HEADER HYDROLASE/HYDROLASE INHIBITOR 29-MAR-01 1IBX TITLE NMR STRUCTURE OF DFF40 AND DFF45 N-TERMINAL DOMAIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA FRAGMENTATION FACTOR 40; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (CIDE DOMAIN); COMPND 5 SYNONYM: DFF40, CASPASE-ACTIVATED DNASE, CASPASE-ACTIVATED NUCLEASE; COMPND 6 EC: 3.-.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: CHIMERA OF IGG BINDING PROTEIN G AND DNA FRAGMENTATION COMPND 10 FACTOR 45; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: B1 DOMAIN OF PROTEIN G FUSED WITH N-TERMINAL DOMAIN (CIDE COMPND 13 DOMAIN) OF DFF45; COMPND 14 SYNONYM: DFF45, INHIBITOR OF CAD; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DFF40; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-30A(+); SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SP., HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: , HUMAN; SOURCE 14 ORGANISM_TAXID: 1306,9606; SOURCE 15 STRAIN: ,; SOURCE 16 GENE: DFF45; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PET-30A(+) KEYWDS DFF40, DFF45, PROTEIN-PROTEIN COMPLEX, CIDE, CIDE DOMAIN COMPLEX, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR P.ZHOU,A.A.LUGOVSKOY,J.S.MCCARTY,P.LI,G.WAGNER REVDAT 5 22-MAY-24 1IBX 1 REMARK REVDAT 4 27-OCT-21 1IBX 1 REMARK SEQADV REVDAT 3 24-FEB-09 1IBX 1 VERSN REVDAT 2 30-MAY-01 1IBX 1 JRNL AUTHOR REVDAT 1 02-MAY-01 1IBX 0 JRNL AUTH P.ZHOU,A.A.LUGOVSKOY,J.S.MCCARTY,P.LI,G.WAGNER JRNL TITL SOLUTION STRUCTURE OF DFF40 AND DFF45 N-TERMINAL DOMAIN JRNL TITL 2 COMPLEX AND MUTUAL CHAPERONE ACTIVITY OF DFF40 AND DFF45. JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 6051 2001 JRNL REFN ISSN 0027-8424 JRNL PMID 11371636 JRNL DOI 10.1073/PNAS.111145098 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 97, X-PLOR 3.851 REMARK 3 AUTHORS : MOLECULAR SIMULATION, INC. (FELIX), BRUNGER (X REMARK 3 -PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IBX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013141. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM DFF40/DFF45 NTD COMPLEX REMARK 210 90% DEUTERATED, U-15N/13C REMARK 210 LABELED DFF40 NON-LABELED DFF45; REMARK 210 0.6 MM DFF40/DFF45 NTD COMPLEX REMARK 210 90% DEUTERATED, U-15N/13C REMARK 210 LABELED DFF45 NON-LABELED DFF40; REMARK 210 0.6 MM DFF40/DFF45 NTD COMPLEX U- REMARK 210 15N LABELED DFF40 NON-LABELED REMARK 210 DFF45; 0.6 MM DFF40/DFF45 NTD REMARK 210 COMPLEX U-15N LABELED DFF45 NON- REMARK 210 LABELED DFF40; 0.6 MM DFF40/ REMARK 210 DFF45 NTD COMPLEX PERDEUTERATED, REMARK 210 U-15N LABELED DFF40 NON-LABELED REMARK 210 DFF45; 0.6 MM DFF40/DFF45 NTD REMARK 210 COMPLEX PERDEUTERATED, U-15N REMARK 210 LABELED DFF45 NON-LABELED DFF40; REMARK 210 0.6 MM DFF40/DFF45 NTD COMPLEX REMARK 210 10% 13C LABELED DFF40 NON- REMARK 210 LABELED DFF45; 0.6 MM DFF40/ REMARK 210 DFF45 NTD COMPLEX 10% 13C REMARK 210 LABELED DFF45 NON-LABELED DFF40; REMARK 210 0.6 MM DFF40/DFF45 NTD COMPLEX U- REMARK 210 13C LABELED DFF40 NON-LABELED REMARK 210 DFF45; 0.6 MM DFF40/DFF45 NTD REMARK 210 COMPLEX U-13C LABELED DFF45 NON- REMARK 210 LABELED DFF40 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY V1.3, DYANA V1.5, X-PLOR