HEADER UBIQUITIN CONJUGATION 19-JAN-99 2E2C TITLE E2-C, AN UBIQUITIN CONJUGATING ENZYME REQUIRED FOR THE DESTRUCTION OF TITLE 2 MITOTIC CYCLINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CONJUGATING ENZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.2.19 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPISULA SOLIDISSIMA; SOURCE 3 ORGANISM_COMMON: ATLANTIC SURF CLAM; SOURCE 4 ORGANISM_TAXID: 6584 KEYWDS UBIQUITIN CONJUGATION, UBIQUITIN CARRIER PROTEIN, THIOESTER BOND, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR F.JIANG,R.BASAVAPPA REVDAT 7 22-MAY-24 2E2C 1 REMARK REVDAT 6 09-AUG-23 2E2C 1 REMARK REVDAT 5 20-MAR-13 2E2C 1 SPRSDE REVDAT 4 16-NOV-11 2E2C 1 VERSN HETATM REVDAT 3 24-FEB-09 2E2C 1 VERSN REVDAT 2 06-APR-99 2E2C 3 COMPND REMARK HETATM CISPEP REVDAT 2 2 3 CRYST1 TER ATOM SPRSDE REVDAT 2 3 3 SHEET HELIX REVDAT 1 27-JAN-99 2E2C 0 SPRSDE 23-MAR-99 2E2C 1E2C 1BR7 JRNL AUTH F.JIANG,R.BASAVAPPA JRNL TITL CRYSTAL STRUCTURE OF THE CYCLIN-SPECIFIC JRNL TITL 2 UBIQUITIN-CONJUGATING ENZYME FROM CLAM, E2-C, AT 2.0 A JRNL TITL 3 RESOLUTION. JRNL REF BIOCHEMISTRY V. 38 6471 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10350465 JRNL DOI 10.1021/BI9901329 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 13327 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 789 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1250 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.340 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.27 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2E2C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178019. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-96 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : DOUBLE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13327 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: 1AAK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.17333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 100.34667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 100.34667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.17333 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: DIMERIC 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 80.25284 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 100.34667 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 271 LIES ON A SPECIAL POSITION. 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 THR A 24 -142.80 54.73 REMARK 500 SER A 25 -3.57 178.63 REMARK 500 GLU A 27 103.10 55.49 REMARK 500 SER A 30 142.18 179.04 REMARK 500 ASP A 55 -16.43 -49.17 REMARK 500 SER A 76 -7.17 84.53 REMARK 500 LYS A 119 -114.21 -131.25 REMARK 500 ALA A 145 -75.88 -53.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 2E2C A 22 177 UNP Q95044 UB2EC_SPISO 22 177 SEQRES 1 A 156 MET THR THR SER LYS GLU ARG HIS SER VAL SER LYS ARG SEQRES 2 A 156 LEU GLN GLN GLU LEU ARG THR LEU LEU MET SER GLY ASP SEQRES 3 A 156 PRO GLY ILE THR ALA PHE PRO ASP GLY ASP ASN LEU PHE SEQRES 4 A 156 LYS TRP VAL ALA THR LEU ASP GLY PRO LYS ASP THR VAL SEQRES 5 A 156 TYR GLU SER LEU LYS TYR LYS LEU THR LEU GLU PHE PRO SEQRES 6 A 156 SER ASP TYR PRO TYR LYS PRO PRO VAL VAL LYS PHE THR SEQRES 7 A 156 THR PRO CYS TRP HIS PRO ASN VAL ASP GLN SER GLY ASN SEQRES 8 A 156 ILE CYS LEU ASP ILE LEU LYS GLU ASN TRP THR ALA SER SEQRES 9 A 156 TYR ASP VAL ARG THR ILE LEU LEU SER LEU GLN SER LEU SEQRES 10 A 156 LEU GLY GLU PRO ASN ASN ALA SER PRO LEU ASN ALA GLN SEQRES 11 A 156 ALA ALA ASP MET TRP SER ASN GLN THR GLU TYR LYS LYS SEQRES 12 A 156 VAL LEU HIS GLU LYS TYR LYS THR ALA GLN SER ASP LYS FORMUL 2 HOH *172(H2 O) HELIX 1 1 VAL A 31 SER A 45 1 15 HELIX 2 2 ASP A 116 LEU A 118 5 3 HELIX 3 3 VAL A 128 LEU A 138 1 11 HELIX 4 4 ALA A 150 SER A 157 1 8 HELIX 5 5 GLN A 159 SER A 175 1 17 SHEET 1 A 4 ILE A 50 PRO A 54 0 SHEET 2 A 4 LYS A 61 ASP A 67 -1 N THR A 65 O THR A 51 SHEET 3 A 4 LYS A 78 GLU A 84 -1 N LEU A 83 O TRP A 62 SHEET 4 A 4 VAL A 95 PHE A 98 -1 N LYS A 97 O THR A 82 CISPEP 1 TYR A 89 PRO A 90 0 -0.33 CRYST1 46.334 46.334 150.520 90.00 90.00 120.00 P 31 2 1 6 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 0.021582 0.012461 0.000000 0.00000 SCALE2 0.000000 0.024921 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006644 0.00000