HEADER UNKNOWN FUNCTION 16-MAY-01 1J7D TITLE CRYSTAL STRUCTURE OF HMMS2-HUBC13 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MMS2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-17 KDA; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: UBC13; COMPND 9 EC: 6.3.2.19; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN, UBC, DNA REPAIR, TRAF6, NFKB,, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR T.F.MORAES,R.A.EDWARDS,S.MCKENNA,L.PASHUSHOK,W.XIAO, AUTHOR 2 J.N.M.GLOVER,M.J.ELLISON REVDAT 3 24-FEB-09 1J7D 1 VERSN REVDAT 2 30-SEP-03 1J7D 1 JRNL DBREF REVDAT 1 08-AUG-01 1J7D 0 JRNL AUTH T.F.MORAES,R.A.EDWARDS,S.MCKENNA,L.PASTUSHOK, JRNL AUTH 2 W.XIAO,J.N.GLOVER,M.J.ELLISON JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN UBIQUITIN JRNL TITL 2 CONJUGATING ENZYME COMPLEX, HMMS2-HUBC13. JRNL REF NAT.STRUCT.BIOL. V. 8 669 2001 JRNL REFN ISSN 1072-8368 JRNL PMID 11473255 JRNL DOI 10.1038/90373 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : CNS TARGETS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 25927 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1317 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2811 REMARK 3 BIN FREE R VALUE : 0.3147 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 46 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 : 2295 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.40 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 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1J7D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-01. REMARK 100 THE RCSB ID CODE IS RCSB013451. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.981958, 0.982127, 1.022130 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26066 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.250 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : 0.03400 REMARK 200 FOR THE DATA SET : 37.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.26300 REMARK 200 R SYM FOR SHELL (I) : 0.26300 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 100MM CITRATE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 22.06600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.74450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.06850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.74450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.06600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.06850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ALA A 2 REMARK 465 VAL A 3 REMARK 465 SER A 4 REMARK 465 THR A 5 REMARK 465 MET B 1 REMARK 465 ASN B 151 REMARK 465 ILE B 152 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 VAL A 7 123.03 -28.97 REMARK 500 ASP A 38 0.30 -65.39 REMARK 500 LEU B 16 34.25 -68.11 REMARK 500 ALA B 17 -62.36 -152.76 REMARK 500 GLU B 18 74.22 -109.80 REMARK 500 GLU B 61 9.50 -65.49 REMARK 500 ILE B 90 0.41 -66.91 REMARK 500 LYS B 92 -70.13 -134.42 REMARK 500 LYS B 94 30.75 -77.10 REMARK 500 PRO B 97 -28.79 -35.63 REMARK 500 GLN B 100 -165.26 62.28 REMARK 500 ARG B 102 0.84 -63.86 REMARK 500 ASN B 123 -89.42 -40.79 REMARK 500 ASP B 124 -21.42 161.