HEADER LIGASE/SIGNALING PROTEIN 17-FEB-15 5AIU TITLE A COMPLEX OF RNF4-RING DOMAIN, UBC13-UB (ISOPEPTIDE CROSSLINK) COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RING DOMAIN, UNP RESIDUES 131-194,131-194; COMPND 5 SYNONYM: RING FINGER PROTEIN 4, SMALL NUCLEAR RING FINGER PROTEIN, COMPND 6 PROTEIN SNURF, "RING DOMAIN, UBC13"; COMPND 7 EC: 6.3.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: THE RING DOMAIN IS DUPLICATED BUT AS A FUSED DIMER. COMPND 11 THAT IS THE SEQUENCE OF THE RING DOMAIN FROM RNF4 (RESIDUES 131 TO COMPND 12 194) IS LINKED BY A SINGLE GLYCINE RESIDUE TO ANOTHER RING DOMAIN COMPND 13 (RESIDUES 131 TO 194).; COMPND 14 MOL_ID: 2; COMPND 15 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 N; COMPND 16 CHAIN: B, E; COMPND 17 SYNONYM: BENDLESS-LIKE UBIQUITIN-CONJUGATING ENZYME, UBC13, UBCH13, COMPND 18 UBIQUITIN CARRIER PROTEIN N, UBIQUITIN-PROTEIN LIGASE N, UBC13; COMPND 19 EC: 6.3.2.19; COMPND 20 ENGINEERED: YES; COMPND 21 MUTATION: YES; COMPND 22 OTHER_DETAILS: CHAIN B COVALENTLY LINKED TO CHAINS C, CHAIN E IS COMPND 23 COVALENTLY LINKED TO CHAIN F; COMPND 24 MOL_ID: 3; COMPND 25 MOLECULE: POLYUBIQUITIN-C; COMPND 26 CHAIN: C, F; COMPND 27 FRAGMENT: UNP RESIDUES 1-76; COMPND 28 ENGINEERED: YES; COMPND 29 OTHER_DETAILS: CHAIN B COVALENTLY LINKED TO CHAINS C, CHAIN E IS COMPND 30 COVALENTLY LINKED TO CHAIN F SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; 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; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGASE-SIGNALING PROTEIN COMPLEX, COMPLEX, FUSION PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.BRANIGAN,J.H.NAISMITH REVDAT 5 31-JUL-19 5AIU 1 REMARK LINK REVDAT 4 28-JUN-17 5AIU 1 REMARK REVDAT 3 19-AUG-15 5AIU 1 JRNL REVDAT 2 15-JUL-15 5AIU 1 TITLE JRNL REVDAT 1 08-JUL-15 5AIU 0 JRNL AUTH E.BRANIGAN,A.PLECHANOVOVA,E.JAFFRAY,J.H.NAISMITH,R.T.HAY JRNL TITL STRUCTURAL BASIS FOR THE RING CATALYZED SYNTHESIS OF K63 JRNL TITL 2 LINKED UBIQUITIN CHAINS JRNL REF NAT.STRUCT.MOL.BIOL. V. 22 597 2015 JRNL REFN ISSN 1545-9993 JRNL PMID 26148049 JRNL DOI 10.1038/NSMB.3052 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 28823 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 + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1536 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1629 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4524 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.37000 REMARK 3 B22 (A**2) : -1.18000 REMARK 3 B33 (A**2) : -1.19000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.328 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.233 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.172 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.731 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.911 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.890 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4654 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4567 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6288 ; 1.696 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10521 ; 1.042 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 