PDB Short entry for 1YYB HEADER APOPTOSIS 24-FEB-05 1YYB TITLE SOLUTION STRUCTURE OF 1-26 FRAGMENT OF HUMAN PROGRAMMED CELL DEATH 5 TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-26; COMPND 5 SYNONYM: PDCD5, TFAR19 PROTEIN, TF-1 CELL APOPTOSIS RELATED GENE-19 COMPND 6 PROTEIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3D KEYWDS PDCD5(1-26), SOLUTION STRUCTURE, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.S.LIU,Y.G.FENG,H.W.YAO,J.F.WANG REVDAT 3 02-MAR-22 1YYB 1 REMARK REVDAT 2 24-FEB-09 1YYB 1 VERSN REVDAT 1 13-SEP-05 1YYB 0 JRNL AUTH D.LIU,H.YAO,Y.CHEN,Y.FENG,Y.CHEN,J.WANG JRNL TITL THE N-TERMINAL 26-RESIDUE FRAGMENT OF HUMAN PROGRAMMED CELL JRNL TITL 2 DEATH 5 PROTEIN CAN FORM A STABLE ALPHA-HELIX HAVING UNIQUE JRNL TITL 3 ELECTROSTATIC POTENTIAL CHARACTER. JRNL REF BIOCHEM.J. V. 392 47 2005 JRNL REFN ISSN 0264-6021 JRNL PMID 16083422 JRNL DOI 10.1042/BJ20050688 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, CNS 1.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 223 INTRAREDIDUAL,SEQUENTIAL AND MEDIUM RANGE NOE RESTRAINTS, REMARK 3 AND 19 PHI AND 19 PSI DIHEDRAL ANGLE RESTRAINTS DRIVING FROM REMARK 3 PROGRAME TALOS. REMARK 4 REMARK 4 1YYB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000032065. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.25 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2-4MM PDCD5(1-26)-15N LABELED; REMARK 210 50MM PHOSPHATE BUFFER, 200MM REMARK 210 NACL, DSS, NAN3; 90% H2O, 10% REMARK 210 D2O; 2MM PDCD5(1-26)-13C LABELED; REMARK 210 50MM PHOSPHATE BUFFER, 200MM REMARK 210 NACL, DSS, NAN3; 100% D2O; 2-4MM REMARK 210 UNLABELED PDCD5(1-26); 50MM REMARK 210 PHOSPHATE BUFFER, 200MM NACL, REMARK 210 DSS, NAN3; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N NOESY-HSQC; 3D_15N TOCSY REMARK 210 -HSQC; 2D_15N HSQC; 2D_13C HMQC; REMARK 210 HMQC-NOESY; HMQC-TOCSY; 2D TOCSY; REMARK 210 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98, CNS 1.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 4 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 0 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 LEU A 6 H ARG A 10 1.45 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 1 ASP A 23 82.64 -176.57 REMARK 500 3 HIS A 21 99.26 -60.16 REMARK 500 4 LYS A 20 -74.59 -105.29 REMARK 500 4 HIS A 21 -67.85 -107.33 REMARK 500 5 HIS A 21 110.79 60.28 REMARK 500 5 PRO A 24 108.21 -52.59 REMARK 500 6 ALA A 19 -65.58 -98.29 REMARK 500 6 HIS A 21 157.29 60.56 REMARK 500 7 HIS A 21 110.46 60.55 REMARK 500 7 ASP A 23 -61.69 -178.26 REMARK 500 8 LYS A 20 -74.45 -63.39 REMARK 500 9 LYS A 20 -74.07 -69.79 REMARK 500 9 HIS A 21 -176.59 -60.43 REMARK 500 10 ASP A 23 84.48 -159.25 REMARK 500 11 ALA A 19 36.74 -98.96 REMARK 500 12 ASP A 23 149.04 62.35 REMARK 500 13 ALA A 19 36.48 -97.87 REMARK 500 16 ASP A 23 167.44 60.31 REMARK 500 16 PRO A 24 -166.36 -70.05 REMARK 500 17 HIS A 21 80.06 60.34 REMARK 500 18 LYS A 20 -74.11 -106.52 REMARK 500 18 ASP A 23 80.01 60.71 REMARK 500 19 HIS A 21 110.55 60.57 REMARK 500 19 PRO A 24 90.90 -52.33 REMARK 500 20 ASP A 23 83.38 60.68 REMARK 500 REMARK 500 REMARK: NULL DBREF 1YYB A 1 26 UNP O14737 PDCD5_HUMAN 1 26 SEQADV 1YYB GLY A 0 UNP O14737 SEE REMARK 999 SEQADV 1YYB SER A 1 UNP O14737 MET 1 SEE REMARK 999 SEQRES 1 A 27 GLY SER ALA ASP GLU GLU LEU GLU ALA LEU ARG ARG GLN SEQRES 2 A 27 ARG LEU ALA GLU LEU GLN ALA LYS HIS GLY ASP PRO GLY SEQRES 3 A 27 ASP HELIX 1 1 SER A 1 LYS A 20 1 20 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