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J74 RELATED DB: PDB REMARK 900 1J74 IS THE MONOMERIC CRYSTAL STRUCTURE OF MMS2 DBREF 1J7D A 1 145 UNP Q15819 UB2V2_HUMAN 1 145 DBREF 1J7D B 1 152 UNP P61088 UBE2N_HUMAN 1 152 SEQRES 1 A 145 MET ALA VAL SER THR GLY VAL LYS VAL PRO ARG ASN PHE SEQRES 2 A 145 ARG LEU LEU GLU GLU LEU GLU GLU GLY GLN LYS GLY VAL SEQRES 3 A 145 GLY ASP GLY THR VAL SER TRP GLY LEU GLU ASP ASP GLU SEQRES 4 A 145 ASP MET THR LEU THR ARG TRP THR GLY MET ILE ILE GLY SEQRES 5 A 145 PRO PRO ARG THR ASN TYR GLU ASN ARG ILE TYR SER LEU SEQRES 6 A 145 LYS VAL GLU CYS GLY PRO LYS TYR PRO GLU ALA PRO PRO SEQRES 7 A 145 SER VAL ARG PHE VAL THR LYS ILE ASN MET ASN GLY ILE SEQRES 8 A 145 ASN ASN SER SER GLY MET VAL ASP ALA ARG SER ILE PRO SEQRES 9 A 145 VAL LEU ALA LYS TRP GLN ASN SER TYR SER ILE LYS VAL SEQRES 10 A 145 VAL LEU GLN GLU LEU ARG ARG LEU MET MET SER LYS GLU SEQRES 11 A 145 ASN MET LYS LEU PRO GLN PRO PRO GLU GLY GLN THR TYR SEQRES 12 A 145 ASN ASN SEQRES 1 B 152 MET ALA GLY LEU PRO ARG ARG ILE ILE LYS GLU THR GLN SEQRES 2 B 152 ARG LEU LEU ALA GLU PRO VAL PRO GLY ILE LYS ALA GLU SEQRES 3 B 152 PRO ASP GLU SER ASN ALA ARG TYR PHE HIS VAL VAL ILE SEQRES 4 B 152 ALA GLY PRO GLN ASP SER PRO PHE GLU GLY GLY THR PHE SEQRES 5 B 152 LYS LEU GLU LEU PHE LEU PRO GLU GLU TYR PRO MET ALA SEQRES 6 B 152 ALA PRO LYS VAL ARG PHE MET THR LYS ILE TYR HIS PRO SEQRES 7 B 152 ASN VAL ASP LYS LEU GLY ARG ILE CYS LEU ASP ILE LEU SEQRES 8 B 152 LYS ASP LYS TRP SER PRO ALA LEU GLN ILE ARG THR VAL SEQRES 9 B 152 LEU LEU SER ILE GLN ALA LEU LEU SER ALA PRO ASN PRO SEQRES 10 B 152 ASP ASP PRO LEU ALA ASN ASP VAL ALA GLU GLN TRP LYS SEQRES 11 B 152 THR ASN GLU ALA GLN ALA ILE GLU THR ALA ARG ALA TRP SEQRES 12 B 152 THR ARG LEU TYR ALA MET ASN ASN ILE FORMUL 3 HOH *190(H2 O) HELIX 1 1 PRO A 10 GLY A 25 1 16 HELIX 2 2 ASP A 99 SER A 102 5 4 HELIX 3 3 ILE A 103 LYS A 108 1 6 HELIX 4 4 SER A 114 MET A 127 1 14 HELIX 5 5 SER A 128 LYS A 133 1 6 HELIX 6 6 PRO B 5 LEU B 16 1 12 HELIX 7 7 LEU B 88 LYS B 92 5 5 HELIX 8 8 GLN B 100 ALA B 114 1 15 HELIX 9 9 ASP B 124 ASN B 132 1 9 HELIX 10 10 ASN B 132 ALA B 148 1 17 SHEET 1 A 4 VAL A 31 LEU A 35 0 SHEET 2 A 4 ARG A 45 ILE A 51 -1 N THR A 47 O GLY A 34 SHEET 3 A 4 ILE A 62 GLU A 68 -1 N TYR A 63 O ILE A 50 SHEET 4 A 4 SER A 79 PHE A 82 -1 O SER A 79 N GLU A 68 SHEET 1 B 4 ILE B 23 PRO B 27 0 SHEET 2 B 4 TYR B 34 ALA B 40 -1 N HIS B 36 O GLU B 26 SHEET 3 B 4 THR B 51 PHE B 57 -1 O PHE B 52 N ILE B 39 SHEET 4 B 4 LYS B 68 PHE B 71 -1 N LYS B 68 O PHE B 57 CISPEP 1 TYR A 73 PRO A 74 0 0.10 CISPEP 2 TYR B 62 PRO B 63 0 -1.23 CRYST1 44.132 74.137 91.489 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 0.022659 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013489 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010930 0.00000 MASTER 264 0 0 10 8 0 0 6 0 0 0 24 END