HEADER NUCLEOTIDE BINDING PROTEIN 23-MAY-14 2MPJ TITLE NMR STRUCTURE OF XENOPUS RECQ4 ZINC KNUCKLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECQL4-HELICASE-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 609-633; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: CLAWED FROG,COMMON PLATANNA,PLATANNA; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 GENE: RTS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ZINC KNUCKLE, RECQ4, HELICASE, DNA/RNA BINDING, PROTEIN, NUCLEOTIDE KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR C.ZUCCHELLI,F.MARINO,A.MOJUMDAR,S.ONESTI,G.MUSCO REVDAT 3 14-JUN-23 2MPJ 1 REMARK LINK REVDAT 2 09-MAR-16 2MPJ 1 JRNL REVDAT 1 05-AUG-15 2MPJ 0 JRNL AUTH F.MARINO,A.MOJUMDAR,C.ZUCCHELLI,A.BHARDWAJ,E.BURATTI, JRNL AUTH 2 A.VINDIGNI,G.MUSCO,S.ONESTI JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF AN RNA/DNA JRNL TITL 2 BINDING MOTIF IN THE N-TERMINAL DOMAIN OF RECQ4 HELICASES JRNL REF SCI REP V. 6 21501 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 26888063 JRNL DOI 10.1038/SREP21501 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.0, ARIA 2.3.1, PROCHECKNMR REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), LINGE, O'DONOGHUE AND REMARK 3 NILGES (ARIA), LASKOWSKI AND MACARTHUR REMARK 3 (PROCHECKNMR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MPJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000103896. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 170 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1 MM RECQ4 ZINC KNUCKLE-1, REMARK 210 1.25 MM ZNCL2-2, 10 % D2O-3, 20 REMARK 210 MM SODIUM PHOSPHATE PH 6.3-4, REMARK 210 150 MM POTASSIUM CHLORIDE-5, 4 REMARK 210 MM DTT-6, 0.3 MM DSS-7, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D 1H; 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC; 2D 1H-1H TOCSY; 2D 1H-1H REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR 2.5.1, ARIA 2.3.1, TALOS, REMARK 210 PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 4 SER A 3 -21.22 -150.39 REMARK 500 7 SER A 3 38.18 -150.56 REMARK 500 8 ARG A 2 53.83 -90.76 REMARK 500 8 SER A 3 24.01 -144.80 REMARK 500 10 ARG A 2 34.48 -161.52 REMARK 500 10 SER A 3 -92.95 46.02 REMARK 500 10 SER A 18 31.36 -88.11 REMARK 500 11 SER A 3 15.15 -143.21 REMARK 500 15 SER A 3 51.27 -148.05 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 7 SG REMARK 620 2 CYS A 10 SG 108.2 REMARK 620 3 HIS A 15 NE2 109.9 110.7 REMARK 620 4 CYS A 20 SG 107.2 109.8 111.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19986 RELATED DB: BMRB DBREF 2MPJ A 1 25 UNP Q4JNX8 Q4JNX8_XENLA 606 630 SEQRES 1 A 25 ASN ARG SER GLY ASP THR CYS PHE ARG CYS GLY GLY MET SEQRES 2 A 25 GLY HIS TRP ALA SER GLN CYS PRO GLY SER VAL PRO HET ZN A 101 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 TRP A 16 CYS A 20 5 5 LINK SG CYS A 7 ZN ZN A 101 1555 1555 2.28 LINK SG CYS A 10 ZN ZN A 101 1555 1555 2.30 LINK NE2 HIS A 15 ZN ZN A 101 1555 1555 2.00 LINK SG CYS A 20 ZN ZN A 101 1555 1555 2.30 SITE 1 AC1 4 CYS A 7 CYS A 10 HIS A 15 CYS A 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 MODEL 1