HEADER LIGASE 14-JUL-03 1PZV TITLE CRYSTAL STRUCTURES OF TWO UBC (E2) ENZYMES OF THE UBIQUITIN- TITLE 2 CONJUGATING SYSTEM IN CAENORHABDITIS ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE UBIQUITIN-CONJUGATING ENZYME E2-19 KDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN; COMPND 5 EC: 6.3.2.19; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: F58A4.10; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS ALPHA-BETA(4)-ALPHA(3), CORE, MEANDER BETA-SHEET PLUS ONE HELIX 2, KEYWDS 2 STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, SOUTHEAST KEYWDS 3 COLLABORATORY FOR STRUCTURAL GENOMICS, SECSG, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR N.SCHORMANN,G.LIN,S.LI,J.SYMERSKY,S.QIU,J.FINLEY,D.LUO,A.STANTON, AUTHOR 2 M.CARSON,M.LUO,SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS AUTHOR 3 (SECSG) REVDAT 4 16-AUG-23 1PZV 1 REMARK REVDAT 3 24-FEB-09 1PZV 1 VERSN REVDAT 2 01-FEB-05 1PZV 1 AUTHOR KEYWDS REMARK REVDAT 1 22-JUL-03 1PZV 0 JRNL AUTH N.SCHORMANN,G.LIN,S.LI,J.SYMERSKY,S.QIU,J.FINLEY,D.LUO, JRNL AUTH 2 A.STANTON,M.CARSON,M.LUO,L.DELUCAS,P.PRUETT,L.NAGY, JRNL AUTH 3 A.ARABASHI,R.GRAY,D.JOHNSON,J.TSAO,B.BUNZEL,W.HUANG,Q.SHANG, JRNL AUTH 4 C.-H.LUAN,S.LU,J.ZHANG,A.MCKINSTRY,H.CHEN JRNL TITL CRYSTAL STRUCTURES OF TWO UBC (E2) ENZYMES OF THE JRNL TITL 2 UBIQUITIN-CONJUGATING SYSTEM IN CAENORHABDITIS ELEGANS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 500016.780 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.9 REMARK 3 NUMBER OF REFLECTIONS : 5401 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) : 0.241 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.800 REMARK 3 FREE R VALUE TEST SET COUNT : 311 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.016 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.52 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 56.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 562 REMARK 3 BIN R VALUE (WORKING SET) : 0.4480 REMARK 3 BIN FREE R VALUE : 0.4500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 30 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.082 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1229 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -28.85000 REMARK 3 B22 (A**2) : -23.61000 REMARK 3 B33 (A**2) : 52.46000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.42 REMARK 3 ESD FROM SIGMAA (A) : 0.80 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.52 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.71 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.540 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.510 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.620 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.020 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.210 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 52.27 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PZV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 1.105 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR SI REMARK 200 -220 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6215 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.520 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2UCZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000 MME, CAPSO, GLYCEROL, REMARK 280 POTASSIUM THIOCYANATE, PH 9.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K 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 24.23700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.44100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.09200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.44100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.23700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.09200 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 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 1 REMARK 465 GLU A 2 REMARK 465 GLN A 3 REMARK 465 GLY A 96 REMARK 465 ASP A 97 REMARK 465 ASP A 98 REMARK 465 LYS A 99 REMARK 465 TRP A 100 REMARK 465 GLY A 101 REMARK 465 TYR A 102 REMARK 465 GLU A 103 REMARK 465 ARG A 104 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 95 CA - N - CD ANGL. DEV. = -16.4 DEGREES 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 21 116.28 -26.58 REMARK 500 ILE A 33 3.79 -64.13 REMARK 500 ASP A 45 31.97 76.66 REMARK 500 PHE A 52 70.65 -112.57 REMARK 500 TYR A 63 -68.82 -28.84 REMARK 500 GLN A 65 57.49 -104.11 REMARK 500 LYS A 66 111.64 175.25 REMARK 500 SER A 74 108.79 88.27 REMARK 500 GLU A 75 131.81 -39.46 REMARK 500 ASP A 82 -178.54 -69.76 REMARK 500 ILE A 91 -6.35 -58.72 REMARK 500 ASP A 94 113.41 -166.88 REMARK 500 PHE A 131 -98.38 -71.16 REMARK 500 GLU A 132 78.25 31.16 REMARK 500 GLU A 145 -62.76 -104.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: F58A4.10 RELATED DB: TARGETDB DBREF 1PZV A 1 164 UNP P34477 UBC7_CAEEL 1 164 SEQRES 1 A 164 MET GLU GLN SER SER LEU LEU LEU LYS LYS GLN LEU ALA SEQRES 2 A 164 ASP MET ARG ARG VAL PRO VAL ASP GLY PHE SER ALA GLY SEQRES 3 A 164 LEU VAL ASP ASP ASN ASP ILE TYR LYS TRP GLU VAL LEU SEQRES 4 A 164 VAL ILE GLY PRO PRO ASP THR LEU TYR GLU GLY GLY PHE SEQRES 5 A 164 PHE LYS ALA ILE LEU ASP PHE PRO ARG ASP TYR PRO GLN SEQRES 6 A 164 LYS PRO PRO LYS MET LYS PHE ILE SER GLU ILE TRP HIS SEQRES 7 A 164 PRO ASN ILE ASP LYS GLU GLY ASN VAL CYS ILE SER ILE SEQRES 8 A 164 LEU HIS ASP PRO GLY ASP ASP LYS TRP GLY TYR GLU ARG SEQRES 9 A 164 PRO GLU GLU ARG TRP LEU PRO VAL HIS THR VAL GLU THR SEQRES 10 A 164 ILE LEU LEU SER VAL ILE SER MET LEU THR ASP PRO ASN SEQRES 11 A 164 PHE GLU SER PRO ALA ASN VAL ASP ALA ALA LYS MET GLN SEQRES 12 A 164 ARG GLU ASN TYR ALA GLU PHE LYS LYS LYS VAL ALA GLN SEQRES 13 A 164 CYS VAL ARG ARG SER GLN GLU GLU FORMUL 2 HOH *41(H2 O) HELIX 1 1 SER A 4 VAL A 18 1 15 HELIX 2 2 ASP A 62 LYS A 66 5 5 HELIX 3 3 ILE A 89 HIS A 93 5 5 HELIX 4 4 THR A 114 ASP A 128 1 15 HELIX 5 5 ASN A 136 GLU A 145 1 10 HELIX 6 6 ASN A 146 GLN A 162 1 17 SHEET 1 A 4 PHE A 23 LEU A 27 0 SHEET 2 A 4 LYS A 35 ILE A 41 -1 O LEU A 39 N SER A 24 SHEET 3 A 4 PHE A 52 ASP A 58 -1 O ALA A 55 N VAL A 38 SHEET 4 A 4 LYS A 69 PHE A 72 -1 O LYS A 69 N ASP A 58 CRYST1 48.474 52.184 68.882 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 0.020630 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019163 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014518 0.00000