PDB Short entry for 1ZU1 HEADER RNA BINDING PROTEIN 29-MAY-05 1ZU1 TITLE SOLUTION STRUCTURE OF THE N-TERMINAL ZINC FINGERS OF THE XENOPUS TITLE 2 LAEVIS DOUBLE STRANDED RNA BINDING PROTEIN ZFA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA BINDING PROTEIN ZFA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DSRBP-ZFA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: T7; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS ZINC FINGER PROTEIN, HELIX-LOOP-HELIX, HELIX-TURN-HELIX, RNA BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.M.MOLLER,M.A.MARTINEZ-YAMOUT,H.J.DYSON,P.E.WRIGHT REVDAT 3 02-MAR-22 1ZU1 1 REMARK LINK REVDAT 2 24-FEB-09 1ZU1 1 VERSN REVDAT 1 20-SEP-05 1ZU1 0 JRNL AUTH H.M.MOLLER,M.A.MARTINEZ-YAMOUT,H.J.DYSON,P.E.WRIGHT JRNL TITL SOLUTION STRUCTURE OF THE N-TERMINAL ZINC FINGERS OF THE JRNL TITL 2 XENOPUS LAEVIS DOUBLE-STRANDED RNA-BINDING PROTEIN ZFA JRNL REF J.MOL.BIOL. V. 351 718 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16051273 JRNL DOI 10.1016/J.JMB.2005.06.032 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.1-3.5, AMBER 8 REMARK 3 AUTHORS : BRUKER (XWINNMR), REMARK 3 D.A.CASE,T.CHEATHAM,T.DARDEN,H.GOHLKE,R.LUO,K.M.J.MERZ, REMARK 3 A.ONUFRIEV,C.SIMMERLING,B.WANG,R.WOODS. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1142 UNIQUE NOE RESTRAINTS, 216 REMARK 3 DIHEDRAL ANGLE RESTRAINTS REMARK 4 REMARK 4 1ZU1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033117. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 100MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM DSRBP-ZFA2-128 U-15N, 25MM REMARK 210 TRIS-BUFFER, 100MM NACL, 2MM DTT, REMARK 210 PH=6.9, 95% H2O, 5% D2O; 1MM REMARK 210 DSRBP-ZFA2-128 U-15N,13C, 25MM REMARK 210 TRIS-BUFFER, 100MM NACL, 2MM DTT, REMARK 210 PH=6.9, 95% H2O, 5% D2O; 1MM REMARK 210 DSRBP-ZFA2-128 U-15N,13C, 25MM REMARK 210 TRIS-BUFFER, 100MM NACL, 2MM DTT, REMARK 210 PH=6.9, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; HNHA; 3D_ REMARK 210 HACAHB-COSY; 13C [13CO] AND 13C REMARK 210 [15N] SPIN-ECHO DIFFERENCE CT REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, NMRVIEW 5.0.4, REMARK 210 CYANA 1.0.5 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 THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE PROTEIN CONSISTS OF TWO DOMAINS THAT TUMBLE MORE OR REMARK 210 LESS INDEPENDENTLY. THE LINKER CONNECTING BOTH DOMAINS IS REMARK 210 COMPLETELY DISORDERD. 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 5 GLU A 127 CG GLU A 127 CD 0.101 REMARK 500 REMARK 500 REMARK: NULL 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 1 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 124 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 GLU A 127 OE1 - CD - OE2 ANGL. DEV. = 44.6 DEGREES REMARK 500 5 GLU A 127 CG - CD - OE1 ANGL. DEV. = -34.4 DEGREES REMARK 500 5 GLU A 127 CG - CD - OE2 ANGL. DEV. = -34.2 DEGREES REMARK 500 6 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 13 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 13 ARG A 124 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 126 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.3 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 THR A 34 10.47 -143.20 REMARK 500 1 SER A 40 55.63 38.50 REMARK 500 1 ASN A 69 47.31 -71.32 REMARK 500 1 ALA A 77 36.75 -67.83 REMARK 500 1 LYS A 81 -35.58 -155.61 REMARK 500 2 PHE A 5 30.72 -152.20 REMARK 500 2 SER A 40 55.45 34.96 REMARK 500 2 ASP A 73 21.74 -141.11 REMARK 500 2 ALA A 83 70.31 -119.77 REMARK 500 2 ALA A 85 -10.62 -141.83 REMARK 500 3 SER A 40 55.92 38.44 REMARK 500 3 ILE A 44 -7.79 -56.25 