HEADER RNA BINDING PROTEIN 05-OCT-21 7PVM TITLE NMR STRUCTURE OF THE C. THERMOPHILUM XRN2 ZINC FINGER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-3' EXORIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.13.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS SOURCE 3 144.50 / IMI 039719); SOURCE 4 ORGANISM_TAXID: 759272; SOURCE 5 STRAIN: DSM 1495 / CBS 144.50 / IMI 039719; SOURCE 6 GENE: CTHT_0008830; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ZINC FINGER, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.H.OVERBECK,R.SPRANGERS,J.P.WURM REVDAT 4 14-JUN-23 7PVM 1 REMARK REVDAT 3 05-OCT-22 7PVM 1 JRNL REVDAT 2 07-SEP-22 7PVM 1 TITLE JRNL REVDAT 1 06-JUL-22 7PVM 0 JRNL AUTH J.H.OVERBECK,D.STELZIG,A.L.FUCHS,J.P.WURM,R.SPRANGERS JRNL TITL OBSERVATION OF CONFORMATIONAL CHANGES THAT UNDERLIE THE JRNL TITL 2 CATALYTIC CYCLE OF XRN2. JRNL REF NAT.CHEM.BIOL. V. 18 1152 2022 JRNL REFN ESSN 1552-4469 JRNL PMID 36008487 JRNL DOI 10.1038/S41589-022-01111-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.13 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7PVM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1292118220. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : 125 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 25 MM HEPES, 125 MM NACL, 0.03 % REMARK 210 NAN3, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D HN(CA)CO; 3D H(CCO) REMARK 210 NH; 3D C(CO)NH; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.98.13, CARA 1.9.1.7, REMARK 210 NMRFAM-SPARKY 1.414 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 GLU A 3 51.79 -111.57 REMARK 500 2 GLN A 28 57.68 -104.40 REMARK 500 3 LYS A 23 95.41 -66.64 REMARK 500 4 LYS A 23 94.99 -69.79 REMARK 500 4 GLU A 25 55.46 -108.05 REMARK 500 5 ALA A 6 96.20 58.94 REMARK 500 7 GLU A 3 -72.90 -112.00 REMARK 500 7 LYS A 5 61.44 -105.24 REMARK 500 7 LYS A 27 78.95 -117.53 REMARK 500 7 GLN A 30 -66.03 -125.73 REMARK 500 8 LYS A 23 94.60 -68.78 REMARK 500 9 GLU A 3 -66.97 -132.23 REMARK 500 10 LYS A 23 94.81 -69.11 REMARK 500 11 GLU A 3 55.64 -90.79 REMARK 500 11 LYS A 23 95.63 -64.81 REMARK 500 11 GLU A 25 57.68 -118.61 REMARK 500 12 LYS A 5 55.11 -113.32 REMARK 500 13 LYS A 23 95.60 -63.96 REMARK 500 14 GLU A 25 74.12 -103.17 REMARK 500 15 LYS A 23 95.92 -66.15 REMARK 500 15 GLU A 25 46.52 -97.88 REMARK 500 15 GLN A 30 -174.95 -68.90 REMARK 500 16 ALA A 6 98.40 61.85 REMARK 500 17 LYS A 23 95.27 -61.97 REMARK 500 18 LYS A 23 95.47 -63.24 REMARK 500 19 LYS A 5 -74.18 -127.90 REMARK 500 19 ALA A 6 109.31 -170.15 REMARK 500 19 LYS A 23 95.62 -64.97 REMARK 500 20 LYS A 23 95.40 -62.28 REMARK 500 20 GLN A 30 74.07 -115.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 9 SG REMARK 620 2 CYS A 12 SG 139.2 REMARK 620 3 HIS A 17 NE2 93.6 110.9 REMARK 620 4 CYS A 22 SG 105.4 101.0 101.5 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7OPK RELATED DB: PDB REMARK 900 7OPK CONTAINS THE CRYSTALLIZED PROTEIN CORE REMARK 900 RELATED ID: 50997 RELATED DB: BMRB REMARK 900 XRN2 ZINC FINGER DBREF 7PVM A 3 31 UNP G0S058 G0S058_CHATD 265 293 SEQADV 7PVM GLY A 1 UNP G0S058 EXPRESSION TAG SEQADV 7PVM GLY A 2 UNP G0S058 EXPRESSION TAG SEQRES 1 A 31 GLY GLY GLU ALA LYS ALA ARG LEU CYS LYS LEU CYS GLY SEQRES 2 A 31 GLN LYS GLY HIS ASP GLU ARG SER CYS LYS GLY GLU ALA SEQRES 3 A 31 LYS GLN LYS GLN GLY HET ZN A 101 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ LINK SG CYS A 9 ZN ZN A 101 1555 1555 2.30 LINK SG CYS A 12 ZN ZN A 101 1555 1555 1.99 LINK NE2 HIS A 17 ZN ZN A 101 1555 1555 2.20 LINK SG CYS A 22 ZN ZN A 101 1555 1555 2.30 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