PDB Short entry for 1KDL HEADER STRUCTURAL PROTEIN 13-NOV-01 1KDL TITLE SOLUTION STRUCTURE OF THE AMPHIPATHIC DOMAIN OF YOPD FROM 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 IS FOUND SOURCE 4 IN THE CYTOSOL AND MEMBRANE LOCATIONS. THE SEQUENCE OF THE PEPTIDE SOURCE 5 IS NATURALLY FOUND IN YERSINIA PESTIS (BACTERIA). KEYWDS YERSINIA, YOPD, AMPHIPATHIC ALPHA HELIX, BETA TURN, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR AUTHOR T.TENGEL,I.SETHSON,M.S.FRANCIS REVDAT 3 29-NOV-17 1KDL 1 REMARK HELIX 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 OF A JRNL TITL 2 PEPTIDE ENCOMPASSING THE AMPHIPATHIC DOMAIN OF YOPD FROM JRNL TITL 3 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 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: REMARK 3 STANDARD SIMULATED ANNEALING PROTOCOL USING XPLOR 3.851. REMARK 3 DIHEDRAL RESTRAINTS WERE OBTAINED WITH TALOS REMARK 4 REMARK 4 1KDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014839. 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 4.5; REMARK 210 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 THE REMARK 210 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 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 O VAL A 284 H ILE A 288 1.42 REMARK 500 O MET A 281 H LEU A 285 1.55 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 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