REMARK 500 3 PRO A 84 39.10 -74.24 REMARK 500 3 ALA A 85 23.72 -140.50 REMARK 500 3 ASP A 89 24.92 -144.55 REMARK 500 3 ARG A 93 -75.47 -6.99 REMARK 500 3 SER A 94 -37.50 37.80 REMARK 500 4 GLU A 4 24.14 -142.54 REMARK 500 4 SER A 40 54.38 32.35 REMARK 500 4 GLU A 72 42.82 -72.51 REMARK 500 4 ALA A 85 -35.29 -156.57 REMARK 500 4 SER A 88 -64.31 -146.26 REMARK 500 4 ASP A 89 -34.09 -156.63 REMARK 500 4 ARG A 93 28.97 -76.91 REMARK 500 5 ASP A 3 -36.29 -142.15 REMARK 500 5 ASP A 12 17.31 -68.47 REMARK 500 5 VAL A 15 25.12 -140.65 REMARK 500 5 SER A 40 53.61 36.65 REMARK 500 5 ASN A 69 3.36 -65.24 REMARK 500 5 ASP A 73 48.49 -72.54 REMARK 500 5 ALA A 77 41.21 -70.81 REMARK 500 5 ILE A 87 34.83 -82.22 REMARK 500 5 GLU A 91 21.19 -141.46 REMARK 500 6 PHE A 5 -30.81 -150.22 REMARK 500 6 SER A 40 56.55 36.47 REMARK 500 6 ILE A 44 2.08 -66.53 REMARK 500 6 PRO A 76 -9.42 -58.34 REMARK 500 6 ALA A 77 45.23 -69.58 REMARK 500 6 ASP A 89 56.26 -140.28 REMARK 500 6 SER A 94 40.55 -73.28 REMARK 500 7 PHE A 5 -1.71 -155.44 REMARK 500 7 ASP A 9 -44.10 -155.16 REMARK 500 7 PRO A 14 166.86 -48.92 REMARK 500 7 VAL A 15 19.77 -144.16 REMARK 500 7 SER A 40 56.87 37.47 REMARK 500 8 PHE A 5 -39.96 -144.53 REMARK 500 8 SER A 40 58.52 37.38 REMARK 500 8 ILE A 44 1.79 -65.36 REMARK 500 8 ILE A 68 -46.08 -131.16 REMARK 500 8 GLU A 72 -39.81 -158.02 REMARK 500 REMARK 500 THIS ENTRY HAS 114 RAMACHANDRAN OUTLIERS. 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 129 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 CYS A 39 SG 113.4 REMARK 620 3 HIS A 52 NE2 110.5 106.3 REMARK 620 4 HIS A 58 ND1 112.0 109.1 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 130 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 97 SG REMARK 620 2 CYS A 100 SG 110.5 REMARK 620 3 HIS A 113 NE2 111.2 106.3 REMARK 620 4 HIS A 119 ND1 109.3 113.6 105.8 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 129 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 130 DBREF 1ZU1 A 2 128 UNP Q8AVN9 Q8AVN9_XENLA 2 128 SEQRES 1 A 127 ALA ASP GLU PHE GLY ASN GLY ASP ALA LEU ASP LEU PRO SEQRES 2 A 127 VAL GLY LYS ASP ALA VAL ASN SER LEU ILE ARG GLU ASN SEQRES 3 A 127 SER HIS ILE PHE SER ASP THR GLN CYS LYS VAL CYS SER SEQRES 4 A 127 ALA VAL LEU ILE SER GLU SER GLN LYS LEU ALA HIS TYR SEQRES 5 A 127 GLN SER ARG LYS HIS ALA ASN LYS VAL ARG ARG TYR MET SEQRES 6 A 127 ALA ILE ASN GLN GLY GLU ASP SER VAL PRO ALA LYS LYS SEQRES 7 A 127 PHE LYS ALA ALA PRO ALA GLU ILE SER ASP GLY GLU ASP SEQRES 8 A 127 ARG SER LYS CYS CYS PRO VAL CYS ASN MET THR PHE SER SEQRES 9 A 127 SER PRO VAL VAL ALA GLU SER HIS TYR ILE GLY LYS THR SEQRES 10 A 127 HIS ILE LYS ASN LEU ARG LEU ARG GLU GLN HET ZN A 129 1 HET ZN A 130 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 GLY A 16 ASN A 27 1 12 HELIX 2 2 SER A 45 SER A 55 1 11 HELIX 3 3 SER A 55 ASN A 69 1 15 HELIX 4 4 SER A 106 ILE A 115 1 10 HELIX 5 5 GLY A 116 GLN A 128 1 13 SHEET 1 A 2 GLN A 35 CYS A 36 0 SHEET 2 A 2 ALA A 41 VAL A 42 -1 O ALA A 41 N CYS A 36 SHEET 1 B 2 CYS A 96 CYS A 97 0 SHEET 2 B 2 MET A 102 THR A 103 -1 O MET A 102 N CYS A 97 LINK SG CYS A 36 ZN ZN A 129 1555 1555 2.30 LINK SG CYS A 39 ZN ZN A 129 1555 1555 2.29 LINK NE2 HIS A 52 ZN ZN A 129 1555 1555 2.08 LINK ND1 HIS A 58 ZN ZN A 129 1555 1555 2.08 LINK SG CYS A 97 ZN ZN A 130 1555 1555 2.29 LINK SG CYS A 100 ZN ZN A 130 1555 1555 2.29 LINK NE2 HIS A 113 ZN ZN A 130 1555 1555 2.08 LINK ND1 HIS A 119 ZN ZN A 130 1555 1555 2.09 SITE 1 AC1 4 CYS A 36 CYS A 39 HIS A 52 HIS A 58 SITE 1 AC2 4 CYS A 97 CYS A 100 HIS A 113 HIS A 119 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