 QUANTITATIVE ANALYSIS OF THE 1H CHEMICAL SHIFTS, HOWEVER, REMARK 210 REVEALED THAT THE FREQUENCIES OF THE HB AND HE3 RESONANCES OF REMARK 210 TRP5 AND TRP14 WERE INCONSISTENT WITH A -60 DEG CHI1 VALUE, REMARK 210 AND INDICATED THAT THE SIDE CHAINS FOR THESE TRYPTOPHANS REMARK 210 ACTUALLY RESIDE PRIMARILY IN THE 180 DEG CHI1 ROTAMER (SKELTON REMARK 210 ET AL., MANUSCRIPT IN PREPARATION). THE CURRENT COORDINATES REMARK 210 RESULT FROM REFINEMENT WITH THE SANDER MODULE OF AMBER (V6.0), REMARK 210 AND INCLUDED NOT ONLY NOE-DERIVED DISTANCE RESTRAINTS AND REMARK 210 DIHEDRAL ANGLE RESTRAINTS, BUT ALSO 1H CHEMICAL SHIFT-BASED REMARK 210 RESTRAINTS. THUS, THE RESULTING UPDATED COORDINATES DIFFER REMARK 210 FROM THE PREVIOUS ONES IN THE SIDE CHAIN ORIENTATIONS OF TRP5 REMARK 210 AND TRP14. HOWEVER, THE REST OF THE STRUCTURE IS SIMILAR WITH REMARK 210 A BACKBONE RMSD BETWEEN THE AVERAGE COORDINATES OF THE TWO REMARK 210 ENSEMBLES OF 0.72 ANGSTROM(RES.43-54). THE TWO STRANDS ARE REMARK 210 HIGHLY TWISTED, AS DESCRIBED PREVIOUSLY, HOWEVER THERE IS A REMARK 210 SLIGHT DIFFERENCE IN THE RELATIVE POSITION OF THE TURN WITH REMARK 210 RESPECT TO THE STRANDS. THE KEY DIFFERENCE, HOWEVER, IS THAT REMARK 210 EACH PAIR OF CROSS-STRAND TRYPTOPHAN RINGS NOW SHOWS EDGE-TO- REMARK 210 FACE PACKING AGAINST ONE ANOTHER. THIS SORT OF PACKING IS REMARK 210 OBSERVED FOR ALL TRYPTOPHAN ZIPPER PEPTIDES, REGARDLESS OF REMARK 210 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 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 SEQADV 1LE3 TRP A 52 UNP P06654 PHE 278 ENGINEERED SEQADV 1LE3 TRP A 54 UNP P06654 VAL 280 ENGINEERED
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