570 ; 6.892 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;36.829 ;24.384 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 830 ;15.543 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;21.067 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 711 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5140 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 989 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2295 ; 1.713 ; 2.264 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2294 ; 1.713 ; 2.264 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2857 ; 2.681 ; 3.383 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2858 ; 2.680 ; 3.383 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2359 ; 2.214 ; 2.516 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2359 ; 2.214 ; 2.516 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3431 ; 3.548 ; 3.665 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4949 ; 4.875 ;17.692 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4949 ; 4.875 ;17.694 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 B 2 151 E 2 151 9090 0.09 0.05 REMARK 3 2 C 1 76 F 1 76 4878 0.08 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.85 REMARK 3 SHRINKAGE RADIUS : 0.75 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY DISORDERED REGIONS WERE REMARK 3 MODELED STEREOCHEMICALLY. THE ISOPEPTIDE LINKAGE WAS INCLUDED AS REMARK 3 A RESTRAINT. REMARK 4 REMARK 4 5AIU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1290063079. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541780 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29485 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 32.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.15000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1,2-ETHANEDIOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 34.59500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 84.60500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.59500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 84.60500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, E, F 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 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 E2010 LIES ON A SPECIAL POSITION. 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 127 REMARK 465 ALA A 128 REMARK 465 MET A 129 REMARK 465 GLY A 130 REMARK 465 HIS A 186 REMARK 465 LYS A 187 REMARK 465 ASN A 250 REMARK 465 HIS A 251 REMARK 465 LYS A 252 REMARK 465 ARG A 253 REMARK 465 GLY B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 ILE B 152 REMARK 465 GLY E -1 REMARK 465 ALA E 0 REMARK 465 MET E 1 REMARK 465 ILE E 152 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 NZ LYS E 87 C GLY F 76 1.33 REMARK 500 NZ LYS B 87 C GLY C 76 1.33 REMARK 500 REMARK 500 REMARK: NULL 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 ASP E 28 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG E 145 NE - CZ - NH1 ANGL. DEV. = 3.3 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 ASN A 175 33.71 -98.41 REMARK 500 SER A 196 -98.25 3.90 REMARK 500 MET A 205 13.32 81.30 REMARK 500 GLN A 213 -48.24 -29.70 REMARK 500 ALA A 239 -38.47 -130.99 REMARK 500 ALA B 92 -106.18 -132.02 REMARK 500 ASN B 132 71.59 -151.23 REMARK 500 GLU C 64 -0.18 76.65 REMARK 500 ASN E 31 108.60 -160.35 REMARK 500 ALA E 92 -104.16 -134.