HEADER TOXIN 23-NOV-23 8V2V TITLE SOLUTION NMR STRUCTURE OF RECIFIN A [Y6F] COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECIFIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: AXINELLA SP. 1 TF-2017; SOURCE 4 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.D.PAYNE,C.I.SCHROEDER,K.J.ROSENGREN REVDAT 1 25-SEP-24 8V2V 0 JRNL AUTH T.B.SMALLWOOD,L.R.H.KRUMPE,C.D.PAYNE,V.G.KLEIN,B.R.O'KEEFE, JRNL AUTH 2 R.J.CLARK,C.I.SCHROEDER,K.J.ROSENGREN JRNL TITL PICKING THE TYROSINE-LOCK: CHEMICAL SYNTHESIS OF THE JRNL TITL 2 TYROSYL-DNA PHOSPHODIESTERASE I INHIBITOR RECIFIN A AND JRNL TITL 3 ANALOGUES. JRNL REF CHEM SCI V. 15 13227 2024 JRNL REFN ISSN 2041-6520 JRNL PMID 39183914 JRNL DOI 10.1039/D4SC01976H REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PRELIMINARY STRUCTURES WERE CALCULATED REMARK 3 USING CYANA AND FINAL STRUCTURES WERE CALCULATED AND WATER REMARK 3 MINIMISED USING CNS. REMARK 4 REMARK 4 8V2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1000278855. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.9 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM RECIFIN A [Y6F], 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-13C HSQC; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CARA, CYANA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 1 CYS A 21 -80.14 56.55 REMARK 500 1 GLN A 33 82.46 62.30 REMARK 500 2 CYS A 21 -89.90 54.03 REMARK 500 2 GLN A 33 82.88 64.17 REMARK 500 3 CYS A 21 -75.73 63.55 REMARK 500 3 ARG A 25 -171.75 63.43 REMARK 500 3 GLN A 33 86.36 58.48 REMARK 500 4 CYS A 22 87.18 -171.11 REMARK 500 4 GLN A 33 90.34 68.37 REMARK 500 5 CYS A 21 -67.44 67.76 REMARK 500 5 GLN A 33 89.58 60.40 REMARK 500 6 CYS A 21 -48.81 74.26 REMARK 500 6 ARG A 25 84.32 -65.76 REMARK 500 6 GLN A 33 80.96 61.62 REMARK 500 7 SER A 17 73.31 -104.98 REMARK 500 7 CYS A 21 -56.06 67.73 REMARK 500 7 GLN A 33 85.62 61.80 REMARK 500 8 CYS A 21 -73.59 69.41 REMARK 500 8 ARG A 25 91.83 58.43 REMARK 500 8 GLN A 33 89.17 70.45 REMARK 500 9 SER A 17 75.97 -107.67 REMARK 500 9 CYS A 21 -65.95 68.88 REMARK 500 9 ARG A 25 -179.19 66.30 REMARK 500 9 GLN A 33 88.60 64.13 REMARK 500 10 SER A 17 71.02 -105.59 REMARK 500 10 CYS A 21 -67.47 62.57 REMARK 500 10 GLN A 33 78.17 56.75 REMARK 500 11 CYS A 21 -71.39 66.81 REMARK 500 11 GLN A 33 78.93 63.43 REMARK 500 12 PHE A 10 30.00 -97.81 REMARK 500 12 SER A 17 72.22 -118.84 REMARK 500 12 CYS A 21 -74.42 67.80 REMARK 500 12 ARG A 25 -169.09 58.60 REMARK 500 12 GLN A 33 82.89 65.43 REMARK 500 13 CYS A 21 -82.49 63.91 REMARK 500 13 GLN A 33 82.00 59.56 REMARK 500 14 CYS A 21 -81.49 -98.37 REMARK 500 14 ARG A 25 173.13 78.93 REMARK 500 14 GLN A 33 80.95 62.88 REMARK 500 15 PRO A 19 88.70 -67.21 REMARK 500 15 ASP A 20 -39.45 143.87 REMARK 500 15 CYS A 21 -40.97 75.78 REMARK 500 15 GLN A 33 82.68 63.50 REMARK 500 16 CYS A 21 -56.80 70.00 REMARK 500 16 ARG A 25 81.13 56.34 REMARK 500 16 GLN A 33 84.07 61.97 REMARK 500 17 PRO A 19 5.44 -68.40 REMARK 500 17 CYS A 21 -90.11 -82.60 REMARK 500 17 GLN A 33 82.91 59.59 REMARK 500 18 CYS A 21 -61.72 73.80 REMARK 500 REMARK 500 THIS ENTRY HAS 56 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31130 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF RECIFIN A [Y6F] DBREF 8V2V A 2 42 PDB 8V2V 8V2V 2 42 SEQRES 1 A 41 GLU ALA PHE CYS PHE SER ASP ARG PHE CYS GLN ASN TYR SEQRES 2 A 41 ILE GLY SER ILE PRO ASP CYS CYS PHE GLY ARG GLY SER SEQRES 3 A 41 TYR SER PHE GLU LEU GLN PRO PRO PRO TRP GLU CYS TYR SEQRES 4 A 41 GLN CYS HET PCA A 101 14 HETNAM PCA PYROGLUTAMIC ACID FORMUL 2 PCA C5 H7 N O3 HELIX 1 AA1 PRO A 35 CYS A 39 5 5 SHEET 1 AA1 3 PHE A 4 PHE A 6 0 SHEET 2 AA1 3 SER A 27 SER A 29 -1 O SER A 27 N PHE A 6 SHEET 3 AA1 3 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 2.04 SSBOND 2 CYS A 11 CYS A 39 1555 1555 2.04 SSBOND 3 CYS A 22 CYS A 42 1555 1555 2.03 LINK N GLU A 2 C PCA A 101 1555 1555 1.29 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 1 626 CONECT 51 292 CONECT 148 565 CONECT 292 51 CONECT 302 613 CONECT 565 148 CONECT 613 302 CONECT 620 621 624 628 CONECT 621 620 622 626 629 CONECT 622 621 623 630 631 CONECT 623 622 624 632 633 CONECT 624 620 623 625 CONECT 625 624 CONECT 626 1 621 627 CONECT 627 626 CONECT 628 620 CONECT 629 621 CONECT 630 622 CONECT 631 622 CONECT 632 623 CONECT 633 623 MASTER 143 0 1 1 3 0 0 6 343 1 21 4 END