HEADER TRANSFERASE 20-JUN-18 6GV3 TITLE STRUCTURE OF THE E2 CONJUGATING ENZYME, SCE1, FROM ARABIDOPSIS TITLE 2 THALIANA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUMO-CONJUGATING ENZYME SCE1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN EMBRYO DEFECTIVE 1637,PROTEIN HUS5 HOMOLOG,SUMO- COMPND 5 CONJUGATING ENZYME 1,ATSCE1; COMPND 6 EC: 2.3.2.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: SCE1, AHUS5, EMB1637, AT3G57870, T10K17.80; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SUMO CONJUGATING ENZYME, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.LIU,L.M.LOIS,D.REVERTER REVDAT 2 15-JAN-20 6GV3 1 JRNL REVDAT 1 03-JUL-19 6GV3 0 JRNL AUTH B.LIU,L.M.LOIS,D.REVERTER JRNL TITL STRUCTURAL INSIGHTS INTO SUMO E1-E2 INTERACTIONS IN JRNL TITL 2 ARABIDOPSIS UNCOVERS A DISTINCTIVE PLATFORM FOR SECURING JRNL TITL 3 SUMO CONJUGATION SPECIFICITY ACROSS EVOLUTION. JRNL REF BIOCHEM.J. V. 476 2127 2019 JRNL REFN ESSN 1470-8728 JRNL PMID 31292170 JRNL DOI 10.1042/BCJ20190232 REMARK 2 REMARK 2 RESOLUTION. 1.20 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 49227 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 2429 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 44.4125 - 3.0873 0.99 2974 154 0.1722 0.2129 REMARK 3 2 3.0873 - 2.4505 1.00 2831 154 0.1960 0.1947 REMARK 3 3 2.4505 - 2.1408 1.00 2811 136 0.1789 0.2260 REMARK 3 4 2.1408 - 1.9450 1.00 2778 126 0.1770 0.2009 REMARK 3 5 1.9450 - 1.8056 1.00 2796 140 0.1830 0.2020 REMARK 3 6 1.8056 - 1.6991 1.00 2763 162 0.1910 0.2180 REMARK 3 7 1.6991 - 1.6141 0.99 2728 153 0.1797 0.2210 REMARK 3 8 1.6141 - 1.5438 1.00 2766 114 0.1908 0.2093 REMARK 3 9 1.5438 - 1.4844 1.00 2715 148 0.1886 0.2111 REMARK 3 10 1.4844 - 1.4331 1.00 2736 130 0.1999 0.2144 REMARK 3 11 1.4331 - 1.3883 1.00 2753 154 0.2084 0.2238 REMARK 3 12 1.3883 - 1.3486 1.00 2728 157 0.2109 0.2240 REMARK 3 13 1.3486 - 1.3131 1.00 2695 145 0.2155 0.2076 REMARK 3 14 1.3131 - 1.2811 1.00 2707 158 0.2276 0.2605 REMARK 3 15 1.2811 - 1.2520 0.97 2661 126 0.2463 0.2771 REMARK 3 16 1.2520 - 1.2253 0.98 2693 126 0.2524 0.2573 REMARK 3 17 1.2253 - 1.2008 0.98 2663 146 0.2615 0.2570 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.310 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 : 0.014 1361 REMARK 3 ANGLE : 1.507 1862 REMARK 3 CHIRALITY : 0.071 187 REMARK 3 PLANARITY : 0.011 249 REMARK 3 DIHEDRAL : 11.923 517 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -9.4754 -2.3564 9.0488 REMARK 3 T TENSOR REMARK 3 T11: 0.0630 T22: 0.0658 REMARK 3 T33: 0.0632 T12: 0.0011 REMARK 3 T13: 0.0030 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.2806 L22: 0.1754 REMARK 3 L33: 0.1550 L12: -0.2747 REMARK 3 L13: 0.1954 L23: -0.1175 REMARK 3 S TENSOR REMARK 3 S11: -0.0314 S12: -0.0604 S13: 0.0530 REMARK 3 S21: -0.0101 S22: 0.0295 S23: -0.0390 REMARK 3 S31: 0.0087 S32: -0.0364 S33: -0.0116 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 6GV3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49524 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.201 REMARK 200 RESOLUTION RANGE LOW (A) : 50.