HEADER LIGASE 11-MAR-05 1Z3D TITLE PROTEIN CRYSTAL GROWTH IMPROVEMENT LEADING TO THE 2.5A TITLE 2 CRYSTALLOGRAPHIC STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME (UBC-1) TITLE 3 FROM CAENORHABDITIS ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-PROTEIN LIGASE 1, UBIQUITIN CARRIER PROTEIN 1; 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: UBC-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET26 KEYWDS E2, UBIQUITINATION, UBIQUITIN-CONJUGATING, CRYSTAL GROWTH, STRUCTURAL KEYWDS 2 GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, SOUTHEAST COLLABORATORY KEYWDS 3 FOR STRUCTURAL GENOMICS, SECSG, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.GAVIRA,E.DIGIAMMARINO,W.TEMPEL,D.TOH,Z.J.LIU,B.C.WANG,E.MEEHAN, AUTHOR 2 J.D.NG,SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS (SECSG) REVDAT 3 23-AUG-23 1Z3D 1 REMARK SEQADV REVDAT 2 24-FEB-09 1Z3D 1 VERSN REVDAT 1 22-MAR-05 1Z3D 0 JRNL AUTH J.A.GAVIRA,E.DIGIAMMARINO,W.TEMPEL,D.TOH,Z.J.LIU,B.C.WANG, JRNL AUTH 2 E.MEEHAN,J.D.NG JRNL TITL PROTEIN CRYSTAL GROWTH IMPROVEMENT LEADING TO THE 2.5A JRNL TITL 2 CRYSTALLOGRAPHIC STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME JRNL TITL 3 (UBC-1) FROM CAENORHABDITIS ELEGANS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1342948.770 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 7080 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) : 0.242 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 731 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 931 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 94 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1224 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.74000 REMARK 3 B22 (A**2) : -0.70000 REMARK 3 B33 (A**2) : 1.44000 REMARK 3 B12 (A**2) : 7.62000 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) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.35 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) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.43 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 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) : 2.800 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.050 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.580 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.850 ; 3.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 17.82 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 1Z3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032246. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7370 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 97.1 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.05800 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) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.32600 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: CNS REMARK 200 STARTING MODEL: 2AAK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 8.5, 0.2 M MGCL2, 30% REMARK 280 PEG 4K, COUNTER-DIFFUSION, TEMPERATURE 277.5K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 23.89333 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 11.94667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.92000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 5.97333 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 29.86667 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLY A 153 REMARK 465 GLU A 154 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 C PHE A 48 H GLU A 49 0.75 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 GLN A 44 -65.21 -27.79 REMARK 500 GLN A 93 -88.24 -107.93 REMARK 500 ASN A 119 -71.58 -48.20 REMARK 500 ASN A 133 58.38 -171.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B10 RELATED DB: TARGETDB DBREF 1Z3D A 1 154 UNP P52478 UBC1_CAEEL 1 154 SEQADV 1Z3D GLY A -2 UNP P52478 CLONING ARTIFACT SEQADV 1Z3D SER A -1 UNP P52478 CLONING ARTIFACT SEQADV 1Z3D HIS A 0 UNP P52478 CLONING ARTIFACT SEQRES 1 A 157 GLY SER HIS MET THR THR PRO SER ARG ARG ARG LEU MET SEQRES 2 A 157 ARG ASP PHE LYS LYS LEU GLN GLU ASP PRO PRO ALA GLY SEQRES 3 A 157 VAL SER GLY ALA PRO THR GLU ASP ASN ILE LEU THR TRP SEQRES 4 A 157 GLU ALA ILE ILE PHE GLY PRO GLN GLU THR PRO PHE GLU SEQRES 5 A 157 ASP GLY THR PHE LYS LEU SER LEU GLU PHE THR GLU GLU SEQRES 6 A 157 TYR PRO ASN LYS PRO PRO THR VAL LYS PHE ILE SER LYS SEQRES 7 A 157 MET PHE HIS PRO ASN VAL TYR ALA ASP GLY SER ILE CYS SEQRES 8 A 157 LEU ASP ILE LEU GLN ASN ARG TRP SER PRO THR TYR ASP SEQRES 9 A 157 VAL ALA ALA ILE LEU THR SER ILE GLN SER LEU LEU ASP SEQRES 10 A 157 GLU PRO ASN PRO ASN SER PRO ALA ASN SER LEU ALA ALA SEQRES 11 A 157 GLN LEU TYR GLN GLU ASN ARG ARG GLU TYR GLU LYS ARG SEQRES 12 A 157 VAL GLN GLN ILE VAL GLU GLN SER TRP LEU ASN PHE GLY SEQRES 13 A 157 GLU FORMUL 2 HOH *17(H2 O) HELIX 1 1 THR A 3 ASP A 19 1 17 HELIX 2 2 LEU A 89 GLN A 93 5 5 HELIX 3 3 ASP A 101 LEU A 112 1 12 HELIX 4 4 ASN A 123 ASN A 133 1 11 HELIX 5 5 ASN A 133 TRP A 149 1 17 SHEET 1 A 4 VAL A 24 THR A 29 0 SHEET 2 A 4 ASN A 32 PHE A 41 -1 O THR A 35 N THR A 29 SHEET 3 A 4 THR A 52 GLU A 58 -1 O LEU A 55 N ALA A 38 SHEET 4 A 4 THR A 69 PHE A 72 -1 O LYS A 71 N SER A 56 CISPEP 1 TYR A 63 PRO A 64 0 -0.28 CRYST1 100.550 100.550 35.840 90.00 90.00 120.00 P 65 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 0.009945 0.005742 0.000000 0.00000 SCALE2 0.000000 0.011484 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027902 0.00000