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 800 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 136 SG REMARK 620 2 CYS A 139 SG 101.7 REMARK 620 3 CYS A 163 SG 119.0 117.3 REMARK 620 4 CYS A 166 SG 112.2 107.0 99.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 158 SG REMARK 620 2 HIS A 160 ND1 110.9 REMARK 620 3 CYS A 177 SG 109.5 114.7 REMARK 620 4 CYS A 180 SG 103.6 107.7 109.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 201 SG REMARK 620 2 CYS A 204 SG 101.7 REMARK 620 3 CYS A 228 SG 115.1 118.2 REMARK 620 4 CYS A 231 SG 110.0 113.5 98.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 803 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 223 SG REMARK 620 2 HIS A 225 ND1 113.1 REMARK 620 3 CYS A 242 SG 111.1 108.3 REMARK 620 4 CYS A 245 SG 101.4 109.6 113.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO E 1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO F 1077 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 1077 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1260 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1153 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AIT RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS IS A HEAD TO TAIL FUSION OF TWO RING DOMAINS. THE REMARK 999 GAMG AT THE N-TERMINUS IS A CLONING ARTEFACT REMARK 999 THE ACTIVE SITE C87 HAS BEEN MUTATED TO K87 FOR ATTACHMENT REMARK 999 OF UBIQUITIN (MOLECULES IN CHAIN C AND F). SECOND MUTATION REMARK 999 K92 TO A. THE N-TERMINAL GA IS A CLONING ARTEFACT REMARK 999 NOTE TERMINAL GLY OF CHAIN C IS ATTACHED TO LYS 87 OF REMARK 999 CHAIN B CHAIN F TERMINAL GLY IS ATTACHED TO CHAIN E LYS 87 DBREF 5AIU A 131 194 UNP O88846 RNF4_RAT 131 194 DBREF 5AIU A 196 259 UNP O88846 RNF4_RAT 131 194 DBREF 5AIU B 1 152 UNP P61088 UBE2N_HUMAN 1 152 DBREF 5AIU C 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 5AIU E 1 152 UNP P61088 UBE2N_HUMAN 1 152 DBREF 5AIU F 1 76 UNP P0CG48 UBC_HUMAN 1 76 SEQADV 5AIU GLY A 127 UNP O88846 EXPRESSION TAG SEQADV 5AIU ALA A 128 UNP O88846 EXPRESSION TAG SEQADV 5AIU MET A 129 UNP O88846 EXPRESSION TAG SEQADV 5AIU GLY A 130 UNP O88846 EXPRESSION TAG SEQADV 5AIU GLY A 195 UNP O88846 LINKER SEQADV 5AIU GLY B -1 UNP P61088 EXPRESSION TAG SEQADV 5AIU ALA B 0 UNP P61088 EXPRESSION TAG SEQADV 5AIU LYS B 87 UNP P61088 CYS 87 ENGINEERED MUTATION SEQADV 5AIU ALA B 92 UNP P61088 LYS 92 ENGINEERED MUTATION SEQADV 5AIU GLY E -1 UNP P61088 EXPRESSION TAG SEQADV 5AIU ALA E 0 UNP P61088 EXPRESSION TAG SEQADV 5AIU LYS E 87 UNP P61088 CYS 87 ENGINEERED MUTATION SEQADV 5AIU ALA E 92 UNP P61088 LYS 92 ENGINEERED MUTATION SEQRES 1 A 133 GLY ALA MET GLY SER GLY THR VAL SER CYS PRO ILE CYS SEQRES 2 A 133 MET ASP GLY TYR SER GLU ILE VAL GLN ASN GLY ARG LEU SEQRES 3 A 133 ILE VAL SER THR GLU CYS GLY HIS VAL PHE CYS SER GLN SEQRES 4 A 133 CYS LEU ARG ASP SER LEU LYS ASN ALA ASN THR CYS PRO SEQRES 5 A 133 THR CYS ARG LYS LYS ILE ASN HIS