HEADER RNA BINDING PROTEIN 14-FEB-15 2MZJ TITLE NMR-STRUCTURE OF THE NOP6-RBD FROM S. CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOLAR PROTEIN 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NOP6-RBD; 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: NOP6, YDL213C, D1018; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET11 KEYWDS RNA BINDING DOMAIN, RBD, RRM, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.WURM,A.LIOUTIKOV,P.KOETTER,K.ENTIAN,J.WOEHNERT REVDAT 2 14-JUN-23 2MZJ 1 REMARK REVDAT 1 13-APR-16 2MZJ 0 JRNL AUTH J.WURM,A.LIOUTIKOV,P.KOETTER,K.ENTIAN,J.WOEHNERT JRNL TITL NOT KNOWN YET JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UNIO, OPAL REMARK 3 AUTHORS : HERRMANN (UNIO), LUGINBUHL P, GUNTERT P, BILLETER REMARK 3 M, WUTHRICH K. (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000104232. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0.13 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] ENTITY, 100 MM REMARK 210 SODIUM CHLORIDE, 8 MM SODIUM REMARK 210 PHOSPHATE, 2 MM POTASSIUM REMARK 210 PHOSPHATE, 2.7 MM POTASSIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 1 MM REMARK 210 [U-13C; U-15N] ENTITY, 100 MM REMARK 210 SODIUM CHLORIDE, 8 MM SODIUM REMARK 210 PHOSPHATE, 2 MM POTASSIUM REMARK 210 PHOSPHATE, 2.7 MM POTASSIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 3D HNCACB; 3D REMARK 210 HN(CA)CO; 3D HNCO; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D REMARK 210 H(CCO)NH; 3D HBHA(CO)NH; 3D C(CO) REMARK 210 NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR 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 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 8 ARG A 3 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 51 NE - CZ - NH2 ANGL. DEV. = -3.1 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 ASN A 2 40.76 -73.72 REMARK 500 1 SER A 28 71.42 49.78 REMARK 500 1 VAL A 80 -65.93 160.60 REMARK 500 2 GLU A 71 14.43 59.12 REMARK 500 2 VAL A 80 86.19 57.52 REMARK 500 3 SER A 28 81.41 56.59 REMARK 500 3 ASP A 50 96.95 -166.01 REMARK 500 4 SER A 10 17.09 82.90 REMARK 500 4 SER A 28 77.14 47.55 REMARK 500 4 ASP A 50 84.02 -157.00 REMARK 500 4 VAL A 80 -39.34 -166.82 REMARK 500 5 ASN A 2 45.31 -151.54 REMARK 500 5 SER A 28 70.44 48.58 REMARK 500 5 VAL A 80 77.77 38.94 REMARK 500 6 VAL A 80 79.13 59.49 REMARK 500 7 SER A 28 75.21 62.81 REMARK 500 7 ASP A 50 86.71 -150.14 REMARK 500 7 VAL A 80 113.03 68.15 REMARK 500 8 SER A 10 6.30 84.99 REMARK 500 8 SER A 28 72.35 60.69 REMARK 500 8 LEU A 63 -6.82 -58.41 REMARK 500 8 VAL A 80 90.59 48.93 REMARK 500 9 VAL A 80 160.40 70.53 REMARK 500 10 ASN A 2 1.26 -67.06 REMARK 500 10 SER A 28 73.53 49.15 REMARK 500 10 ASP A 50 86.13 -158.45 REMARK 500 11 SER A 28 79.78 37.32 REMARK 500 11 ASP A 50 85.04 -168.42 REMARK 500 11 THR A 79 82.42 -153.54 REMARK 500 12 SER A 28 69.54 63.74 REMARK 500 12 ASP A 50 96.29 -162.22 REMARK 500 12 VAL A 80 -49.38 68.70 REMARK 500 13 ASN A 2 37.50 -141.74 REMARK 500 13 ASP A 50 90.40 -163.81 REMARK 500 13 VAL A 80 95.24 64.54 REMARK 500 14 SER A 28 77.33 41.68 REMARK 500 14 ASP A 50 71.91 -108.57 REMARK 500 14 VAL A 80 -44.89 -167.89 REMARK 500 15 ASN A 2 52.18 -152.12 REMARK 500 15 SER A 28 74.15 49.17 REMARK 500 15 ASP A 50 90.33 -166.03 REMARK 500 15 VAL A 80 86.65 53.27 REMARK 500 16 ASN A 2 40.49 -77.35 REMARK 500 16 SER A 28 79.95 54.40 REMARK 500 16 ARG A 35 79.40 -115.17 REMARK 500 16 ASP A 50 88.48 -161.35 REMARK 500 16 VAL A 80 91.42 46.01 REMARK 500 17 ASP A 50 73.84 -116.34 REMARK 500 17 VAL A 80 85.58 50.07 REMARK 500 18 ASN A 2 5.57 -60.35 REMARK 500 REMARK 500 THIS ENTRY HAS 58 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 51 0.12 SIDE CHAIN REMARK 500 4 ARG A 57 0.11 SIDE CHAIN REMARK 500 7 ARG A 13 0.09 SIDE CHAIN REMARK 500 8 ARG A 3 0.12 SIDE CHAIN REMARK 500 9 ARG A 57 0.10 SIDE CHAIN REMARK 500 10 ARG A 57 0.09 SIDE CHAIN REMARK 500 11 ARG A 33 0.08 SIDE CHAIN REMARK 500 12 ARG A 57 0.08 SIDE CHAIN REMARK 500 18 ARG A 3 0.08 SIDE CHAIN REMARK 500 18 ARG A 51 0.09 SIDE CHAIN REMARK 500 18 ARG A 56 0.09 SIDE CHAIN REMARK 500 19 ARG A 51 0.09 SIDE CHAIN REMARK 500 20 ARG A 57 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19098 RELATED DB: BMRB DBREF 2MZJ A 1 82 UNP Q07623 NOP6_YEAST 75 156 SEQRES 1 A 82 GLY ASN ARG PHE ILE VAL PHE VAL GLY SER LEU PRO ARG SEQRES 2 A 82 ASP ILE THR ALA VAL GLU LEU GLN ASN HIS PHE LYS ASN SEQRES 3 A 82 SER SER PRO ASP GLN ILE ARG LEU ARG ALA ASP LYS GLY SEQRES 4 A 82 ILE ALA PHE LEU GLU PHE ASP ALA ASP LYS ASP ARG THR SEQRES 5 A 82 GLY ILE GLN ARG ARG MET ASP ILE ALA LEU LEU GLN HIS SEQRES 6 A 82 GLY THR LEU LEU LYS GLU LYS LYS ILE ASN VAL GLU LEU SEQRES 7 A 82 THR VAL GLY GLY HELIX 1 1 THR A 16 LYS A 25 1 10 HELIX 2 2 ALA A 36 LYS A 38 5 3 HELIX 3 3 ASP A 48 ASP A 50 5 3 HELIX 4 4 GLY A 53 LEU A 63 1 11 SHEET 1 A 4 ARG A 33 ARG A 35 0 SHEET 2 A 4 ILE A 40 ASP A 46 -1 O ILE A 40 N ARG A 35 SHEET 3 A 4 ARG A 3 GLY A 9 -1 N PHE A 4 O PHE A 45 SHEET 4 A 4 ASN A 75 THR A 79 -1 O GLU A 77 N PHE A 7 SHEET 1 B 2 LEU A 68 LEU A 69 0 SHEET 2 B 2 LYS A 72 LYS A 73 -1 O LYS A 72 N LEU A 69 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