HEADER RNA BINDING PROTEIN 13-AUG-15 5D77 TITLE STRUCTURE OF MIP6 RRM3 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN MIP6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MEX67-INTERACTING PROTEIN 6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 GENE: MIP6, YHR015W; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: CODON PLUS KEYWDS RNA BINDING PROTEIN, RNA BINDING DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR N.MOHAMAD,J.BRAVO REVDAT 2 10-JAN-24 5D77 1 REMARK REVDAT 1 17-AUG-16 5D77 0 JRNL AUTH N.MOHAMAD,J.BRAVO JRNL TITL STRUCTURE OF MIP6 RRM3 DOMAIN AT 1.3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 15738 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 782 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.7769 - 2.3620 1.00 2702 140 0.1527 0.1651 REMARK 3 2 2.3620 - 1.8749 1.00 2529 132 0.1472 0.1867 REMARK 3 3 1.8749 - 1.6379 1.00 2476 139 0.1446 0.1911 REMARK 3 4 1.6379 - 1.4881 1.00 2475 131 0.1487 0.2345 REMARK 3 5 1.4881 - 1.3815 1.00 2450 124 0.1590 0.2086 REMARK 3 6 1.3815 - 1.3000 0.95 2324 116 0.1741 0.2603 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 699 REMARK 3 ANGLE : 1.278 944 REMARK 3 CHIRALITY : 0.077 103 REMARK 3 PLANARITY : 0.006 121 REMARK 3 DIHEDRAL : 19.177 276 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5D77 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212748. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15814 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.45000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3FEY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M SODIUM CITRATE TRIBASIC DIHYDRATE REMARK 280 PH 6.5; AMMONIUM NITRATE, VAPOR DIFFUSION, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.90800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.15500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.15500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.86200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.15500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.15500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.95400 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.15500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.15500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 68.86200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.15500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.15500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.95400 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 45.90800 REMARK 290 REMARK 290 REMARK: NULL 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: 570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 504 O HOH A 542 2.12 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 ASN A 379 -8.65 78.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 DBREF 5D77 A 313 388 UNP P38760 MIP6_YEAST 313 388 SEQADV 5D77 GLY A -5 UNP P38760 EXPRESSION TAG SEQADV 5D77 PRO A -4 UNP P38760 EXPRESSION TAG SEQADV 5D77 LEU A -3 UNP P38760 EXPRESSION TAG SEQADV 5D77 GLY A -2 UNP P38760 EXPRESSION TAG SEQADV 5D77 SER A -1 UNP P38760 EXPRESSION TAG SEQADV 5D77 MET A 0 UNP P38760 EXPRESSION TAG SEQRES 1 A 82 GLY PRO LEU GLY SER MET LYS THR ILE LEU VAL LYS ASN SEQRES 2 A 82 LEU PRO SER ASP THR THR GLN GLU GLU VAL LEU ASP TYR SEQRES 3 A 82 PHE SER THR ILE GLY PRO ILE LYS SER VAL PHE ILE SER SEQRES 4 A 82 GLU LYS GLN ALA ASN THR PRO HIS LYS ALA PHE VAL THR SEQRES 5 A 82 TYR LYS ASN GLU GLU GLU SER LYS LYS ALA GLN LYS CSO SEQRES 6 A 82 LEU ASN LYS THR ILE PHE LYS ASN HIS THR ILE TRP VAL SEQRES 7 A 82 GLY PRO GLY LYS MODRES 5D77 CSO A 371 CYS MODIFIED RESIDUE HET CSO A 371 12 HET CIT A 401 18 HET NO3 A 402 4 HET NO3 A 403 4 HET NA A 404 1 HETNAM CSO S-HYDROXYCYSTEINE HETNAM CIT CITRIC ACID HETNAM NO3 NITRATE ION HETNAM NA SODIUM ION FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 CIT C6 H8 O7 FORMUL 3 NO3 2(N O3 1-) FORMUL 5 NA NA 1+ FORMUL 6 HOH *51(H2 O) HELIX 1 AA1 THR A 325 SER A 334 1 10 HELIX 2 AA2 ASN A 361 ASN A 373 1 13 SHEET 1 AA1 4 ILE A 339 ILE A 344 0 SHEET 2 AA1 4 HIS A 353 TYR A 359 -1 O THR A 358 N LYS A 340 SHEET 3 AA1 4 THR A 314 LEU A 320 -1 N ILE A 315 O VAL A 357 SHEET 4 AA1 4 TRP A 383 PRO A 386 -1 O TRP A 383 N LYS A 318 SHEET 1 AA2 2 ILE A 376 PHE A 377 0 SHEET 2 AA2 2 HIS A 380 THR A 381 -1 O HIS A 380 N PHE A 377 LINK C LYS A 370 N CSO A 371 1555 1555 1.33 LINK C CSO A 371 N LEU A 372 1555 1555 1.33 LINK OG SER A 345 NA NA A 404 1555 1555 2.72 CISPEP 1 GLY A -5 PRO A -4 0 3.55 SITE 1 AC1 10 LYS A 318 SER A 322 ASP A 323 PRO A 338 SITE 2 AC1 10 ALA A 349 LYS A 360 LYS A 374 HOH A 510 SITE 3 AC1 10 HOH A 511 HOH A 532 SITE 1 AC2 11 LYS A 318 ASN A 319 ASP A 323 PRO A 352 SITE 2 AC2 11 HIS A 353 LYS A 354 LYS A 378 TRP A 383 SITE 3 AC2 11 HOH A 505 HOH A 518 HOH A 537 SITE 1 AC3 9 PRO A -4 LEU A 316 LYS A 318 PRO A 321 SITE 2 AC3 9 PHE A 343 LYS A 354 LYS A 378 HIS A 380 SITE 3 AC3 9 HOH A 504 SITE 1 AC4 5 GLN A 326 ILE A 344 SER A 345 GLU A 346 SITE 2 AC4 5 ASN A 379 CRYST1 36.310 36.310 91.816 90.00 90.00 90.00 P 43 21 2 8 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 0.027541 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027541 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010891 0.00000