Header list of 1le3.pdb file
Complete list - 10 20 Bytes
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
Complete list - 10 20 Bytes