LYS ARG TYR HIS PRO SEQRES 6 A 133 ILE TYR ILE GLY SER GLY THR VAL SER CYS PRO ILE CYS SEQRES 7 A 133 MET ASP GLY TYR SER GLU ILE VAL GLN ASN GLY ARG LEU SEQRES 8 A 133 ILE VAL SER THR GLU CYS GLY HIS VAL PHE CYS SER GLN SEQRES 9 A 133 CYS LEU ARG ASP SER LEU LYS ASN ALA ASN THR CYS PRO SEQRES 10 A 133 THR CYS ARG LYS LYS ILE ASN HIS LYS ARG TYR HIS PRO SEQRES 11 A 133 ILE TYR ILE SEQRES 1 B 154 GLY ALA MET ALA GLY LEU PRO ARG ARG ILE ILE LYS GLU SEQRES 2 B 154 THR GLN ARG LEU LEU ALA GLU PRO VAL PRO GLY ILE LYS SEQRES 3 B 154 ALA GLU PRO ASP GLU SER ASN ALA ARG TYR PHE HIS VAL SEQRES 4 B 154 VAL ILE ALA GLY PRO GLN ASP SER PRO PHE GLU GLY GLY SEQRES 5 B 154 THR PHE LYS LEU GLU LEU PHE LEU PRO GLU GLU TYR PRO SEQRES 6 B 154 MET ALA ALA PRO LYS VAL ARG PHE MET THR LYS ILE TYR SEQRES 7 B 154 HIS PRO ASN VAL ASP LYS LEU GLY ARG ILE LYS LEU ASP SEQRES 8 B 154 ILE LEU ALA ASP LYS TRP SER PRO ALA LEU GLN ILE ARG SEQRES 9 B 154 THR VAL LEU LEU SER ILE GLN ALA LEU LEU SER ALA PRO SEQRES 10 B 154 ASN PRO ASP ASP PRO LEU ALA ASN ASP VAL ALA GLU GLN SEQRES 11 B 154 TRP LYS THR ASN GLU ALA GLN ALA ILE GLU THR ALA ARG SEQRES 12 B 154 ALA TRP THR ARG LEU TYR ALA MET ASN ASN ILE SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 E 154 GLY ALA MET ALA GLY LEU PRO ARG ARG ILE ILE LYS GLU SEQRES 2 E 154 THR GLN ARG LEU LEU ALA GLU PRO VAL PRO GLY ILE LYS SEQRES 3 E 154 ALA GLU PRO ASP GLU SER ASN ALA ARG TYR PHE HIS VAL SEQRES 4 E 154 VAL ILE ALA GLY PRO GLN ASP SER PRO PHE GLU GLY GLY SEQRES 5 E 154 THR PHE LYS LEU GLU LEU PHE LEU PRO GLU GLU TYR PRO SEQRES 6 E 154 MET ALA ALA PRO LYS VAL ARG PHE MET THR LYS ILE TYR SEQRES 7 E 154 HIS PRO ASN VAL ASP LYS LEU GLY ARG ILE LYS LEU ASP SEQRES 8 E 154 ILE LEU ALA ASP LYS TRP SER PRO ALA LEU GLN ILE ARG SEQRES 9 E 154 THR VAL LEU LEU SER ILE GLN ALA LEU LEU SER ALA PRO SEQRES 10 E 154 ASN PRO ASP ASP PRO LEU ALA ASN ASP VAL ALA GLU GLN SEQRES 11 E 154 TRP LYS THR ASN GLU ALA GLN ALA ILE GLU THR ALA ARG SEQRES 12 E 154 ALA TRP THR ARG LEU TYR ALA MET ASN ASN ILE SEQRES 1 F 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 F 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 F 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 F 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 F 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 F 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET ZN A 800 1 HET ZN A 801 1 HET ZN A 802 1 HET ZN A 803 1 HET EDO A1260 4 HET EDO B1152 4 HET EDO B1153 4 HET EDO C1077 4 HET EDO E1152 4 HET EDO F1077 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 6 ZN 4(ZN 2+) FORMUL 10 EDO 6(C2 H6 O2) FORMUL 16 HOH *33(H2 O) HELIX 1 1 GLY A 142 ASN A 149 1 8 HELIX 2 2 SER A 164 ALA A 174 1 11 HELIX 3 3 GLY A 207 ASN A 214 1 8 HELIX 4 4 SER A 229 ALA A 239 1 11 HELIX 5 5 PRO B 5 GLU B 18 1 14 HELIX 6 6 ASP B 89 ALA B 92 5 4 HELIX 7 7 GLN B 100 ALA B 114 1 15 HELIX 8 8 ALA B 122 ASN B 132 1 11 HELIX 9 9 ASN B 132 MET B 149 1 18 HELIX 10 10 THR C 22 GLY C 35 1 14 HELIX 11 11 PRO C 37 ASP C 39 5 3 HELIX 12 12 PRO E 5 GLU E 18 1 14 HELIX 13 13 ASP E 89 ALA E 92 5 4 HELIX 14 14 GLN E 100 ALA E 114 1 15 HELIX 15 15 ALA E 122 ASN E 132 