HEADER METAL BINDING PROTEIN 12-JAN-16 2NAX TITLE STRUCTURE OF CCHC ZINC FINGER DOMAIN OF PCF11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN PCF11; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN 1 OF CF I; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: PCF11, YDR228C, YD9934.13C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-28A KEYWDS ZINC FINGER, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.YANG,G.VARANI REVDAT 4 15-MAY-24 2NAX 1 REMARK REVDAT 3 14-JUN-23 2NAX 1 REMARK SEQADV LINK REVDAT 2 26-APR-17 2NAX 1 JRNL REVDAT 1 23-NOV-16 2NAX 0 JRNL AUTH F.YANG,P.HSU,S.D.LEE,W.YANG,D.HOSKINSON,W.XU,C.MOORE, JRNL AUTH 2 G.VARANI JRNL TITL THE C TERMINUS OF PCF11 FORMS A NOVEL ZINC-FINGER STRUCTURE JRNL TITL 2 THAT PLAYS AN ESSENTIAL ROLE IN MRNA 3'-END PROCESSING. JRNL REF RNA V. 23 98 2017 JRNL REFN ESSN 1469-9001 JRNL PMID 27780845 JRNL DOI 10.1261/RNA.058354.116 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NAX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000104639. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN_1, 90% H2O/10% D2O; 1 MM REMARK 210 [U-99% 15N] PROTEIN_1, 90% H2O/ REMARK 210 10% D2O; 1 MM [U-99% 13C; U-99% REMARK 210 15N] PROTEIN_1, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY-HSQC; REMARK 210 3D 1H-13C NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, CCPNMR, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 ARG A 547 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 540 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 547 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 540 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES 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 ARG A 540 31.17 -77.98 REMARK 500 1 SER A 541 172.08 62.27 REMARK 500 1 SER A 604 88.35 -65.04 REMARK 500 1 SER A 607 -42.96 -165.31 REMARK 500 2 GLU A 581 -162.63 -121.83 REMARK 500 3 PHE A 537 -61.75 -157.73 REMARK 500 3 HIS A 601 -81.67 -75.16 REMARK 500 4 GLN A 605 -39.39 -160.30 REMARK 500 5 ASP A 539 -165.75 56.82 REMARK 500 5 GLU A 543 -29.61 -152.30 REMARK 500 5 ASP A 559 15.32 53.92 REMARK 500 6 GLU A 536 6.06 -68.84 REMARK 500 6 GLU A 555 -24.63 63.48 REMARK 500 6 GLN A 558 -36.78 68.26 REMARK 500 8 THR A 603 -65.94 -101.25 REMARK 500 8 SER A 604 -49.67 55.22 REMARK 500 10 SER A 535 0.83 -157.00 REMARK 500 10 SER A 538 -162.64 -163.85 REMARK 500 10 ASP A 539 1.34 -68.60 REMARK 500 10 GLN A 558 -62.37 59.35 REMARK 500 10 SER A 604 -72.09 -56.23 REMARK 500 10 GLN A 605 -88.93 40.66 REMARK 500 11 ARG A 540 28.42 -72.16 REMARK 500 13 SER A 541 -145.72 -74.23 REMARK 500 13 ASN A 542 11.53 -65.28 REMARK 500 13 GLN A 558 -84.43 45.36 REMARK 500 13 ASN A 606 -91.92 54.32 REMARK 500 15 GLU A 543 -65.42 -91.56 REMARK 500 15 LEU A 544 -8.50 -155.65 REMARK 500 16 SER A 538 -81.51 -80.83 REMARK 500 16 GLN A 558 -49.17 59.76 REMARK 500 16 ASN A 606 -88.95 -79.78 REMARK 500 16 SER A 607 -164.20 53.89 REMARK 500 17 SER A 538 50.26 -160.75 REMARK 500 17 ASP A 559 -11.93 60.75 REMARK 500 18 GLU A 536 -4.20 58.17 REMARK 500 18 SER A 538 150.14 -49.23 REMARK 500 18 SER A 541 -63.85 54.42 REMARK 500 18 SER A 557 43.17 -74.99 REMARK 500 18 GLN A 558 -99.13 46.84 REMARK 500 18 GLU A 581 -167.46 -111.33 REMARK 500 18 SER A 604 38.33 -95.02 REMARK 500 19 ASP A 559 19.28 56.33 REMARK 500 20 SER A 538 -52.87 -149.41 REMARK 500 20 SER A 607 -165.32 58.69 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 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 564 SG REMARK 620 2 CYS A 567 SG 112.5 REMARK 620 3 HIS A 596 ND1 97.3 106.4 REMARK 620 4 CYS A 599 SG 118.6 115.7 103.1 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 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25953 RELATED DB: BMRB DBREF 2NAX A 538 608 UNP P39081 PCF11_YEAST 538 608 SEQADV 2NAX GLY A 533 UNP P39081 EXPRESSION TAG SEQADV 2NAX GLY A 534 UNP P39081 EXPRESSION TAG SEQADV 2NAX SER A 535 UNP P39081 EXPRESSION TAG SEQADV 2NAX GLU A 536 UNP P39081 EXPRESSION TAG SEQADV 2NAX PHE A 537 UNP P39081 EXPRESSION TAG SEQRES 1 A 76 GLY GLY SER GLU PHE SER ASP ARG SER ASN GLU LEU GLU SEQRES 2 A 76 ILE ARG GLY LYS TYR VAL VAL VAL PRO GLU THR SER GLN SEQRES 3 A 76 ASP MET ALA PHE LYS CYS PRO ILE CYS LYS GLU THR VAL SEQRES 4 A 76 THR GLY VAL TYR ASP GLU GLU SER GLY GLU TRP VAL TRP SEQRES 5 A 76 LYS ASN THR ILE GLU VAL ASN GLY LYS TYR PHE HIS SER SEQRES 6 A 76 THR CYS TYR HIS GLU THR SER GLN ASN SER SER HET ZN A 701 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASN A 542 GLY A 548 1 7 HELIX 2 2 SER A 597 SER A 604 1 8 SHEET 1 A 4 TYR A 550 VAL A 553 0 SHEET 2 A 4 GLU A 581 LYS A 585 -1 O TRP A 584 N VAL A 551 SHEET 3 A 4 GLU A 569 ASP A 576 -1 N ASP A 576 O GLU A 581 SHEET 4 A 4 ALA A 561 CYS A 564 -1 N CYS A 564 O GLU A 569 SHEET 1 B 2 THR A 587 VAL A 590 0 SHEET 2 B 2 LYS A 593 HIS A 596 -1 O LYS A 593 N VAL A 590 LINK SG CYS A 564 ZN ZN A 701 1555 1555 2.36 LINK SG CYS A 567 ZN ZN A 701 1555 1555 2.34 LINK ND1 HIS A 596 ZN ZN A 701 1555 1555 2.18 LINK SG CYS A 599 ZN ZN A 701 1555 1555 2.40 SITE 1 AC1 4 CYS A 564 CYS A 567 HIS A 596 CYS A 599 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