HEADER PROTEIN BINDING 17-SEP-15 5DTC TITLE UBL STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME BIOGENESIS PROTEIN YTM1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 5-92; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_TAXID: 1294333; SOURCE 4 STRAIN: YJM1133; SOURCE 5 GENE: YTM1, H781_YJM1133O00421; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGST2 KEYWDS UBIQUITIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR E.M.ROMES,R.E.STANLEY REVDAT 5 27-SEP-23 5DTC 1 REMARK REVDAT 4 27-NOV-19 5DTC 1 JRNL REMARK REVDAT 3 20-JAN-16 5DTC 1 JRNL REVDAT 2 09-DEC-15 5DTC 1 JRNL REVDAT 1 02-DEC-15 5DTC 0 JRNL AUTH E.M.ROMES,M.SOBHANY,R.E.STANLEY JRNL TITL THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE DOMAIN OF JRNL TITL 2 RIBOSOME ASSEMBLY FACTOR YTM1 AND CHARACTERIZATION OF ITS JRNL TITL 3 INTERACTION WITH THE AAA-ATPASE MIDASIN. JRNL REF J.BIOL.CHEM. V. 291 882 2016 JRNL REFN ESSN 1083-351X JRNL PMID 26601951 JRNL DOI 10.1074/JBC.M115.693259 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 18657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 942 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 37.0657 - 3.2573 0.98 2612 136 0.1885 0.2281 REMARK 3 2 3.2573 - 2.5856 0.98 2605 134 0.1888 0.2366 REMARK 3 3 2.5856 - 2.2588 0.97 2601 145 0.1623 0.2292 REMARK 3 4 2.2588 - 2.0523 0.97 2572 143 0.1391 0.2060 REMARK 3 5 2.0523 - 1.9052 0.96 2564 126 0.1409 0.2260 REMARK 3 6 1.9052 - 1.7929 0.94 2476 130 0.1638 0.2419 REMARK 3 7 1.7929 - 1.7000 0.86 2285 128 0.1886 0.3173 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.700 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 : 0.006 1442 REMARK 3 ANGLE : 0.930 1944 REMARK 3 CHIRALITY : 0.038 222 REMARK 3 PLANARITY : 0.004 244 REMARK 3 DIHEDRAL : 11.804 552 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 5DTC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213765. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2-6.8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18667 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: PDB ENTRY 4WJS REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE, 1M SODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LEU A 92 REMARK 465 LEU B 92 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 B 135 O HOH B 161 1.82 REMARK 500 O HOH A 170 O HOH A 173 1.89 REMARK 500 O HOH B 106 O HOH B 145 1.90 REMARK 500 O HOH B 144 O HOH B 156 1.96 REMARK 500 O HOH A 166 O HOH B 124 1.98 REMARK 500 O HOH A 115 O HOH A 154 2.05 REMARK 500 O HOH B 148 O HOH B 158 2.06 REMARK 500 O HOH A 168 O HOH A 169 2.08 REMARK 500 O HOH A 150 O HOH A 167 2.10 REMARK 500 OD2 ASP B 25 O HOH B 101 2.15 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 LYS A 35 -162.20 -122.50 REMARK 500 THR A 66 -135.31 -138.48 REMARK 500 LYS B 35 -166.46 -116.89 REMARK 500 THR B 66 -156.64 -130.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 174 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 175 DISTANCE = 6.23 ANGSTROMS DBREF1 5DTC A 5 92 UNP A0A0D4FJ11_YEASX DBREF2 5DTC A A0A0D4FJ11 5 92 DBREF1 5DTC B 5 92 UNP A0A0D4FJ11_YEASX DBREF2 5DTC B A0A0D4FJ11 5 92 SEQRES 1 A 88 LYS SER GLN VAL LYS ILE ARG PHE PHE THR ARG GLU LYS SEQRES 2 A 88 ASP GLU LEU LEU HIS VAL GLN ASP THR PRO MET TYR ALA SEQRES 3 A 88 PRO ILE SER LEU LYS ARG TYR GLY LEU SER GLU ILE VAL SEQRES 4 A 88 ASN HIS LEU LEU GLY SER GLU LYS PRO VAL PRO PHE ASP SEQRES 5 A 88 PHE LEU ILE GLU GLY GLU LEU LEU ARG THR SER LEU HIS SEQRES 6 A 88 ASP TYR LEU THR LYS LYS GLY LEU SER SER GLU ALA SER SEQRES 7 A 88 LEU ASN VAL GLU TYR THR ARG ALA ILE LEU SEQRES 1 B 88 LYS SER GLN VAL LYS ILE ARG PHE PHE THR ARG GLU LYS SEQRES 2 B 88 ASP GLU LEU LEU HIS VAL GLN ASP THR PRO MET TYR ALA SEQRES 3 B 88 PRO ILE SER LEU LYS ARG TYR GLY LEU SER GLU ILE VAL SEQRES 4 B 88 ASN HIS LEU LEU GLY SER GLU LYS PRO VAL PRO PHE ASP SEQRES 5 B 88 PHE LEU ILE GLU GLY GLU LEU LEU ARG THR SER LEU HIS SEQRES 6 B 88 ASP TYR LEU THR LYS LYS GLY LEU SER SER GLU ALA SER SEQRES 7 B 88 LEU ASN VAL GLU TYR THR ARG ALA ILE LEU FORMUL 3 HOH *137(H2 O) HELIX 1 AA1 ASP A 18 HIS A 22 5 5 HELIX 2 AA2 LYS A 35 GLY A 48 1 14 HELIX 3 AA3 SER A 67 GLY A 76 1 10 HELIX 4 AA4 ASP B 18 HIS B 22 5 5 HELIX 5 AA5 LYS B 35 GLY B 48 1 14 HELIX 6 AA6 SER B 67 GLY B 76 1 10 SHEET 1 AA1 5 MET A 28 PRO A 31 0 SHEET 2 AA1 5 GLN A 7 THR A 14 -1 N ILE A 10 O MET A 28 SHEET 3 AA1 5 SER A 82 ARG A 89 1 O LEU A 83 N LYS A 9 SHEET 4 AA1 5 PHE A 55 ILE A 59 -1 N ASP A 56 O THR A 88 SHEET 5 AA1 5 GLU A 62 LEU A 63 -1 O GLU A 62 N ILE A 59 SHEET 1 AA2 5 MET B 28 PRO B 31 0 SHEET 2 AA2 5 GLN B 7 THR B 14 -1 N ILE B 10 O MET B 28 SHEET 3 AA2 5 SER B 82 ARG B 89 1 O VAL B 85 N ARG B 11 SHEET 4 AA2 5 PHE B 55 ILE B 59 -1 N ASP B 56 O THR B 88 SHEET 5 AA2 5 GLU B 62 LEU B 63 -1 O GLU B 62 N ILE B 59 CRYST1 35.298 37.738 41.134 82.54 64.31 69.62 P 1 2 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 0.028330 -0.010524 -0.013895 0.00000 SCALE2 0.000000 0.028268 0.000709 0.00000 SCALE3 0.000000 0.000000 0.026985 0.00000