HEADER LIGASE 28-AUG-10 3ONH TITLE CRYSTAL STRUCTURE OF UBA2UFD-UBC9: INSIGHTS INTO E1-E2 INTERACTIONS IN TITLE 2 SUMO PATHWAYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-ACTIVATING ENZYME E1-LIKE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 439-563; COMPND 5 SYNONYM: SMT3-ACTIVATING ENZYME SUBUNIT 2, POLYMERASE-INTERACTING COMPND 6 PROTEIN 2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: UBA2, PIP2, UAL1, YDR390C, D9509.10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGASE, SUMO CONJUGATION, UBC9 EXPDTA X-RAY DIFFRACTION AUTHOR J.WANG,A.M.TAHERBHOY,H.W.HUNT,S.N.SEYEDIN,D.W.MILLER,D.T.HUANG, AUTHOR 2 B.A.SCHULMAN REVDAT 3 06-SEP-23 3ONH 1 SEQADV REVDAT 2 23-JAN-13 3ONH 1 JRNL VERSN REVDAT 1 12-JAN-11 3ONH 0 JRNL AUTH J.WANG,A.M.TAHERBHOY,H.W.HUNT,S.N.SEYEDIN,D.W.MILLER, JRNL AUTH 2 D.J.MILLER,D.T.HUANG,B.A.SCHULMAN JRNL TITL CRYSTAL STRUCTURE OF UBA2(UFD)-UBC9: INSIGHTS INTO E1-E2 JRNL TITL 2 INTERACTIONS IN SUMO PATHWAYS. JRNL REF PLOS ONE V. 5 15805 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 21209884 JRNL DOI 10.1371/JOURNAL.PONE.0015805 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 20193 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1041 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 25.3621 - 3.0619 0.93 2879 151 0.1108 0.1350 REMARK 3 2 3.0619 - 2.4310 0.94 2868 175 0.1568 0.1842 REMARK 3 3 2.4310 - 2.1239 0.94 2864 134 0.1724 0.1882 REMARK 3 4 2.1239 - 1.9297 0.94 2818 153 0.1850 0.2043 REMARK 3 5 1.9297 - 1.7915 0.90 2738 163 0.2034 0.2014 REMARK 3 6 1.7915 - 1.6859 0.86 2602 112 0.2339 0.2651 REMARK 3 7 1.6859 - 1.6010 0.80 2403 122 0.2545 0.2563 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 : 0.39 REMARK 3 B_SOL : 39.88 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.960 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) : -0.89880 REMARK 3 B22 (A**2) : -0.89880 REMARK 3 B33 (A**2) : 1.79750 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.006 896 REMARK 3 ANGLE : 0.982 1212 REMARK 3 CHIRALITY : 0.064 145 REMARK 3 PLANARITY : 0.003 157 REMARK 3 DIHEDRAL : 17.956 336 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 3ONH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : KOHZU REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20193 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 3ONG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3M (NH4)2SO4, 1% MPD, PH 7.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.09600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.09600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.36400 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.09600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.09600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.36400 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 40.09600 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 40.09600 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.36400 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 40.09600 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 40.09600 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.36400 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 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 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 GLY A 437 REMARK 465 SER A 438 REMARK 465 SER A 439 REMARK 465 ASN A 553 REMARK 465 ASN A 554 REMARK 465 SER A 555 REMARK 465 PRO A 556 REMARK 465 SER A 557 REMARK 465 LYS A 558 REMARK 465 ASN A 559 REMARK 465 GLU A 560 REMARK 465 GLU A 561 REMARK 465 GLU A 562 REMARK 465 GLU A 563 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 533 CG OD1 OD2 REMARK 470 GLU A 534 CG CD OE1 OE2 REMARK 470 LYS A 551 CG CD CE NZ 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 2 O HOH A 16 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 4 O HOH A 16 6555 2.08 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 ASP A 490 -12.07 -148.70 REMARK 500 ASP A 518 -78.30 -64.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ONG RELATED DB: PDB DBREF 3ONH A 439 563 UNP P52488 UBA2_YEAST 439 563 SEQADV 3ONH GLY A 437 UNP P52488 EXPRESSION TAG SEQADV 3ONH SER A 438 UNP P52488 EXPRESSION TAG SEQRES 1 A 127 GLY SER SER LYS VAL CYS ARG GLY VAL ILE LYS LEU SER SEQRES 2 A 127 SER ASP CYS LEU ASN LYS MET LYS LEU SER ASP PHE VAL SEQRES 3 A 127 VAL LEU ILE ARG GLU LYS TYR SER TYR PRO GLN ASP ILE SEQRES 4 A 127 SER LEU LEU ASP ALA SER ASN GLN ARG LEU LEU PHE ASP SEQRES 5 A 127 TYR ASP PHE GLU ASP LEU ASN ASP ARG THR LEU SER GLU SEQRES 6 A 127 ILE ASN LEU GLY ASN GLY SER ILE ILE LEU PHE SER ASP SEQRES 7 A 127 GLU GLU GLY ASP THR MET ILE ARG LYS ALA ILE GLU LEU SEQRES 8 A 127 PHE LEU ASP VAL ASP ASP GLU LEU PRO CYS ASN THR CYS SEQRES 9 A 127 SER LEU PRO ASP VAL GLU VAL PRO LEU ILE LYS ALA ASN SEQRES 10 A 127 ASN SER PRO SER LYS ASN GLU GLU GLU GLU FORMUL 2 HOH *81(H2 O) HELIX 1 1 SER A 449 MET A 456 1 8 HELIX 2 2 LYS A 457 SER A 470 1 14 SHEET 1 A 6 ARG A 484 ASP A 488 0 SHEET 2 A 6 ILE A 475 ASP A 479 -1 N LEU A 477 O PHE A 487 SHEET 3 A 6 ILE A 509 ASP A 514 -1 O SER A 513 N SER A 476 SHEET 4 A 6 ILE A 525 VAL A 531 -1 O LEU A 527 N ILE A 510 SHEET 5 A 6 CYS A 442 LEU A 448 1 N CYS A 442 O GLU A 526 SHEET 6 A 6 CYS A 540 SER A 541 -1 O SER A 541 N LYS A 447 SHEET 1 B 2 MET A 520 ARG A 522 0 SHEET 2 B 2 LEU A 549 LYS A 551 -1 O ILE A 550 N ILE A 521 CISPEP 1 ASP A 533 GLU A 534 0 4.55 CRYST1 80.192 80.192 50.728 90.00 90.00 90.00 I 4 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 0.012470 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019713 0.00000