1 11 HELIX 16 16 ASN E 132 MET E 149 1 18 HELIX 17 17 THR F 22 GLY F 35 1 14 HELIX 18 18 PRO F 37 ASP F 39 5 3 SHEET 1 AA 3 VAL A 161 CYS A 163 0 SHEET 2 AA 3 ILE A 153 THR A 156 -1 O VAL A 154 N PHE A 162 SHEET 3 AA 3 TYR A 189 PRO A 191 -1 O HIS A 190 N SER A 155 SHEET 1 AB 3 VAL A 226 CYS A 228 0 SHEET 2 AB 3 ILE A 218 SER A 220 -1 O VAL A 219 N PHE A 227 SHEET 3 AB 3 HIS A 255 PRO A 256 -1 O HIS A 255 N SER A 220 SHEET 1 BA 4 ILE B 23 ASP B 28 0 SHEET 2 BA 4 ASN B 31 ALA B 40 -1 N ASN B 31 O ASP B 28 SHEET 3 BA 4 THR B 51 PHE B 57 -1 O PHE B 52 N ILE B 39 SHEET 4 BA 4 LYS B 68 PHE B 71 -1 O LYS B 68 N PHE B 57 SHEET 1 CA 5 THR C 12 GLU C 16 0 SHEET 2 CA 5 GLN C 2 LYS C 6 -1 O ILE C 3 N LEU C 15 SHEET 3 CA 5 THR C 66 LEU C 71 1 O LEU C 67 N LYS C 6 SHEET 4 CA 5 GLN C 41 PHE C 45 -1 O ARG C 42 N VAL C 70 SHEET 5 CA 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 EA 4 ILE E 23 ASP E 28 0 SHEET 2 EA 4 ASN E 31 ALA E 40 -1 N ASN E 31 O ASP E 28 SHEET 3 EA 4 THR E 51 PHE E 57 -1 O PHE E 52 N ILE E 39 SHEET 4 EA 4 LYS E 68 PHE E 71 -1 O LYS E 68 N PHE E 57 SHEET 1 FA 5 THR F 12 GLU F 16 0 SHEET 2 FA 5 GLN F 2 LYS F 6 -1 O ILE F 3 N LEU F 15 SHEET 3 FA 5 THR F 66 LEU F 71 1 O LEU F 67 N LYS F 6 SHEET 4 FA 5 GLN F 41 PHE F 45 -1 O ARG F 42 N VAL F 70 SHEET 5 FA 5 LYS F 48 GLN F 49 -1 O LYS F 48 N PHE F 45 LINK SG CYS A 136 ZN ZN A 800 1555 1555 2.30 LINK SG CYS A 139 ZN ZN A 800 1555 1555 2.29 LINK SG CYS A 158 ZN ZN A 801 1555 1555 2.34 LINK ND1 HIS A 160 ZN ZN A 801 1555 1555 2.11 LINK SG CYS A 163 ZN ZN A 800 1555 1555 2.32 LINK SG CYS A 166 ZN ZN A 800 1555 1555 2.30 LINK SG CYS A 177 ZN ZN A 801 1555 1555 2.28 LINK SG CYS A 180 ZN ZN A 801 1555 1555 2.31 LINK SG CYS A 201 ZN ZN A 802 1555 1555 2.31 LINK SG CYS A 204 ZN ZN A 802 1555 1555 2.31 LINK SG CYS A 223 ZN ZN A 803 1555 1555 2.32 LINK ND1 HIS A 225 ZN ZN A 803 1555 1555 2.12 LINK SG CYS A 228 ZN ZN A 802 1555 1555 2.33 LINK SG CYS A 231 ZN ZN A 802 1555 1555 2.30 LINK SG CYS A 242 ZN ZN A 803 1555 1555 2.31 LINK SG CYS A 245 ZN ZN A 803 1555 1555 2.36 CISPEP 1 TYR B 62 PRO B 63 0 9.99 CISPEP 2 TYR E 62 PRO E 63 0 15.90 SITE 1 AC1 4 CYS A 136 CYS A 139 CYS A 163 CYS A 166 SITE 1 AC2 4 CYS A 158 HIS A 160 CYS A 177 CYS A 180 SITE 1 AC3 4 CYS A 201 CYS A 204 CYS A 228 CYS A 231 SITE 1 AC4 4 CYS A 223 HIS A 225 CYS A 242 CYS A 245 SITE 1 AC5 10 PHE E 47 PHE E 52 LYS E 74 ILE E 75 SITE 2 AC5 10 TYR E 76 ALA E 140 TRP E 143 THR E 144 SITE 3 AC5 10 TYR E 147 ALA E 148 SITE 1 AC6 5 HOH E2001 PHE F 45 ALA F 46 GLY F 47 SITE 2 AC6 5 HIS F 68 SITE 1 AC7 9 PHE B 47 PHE B 52 LYS B 74 ILE B 75 SITE 2 AC7 9 TYR B 76 ALA B 140 TRP B 143 THR B 144 SITE 3 AC7 9 TYR B 147 SITE 1 AC8 5 LEU B 106 PHE C 45 ALA C 46 GLY C 47 SITE 2 AC8 5 HIS C 68 SITE 1 AC9 6 TYR A 193 PRO A 202 HIS A 225 VAL A 226 SITE 2 AC9 6 PHE A 227 THR A 244 SITE 1 BC1 6 LEU B 15 PRO B 19 VAL B 20 ILE B 23 SITE 2 BC1 6 LYS B 24 ALA B 25 CRYST1 69.190 169.210 52.620 90.00 90.00 90.00 P 21 21 2 8 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 0.014453 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005910 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019004 0.00000