HEADER TOXIN 02-JUL-20 6XN9 TITLE SOLUTION NMR STRUCTURE OF RECIFIN, A CYSTEINE-RICH TYROSYL-DNA TITLE 2 PHOSPHODIESTERASE I MODULATORY PEPTIDE FROM THE MARINE SPONGE TITLE 3 AXINELLA SP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECIFIN MODULATORY PEPTIDE; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AXINELLA SP. 1 TF-2017; SOURCE 3 ORGANISM_TAXID: 2041915 KEYWDS CYSTINE-RICH PEPTIDE, PROTEIN KNOT, TYROSYL-DNA PHOSPHODIESTERASE I KEYWDS 2 INHIBITOR, MARINE NATURAL PRODUCT, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.I.SCHROEDER,K.J.ROSENGREN,B.R.O'KEEFE REVDAT 1 10-FEB-21 6XN9 0 JRNL AUTH L.R.H.KRUMPE,B.A.P.WILSON,C.MARCHAND,S.N.SUNASSEE, JRNL AUTH 2 A.BERMINGHAM,W.WANG,E.PRICE,T.GUSZCZYNSKI,J.A.KELLEY, JRNL AUTH 3 K.R.GUSTAFSON,Y.POMMIER,K.J.ROSENGREN,C.I.SCHROEDER, JRNL AUTH 4 B.R.O'KEEFE JRNL TITL RECIFIN A, INITIAL EXAMPLE OF THE TYR-LOCK PEPTIDE JRNL TITL 2 STRUCTURAL FAMILY, IS A SELECTIVE ALLOSTERIC INHIBITOR OF JRNL TITL 3 TYROSYL-DNA PHOSPHODIESTERASE I. JRNL REF J.AM.CHEM.SOC. V. 142 21178 2020 JRNL REFN ESSN 1520-5126 JRNL PMID 33263997 JRNL DOI 10.1021/JACS.0C10418 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES CALCULATED WITH EROSION REMARK 3 ANGLE DYNAMICS THEN REFINED AND MINIMIZED IN EXPLICIT WATER REMARK 3 USING CARTESIAN DYNAMICS REMARK 4 REMARK 4 6XN9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250181. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.85 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 4 MG/ML RECIFIN, 90% H2O/10% REMARK 210 D2O; 4 MG/ML RECIFIN, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.5, CCPNMR ANALYSIS REMARK 210 2.4.1, XEASY, CYANA 3.97 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY 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: 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 7 GLN A 33 70.26 50.52 REMARK 500 9 ASP A 20 58.13 -94.93 REMARK 500 9 GLN A 33 71.57 49.74 REMARK 500 10 GLN A 33 70.62 52.10 REMARK 500 11 SER A 7 39.95 -85.58 REMARK 500 11 ASP A 20 45.65 -85.03 REMARK 500 12 GLN A 33 71.19 48.97 REMARK 500 13 GLN A 33 79.82 38.08 REMARK 500 14 SER A 7 41.66 -77.53 REMARK 500 18 CYS A 22 20.66 -79.02 REMARK 500 18 GLN A 33 74.52 43.71 REMARK 500 19 SER A 7 37.98 -82.76 REMARK 500 20 SER A 7 24.83 -77.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30767 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF RECIFIN, A CYSTEINE-RICH TYROSYL-DNA REMARK 900 PHOSPHODIESTERASE I MODULATORY PEPTIDE FROM THE MARINE SPONGE REMARK 900 AXINELLA SP. DBREF 6XN9 A 1 42 PDB 6XN9 6XN9 1 42 SEQRES 1 A 42 PCA GLU ALA PHE CYS TYR SER ASP ARG PHE CYS GLN ASN SEQRES 2 A 42 TYR ILE GLY SER ILE PRO ASP CYS CYS PHE GLY ARG GLY SEQRES 3 A 42 SER TYR SER PHE GLU LEU GLN PRO PRO PRO TRP GLU CYS SEQRES 4 A 42 TYR GLN CYS HET PCA A 1 14 HETNAM PCA PYROGLUTAMIC ACID FORMUL 1 PCA C5 H7 N O3 HELIX 1 AA1 ASP A 20 GLY A 24 5 5 HELIX 2 AA2 PRO A 35 CYS A 39 5 5 SHEET 1 AA1 4 TYR A 14 ILE A 18 0 SHEET 2 AA1 4 ALA A 3 TYR A 6 -1 N CYS A 5 O GLY A 16 SHEET 3 AA1 4 SER A 27 SER A 29 -1 O SER A 27 N TYR A 6 SHEET 4 AA1 4 TYR A 40 GLN A 41 -1 O TYR A 40 N TYR A 28 SSBOND 1 CYS A 5 CYS A 21 1555 1555 2.03 SSBOND 2 CYS A 11 CYS A 39 1555 1555 2.01 SSBOND 3 CYS A 22 CYS A 42 1555 1555 2.04 LINK C PCA A 1 N GLU A 2 1555 1555 1.31 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 HETATM 1 N PCA A 1 -8.459 7.403 3.140 1.00 0.00 N HETATM 2 CA PCA A 1 -7.209 8.123 2.921 1.00 0.00 C HETATM 3 CB PCA A 1 -7.200 9.252 3.947 1.00 0.00 C HETATM 4 CG PCA A 1 -8.417 9.034 4.826 1.00 0.00 C HETATM 5 CD PCA A 1 -8.976 7.719 4.319 1.00 0.00 C HETATM 6 OE PCA A 1 -9.759 7.028 4.955 1.00 0.00 O HETATM 7 C PCA A 1 -6.034 7.191 3.178 1.00 0.00 C HETATM 8 O PCA A 1 -4.941 7.373 2.650 1.00 0.00 O HETATM 9 H PCA A 1 -8.849 6.774 2.496 1.00 0.00 H HETATM 10 HA PCA A 1 -7.147 8.510 1.915 1.00 0.00 H HETATM 11 HB2 PCA A 1 -7.263 10.217 3.445 1.00 0.00 H HETATM 12 HB3 PCA A 1 -6.290 9.204 4.547 1.00 0.00 H HETATM 13 HG2 PCA A 1 -9.159 9.818 4.676 1.00 0.00 H HETATM 14 HG3 PCA A 1 -8.124 8.965 5.875 1.00 0.00 H