REMARK 210 V3.8 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS/SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. CHAIN B, IS PRODUCED AS A CHIMERIC PROTEIN REMARK 210 CONTAINING PROTEIN G B1 DOMAIN (-44 TO 11) AND DFF45 (12 TO 100) REMARK 210 . THE RESIDUES OF THE PROTEIN G B1 DOMAIN ARE USED AS A REMARK 210 SOLUBILITY ENHANCEMENT TAG TO IMPROVE SOLUBILITY AND STABILITY REMARK 210 OF TARGET PROTEIN. THESE RESIDUES ARE NOT INCLUDED IN THE REMARK 210 STRUCTURAL CALCULATION, THUS THE COORDINATES ARE NOT DEPOSITED. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 HIS A 82 REMARK 465 HIS A 83 REMARK 465 HIS A 84 REMARK 465 HIS A 85 REMARK 465 HIS A 86 REMARK 465 MET B -44 REMARK 465 GLN B -43 REMARK 465 TYR B -42 REMARK 465 LYS B -41 REMARK 465 LEU B -40 REMARK 465 ILE B -39 REMARK 465 LEU B -38 REMARK 465 ASN B -37 REMARK 465 GLY B -36 REMARK 465 LYS B -35 REMARK 465 THR B -34 REMARK 465 LEU B -33 REMARK 465 LYS B -32 REMARK 465 GLY B -31 REMARK 465 GLU B -30 REMARK 465 THR B -29 REMARK 465 THR B -28 REMARK 465 THR B -27 REMARK 465 GLU B -26 REMARK 465 ALA B -25 REMARK 465 VAL B -24 REMARK 465 ASP B -23 REMARK 465 ALA B -22 REMARK 465 ALA B -21 REMARK 465 THR B -20 REMARK 465 ALA B -19 REMARK 465 GLU B -18 REMARK 465 LYS B -17 REMARK 465 VAL B -16 REMARK 465 PHE B -15 REMARK 465 LYS B -14 REMARK 465 GLN B -13 REMARK 465 TYR B -12 REMARK 465 ALA B -11 REMARK 465 ASN B -10 REMARK 465 ASP B -9 REMARK 465 ASN B -8 REMARK 465 GLY B -7 REMARK 465 VAL B -6 REMARK 465 ASP B -5 REMARK 465 GLY B -4 REMARK 465 GLU B -3 REMARK 465 TRP B -2 REMARK 465 THR B -1 REMARK 465 TYR B 0 REMARK 465 ASP B 1 REMARK 465 ASP B 2 REMARK 465 ALA B 3 REMARK 465 THR B 4 REMARK 465 LYS B 5 REMARK 465 THR B 6 REMARK 465 PHE B 7 REMARK 465 THR B 8 REMARK 465 VAL B 9 REMARK 465 THR B 10 REMARK 465 GLU B 11 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 1 LYS A 4 58.96 -175.49 REMARK 500 1 CYS A 26 -81.24 -51.58 REMARK 500 1 GLN A 27 -39.08 -39.20 REMARK 500 1 LYS A 32 -77.91 -77.63 REMARK 500 1 GLU A 41 -81.80 -74.94 REMARK 500 1 TYR A 49 -62.04 -90.30 REMARK 500 1 THR A 53 -75.79 -60.15 REMARK 500 1 ASP A 58 -70.37 -49.38 REMARK 500 1 VAL A 63 79.12 -119.87 REMARK 500 1 LYS B 54 30.16 -87.48 REMARK 500 1 GLU B 65 -63.89 -90.50 REMARK 500 1 ASP B 74 -78.05 -39.76 REMARK 500 1 SER B 90 -32.37 -34.78 REMARK 500 1 LYS B 93 87.26 -53.50 REMARK 500 2 LEU A 2 -173.02 -51.00 REMARK 500 2 GLN A 3 32.49 -95.04 REMARK 500 2 LEU A 13 -60.05 -109.62 REMARK 500 2 CYS A 26 -82.17 -57.41 REMARK 500 2 LYS A 32 -79.73 -61.56 REMARK 500 2 GLU A 41 -80.73 -72.23 REMARK 500 2 THR A 53 -75.90 -63.37 REMARK 500 2 ALA A 67 78.78 -116.05 REMARK 500 2 ASP B 74 -80.53 -41.85 REMARK 500 2 SER B 90 -31.48 -34.63 REMARK 500 2 GLU B 92 0.17 -61.85 REMARK 500 2 LYS B 93 94.71 -53.04 REMARK 500 3 GLN A 3 33.05 -97.23 REMARK 500 3 CYS A 26 -83.30 -54.34 REMARK 500 3 LYS A 32 -82.94 -59.96 REMARK 500 3 GLU A 41 -80.38 -72.57 REMARK 500 3 THR A 53 -75.14 -65.79 REMARK 500 3 ALA A 67 76.24 -118.35 REMARK 500 3 ARG B 16 -68.65 -93.10 REMARK 500 3 LYS B 54 30.19 -86.05 REMARK 500 3 LEU B 56 2.72 -69.88 REMARK 500 3 ASP B 74 -80.29 -44.81 REMARK 500 3 SER B 90 -33.78 -33.41 REMARK 500 3 GLU B 92 0.05 -61.57 REMARK 500 3 LYS B 93 90.19 -53.17 REMARK 500 4 LEU A 2 -172.51 -68.63 REMARK 500 4 GLN A 3 32.28 -93.80 REMARK 500 4 CYS A 26 -85.63 -42.13 REMARK 500 4 LYS A 32 -81.66 -72.36 REMARK 500 4 GLN A 38 67.26 60.64 REMARK 500 4 GLU A 41 -77.49 -70.93 REMARK 500 4 THR A 53 -75.92 -61.83 REMARK 500 4 ARG B 16 -75.73 -90.22 REMARK 500 4 ASP B 74 -79.75 -41.39 REMARK 500 4 SER B 90 -30.80 -36.09 REMARK 500 4 LYS B 93 97.40 -53.68 REMARK 500 REMARK 500 THIS ENTRY HAS 131 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 "HIS A 81" IN DFF40 IS THE FIRST RESIDUE OF A C-TERMINAL REMARK 999 HIS6 TAG. ALL OTHER FIVE HIS RESIDUES ARE NOT REMARK 999 OBSERVABLE IN THE EXPERIMENT. REMARK 999 CHAIN B, IS PRODUCED AS A CHIMERIC PROTEIN CONTAINING REMARK 999 PROTEIN G B1 DOMAIN (-44 TO 11) AND DFF45 (12 TO 100). REMARK 999 THE SEQUENCE FOR PROTEIN G B1 CAN ALSO BE FOUND IN REMARK 999 PDB ENTRY 1GB1 AS RESIDUES 1 TO 56. THE ENGINEERED REMARK 999 MUTATION WHEN USING PDB ENTRY 1GB1 NUMBERING, IS T2Q. DBREF 1IBX A 1 80 UNP O76075 DFFB_HUMAN 1 80 DBREF 1IBX B -44 11 UNP P19909 SPG2_STRSP 302 357 DBREF 1IBX B 12 100 GB 2065561 AAC51249 12 100 SEQADV 1IBX HIS A 81 UNP O76075 EXPRESSION TAG SEQADV 1IBX HIS A 82 UNP O76075 EXPRESSION TAG SEQADV 1IBX HIS A 83 UNP O76075 EXPRESSION TAG SEQADV 1IBX HIS A 84 UNP O76075 EXPRESSION TAG SEQADV 1IBX HIS A 85 UNP O76075 EXPRESSION TAG SEQADV 1IBX HIS A 86 UNP O76075 EXPRESSION TAG SEQADV 1IBX MET B -44 GB P19909 INITIATING METHIONINE SEQADV 1IBX GLN B -43 GB P19909 THR 303 ENGINEERED MUTATION SEQRES 1 A 86 MET LEU GLN LYS PRO LYS SER VAL LYS LEU ARG ALA LEU SEQRES 2 A 86 ARG SER PRO ARG LYS PHE GLY VAL ALA GLY ARG SER CYS SEQRES 3 A 86 GLN GLU VAL LEU ARG LYS GLY CYS LEU ARG PHE GLN LEU SEQRES 4 A 86 PRO GLU ARG GLY SER ARG LEU CYS LEU TYR GLU ASP GLY SEQRES 5 A 86 THR GLU LEU THR GLU ASP TYR PHE PRO SER VAL PRO ASP SEQRES 6 A 86 ASN ALA GLU LEU VAL LEU LEU THR LEU GLY GLN ALA TRP SEQRES 7 A 86 GLN GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 145 MET GLN TYR LYS LEU ILE LEU ASN GLY LYS THR LEU LYS SEQRES 2 B 145 GLY GLU THR THR THR GLU ALA VAL ASP ALA ALA THR ALA SEQRES 3 B 145 GLU LYS VAL PHE LYS GLN TYR ALA ASN ASP ASN GLY VAL SEQRES 4 B 145 ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 B 145 THR VAL THR GLU SER GLY GLU ILE ARG THR LEU LYS PRO SEQRES 6 B 145 CYS LEU LEU ARG ARG ASN TYR SER ARG GLU GLN HIS GLY SEQRES 7 B 145 VAL ALA ALA SER CYS LEU GLU ASP LEU ARG SER LYS ALA SEQRES 8 B 145 CYS ASP ILE LEU ALA ILE ASP LYS SER LEU THR PRO VAL SEQRES 9 B 145 THR LEU VAL LEU ALA GLU ASP GLY THR ILE VAL ASP ASP SEQRES 10 B 145 ASP ASP TYR PHE LEU CYS LEU PRO SER ASN THR LYS PHE SEQRES 11 B 145 VAL ALA LEU ALA SER ASN GLU LYS TRP ALA TYR ASN ASN SEQRES 12 B 145 SER ASP HELIX 1 1 SER A 25 PHE A 37 1 13 HELIX 2 2 CYS B 38 ALA B 51 1 14 HELIX 3 3 ASP B 72 LEU B 79 1 8 SHEET 1 A 3 LEU A 10 ARG A 11 0 SHEET 2 A 3 LEU A 69 LEU A 72 1 O LEU A 69 N ARG A 11 SHEET 3 A 3 ARG A 45 LEU A 48 -1 N ARG A 45 O LEU A 72 SHEET 1 B 2 THR B 60 LEU B 63 0 SHEET 2 B 2 PHE B 85 LEU B 88 -1 O VAL B 86 N VAL B 62 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