10 20 30 40 50 60 70 80 1KDL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL PROTEIN 13-NOV-01 1KDL
TITLE SOLUTION STRUCTURE OF THE AMPHIPATHIC DOMAIN OF YOPD FROM TITLE 2 YERSINIA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: YOPD PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 278-300; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED AND SOURCE 4 IS FOUND IN THE CYTOSOL AND MEMBRANE LOCATIONS. THE SOURCE 5 SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN YERSINIA SOURCE 6 PESTIS (BACTERIA).
KEYWDS YERSINIA, YOPD, AMPHIPATHIC ALPHA HELIX, BETA TURN, KEYWDS 2 STRUCTURAL PROTEIN
EXPDTA SOLUTION NMR
AUTHOR T.TENGEL,I.SETHSON,M.S.FRANCIS
REVDAT 2 24-FEB-09 1KDL 1 VERSN REVDAT 1 21-AUG-02 1KDL 0
JRNL AUTH T.TENGEL,I.SETHSON,M.S.FRANCIS JRNL TITL CONFORMATIONAL ANALYSIS BY CD AND NMR SPECTROSCOPY JRNL TITL 2 OF A PEPTIDE ENCOMPASSING THE AMPHIPATHIC DOMAIN JRNL TITL 3 OF YOPD FROM YERSINIA. JRNL REF EUR.J.BIOCHEM. V. 269 3659 2002 JRNL REFN ISSN 0014-2956 JRNL PMID 12153562 JRNL DOI 10.1046/J.1432-1033.2002.03051.X
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STANDARD SIMULATED ANNEALING REMARK 3 PROTOCOL USING XPLOR 3.851. DIHEDRAL RESTRAINTS WERE OBTAINED REMARK 3 WITH TALOS
REMARK 4 REMARK 4 1KDL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-01. REMARK 100 THE RCSB ID CODE IS RCSB014839.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOSPHATE BUFFER REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 3.5 MM YOPD(278-300); 20 MM REMARK 210 SODIUM PHOSPHATE BUFFER, PH REMARK 210 4.5; 1 MM SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY, REMARK 210 15N HSQC, 13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX, AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, MARDIGRAS 3.0, REMARK 210 TALOS 98.040.21.02 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 150 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS, STRUCTURES WITH REMARK 210 THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL
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 ASN A 279 30.08 -93.03 REMARK 500 HIS A 295 49.20 -93.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 286 0.31 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1KDL A 278 300 UNP Q06131 YOPD_YERPS 278 300
SEQRES 1 A 23 ASP ASN PHE MET LYS ASP VAL LEU ARG LEU ILE GLU GLN SEQRES 2 A 23 TYR VAL SER SER HIS THR HIS ALA MET LYS
HELIX 1 H1 PHE A 280 VAL A 292 1 13
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