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CARBOXYLIC ACID 0,1 M; BUFFER SYSTEM 1 REMARK 280 0,1 M (MORPHEUS, MD); PEG550MME-PEG20000 30%, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 16.46200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.88800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.19100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.88800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.46200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.19100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 159 REMARK 465 VAL A 160 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 HIS A 84 144.98 -170.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 157 ALA A 158 145.22 REMARK 500 REMARK 500 REMARK: NULL DBREF 6GV3 A 1 160 UNP Q42551 SCE1_ARATH 1 160 SEQADV 6GV3 MET A -19 UNP Q42551 INITIATING METHIONINE SEQADV 6GV3 GLY A -18 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 SER A -17 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 SER A -16 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 HIS A -15 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 HIS A -14 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 HIS A -13 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 HIS A -12 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 HIS A -11 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 HIS A -10 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 SER A -9 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 SER A -8 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 GLY A -7 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 LEU A -6 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 VAL A -5 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 PRO A -4 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 ARG A -3 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 GLY A -2 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 SER A -1 UNP Q42551 EXPRESSION TAG SEQADV 6GV3 HIS A 0 UNP Q42551 EXPRESSION TAG SEQRES 1 A 180 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 180 LEU VAL PRO ARG GLY SER HIS MET ALA SER GLY ILE ALA SEQRES 3 A 180 ARG GLY ARG LEU ALA GLU GLU ARG LYS SER TRP ARG LYS SEQRES 4 A 180 ASN HIS PRO HIS GLY PHE VAL ALA LYS PRO GLU THR GLY SEQRES 5 A 180 GLN ASP GLY THR VAL ASN LEU MET VAL TRP HIS CYS THR SEQRES 6 A 180 ILE PRO GLY LYS ALA GLY THR ASP TRP GLU GLY GLY PHE SEQRES 7 A 180 PHE PRO LEU THR MET HIS PHE SER GLU ASP TYR PRO SER SEQRES 8 A 180 LYS PRO PRO LYS CYS LYS PHE PRO GLN GLY PHE PHE HIS SEQRES 9 A 180 PRO ASN VAL TYR PRO SER GLY THR VAL CYS LEU SER ILE SEQRES 10 A 180 LEU ASN GLU ASP TYR GLY TRP ARG PRO ALA ILE THR VAL SEQRES 11 A 180 LYS GLN ILE LEU VAL GLY ILE GLN ASP LEU LEU ASP THR SEQRES 12 A 180 PRO ASN PRO ALA ASP PRO ALA GLN THR ASP GLY TYR HIS SEQRES 13 A 180 LEU PHE CYS GLN ASP PRO VAL GLU TYR LYS LYS ARG VAL SEQRES 14 A 180 LYS LEU GLN SER LYS GLN TYR PRO ALA LEU VAL FORMUL 2 HOH *179(H2 O) HELIX 1 AA1 GLY A 4 ASN A 20 1 17 HELIX 2 AA2 LEU A 95 ASN A 99 5 5 HELIX 3 AA3 THR A 109 THR A 123 1 15 HELIX 4 AA4 GLN A 131 ASP A 141 1 11 HELIX 5 AA5 ASP A 141 TYR A 156 1 16 SHEET 1 AA1 4 VAL A 26 THR A 31 0 SHEET 2 AA1 4 VAL A 37 PRO A 47 -1 O VAL A 41 N GLU A 30 SHEET 3 AA1 4 PHE A 58 HIS A 64 -1 O MET A 63 N TRP A 42 SHEET 4 AA1 4 LYS A 75 LYS A 77 -1 O LYS A 75 N HIS A 64 CISPEP 1 TYR A 69 PRO A 70 0 7.96 CRYST1 32.924 50.382 93.776 90.00 90.00 90.00 P 21 21 21 4 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 0.030373 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019848 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010664 0.00000