PDB Short entry for 3E46 HEADER LIGASE 09-AUG-08 3E46 TITLE CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME E2-25KDA (HUNTINGTON TITLE 2 INTERACTING PROTEIN 2) M172A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-25 KDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-CONJUGATING ENZYME E2 K, E2(25K), UBIQUITIN- COMPND 5 PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN, HUNTINGTIN-INTERACTING COMPND 6 PROTEIN 2, HIP-2; COMPND 7 EC: 6.3.2.19; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: UBE2K, HIP2, LIG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS UBIQUITIN-CONJUGATING, HUNTINGTON INTERACTING, E2-25K, LIGASE, KEYWDS 2 ALTERNATIVE SPLICING, CYTOPLASM, UBL CONJUGATION, UBL CONJUGATION KEYWDS 3 PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR R.C.HUGHES,R.C.WILSON,J.W.FLATT,E.J.MEEHAN,J.D.NG,P.D.TWIGG REVDAT 5 30-AUG-23 3E46 1 REMARK REVDAT 4 20-OCT-21 3E46 1 REMARK SEQADV LINK REVDAT 3 12-MAY-09 3E46 1 JRNL REVDAT 2 24-FEB-09 3E46 1 VERSN REVDAT 1 26-AUG-08 3E46 0 JRNL AUTH R.C.WILSON,R.C.HUGHES,J.W.FLATT,E.J.MEEHAN,J.D.NG,P.D.TWIGG JRNL TITL STRUCTURE OF FULL-LENGTH UBIQUITIN-CONJUGATING ENZYME E2-25K JRNL TITL 2 (HUNTINGTIN-INTERACTING PROTEIN 2). JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 65 440 2009 JRNL REFN ESSN 1744-3091 JRNL PMID 19407372 JRNL DOI 10.1107/S1744309109011117 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 27404 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1403 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1066 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 52.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.4160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1570 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.02000 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): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.829 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1631 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1084 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2233 ; 1.514 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2673 ; 0.939 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 211 ; 5.429 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 72 ;38.906 ;25.278 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 273 ;12.945 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;16.114 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 258 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1821 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 303 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 379 ; 0.233 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1158 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 831 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 799 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 158 ; 0.208 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.258 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 8 ; 0.320 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 18 ; 0.186 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.130 ; 0.200 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): 1068 ; 1.361 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 402 ; 0.252 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1676 ; 2.099 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 662 ; 3.253 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 552 ; 5.299 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3E46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 0.97000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27414 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 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 (%) : 93.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.980 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 2BEP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CALCIUM ACETATE, SODIUM ACETATE, NACL, REMARK 280 PEG 8000, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 67.24500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.24500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.20200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 67.24500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.24500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.20200 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 67.24500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 67.24500 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 19.20200 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 67.24500 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 67.24500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 19.20200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 -52 REMARK 465 HIS A -51 REMARK 465 HIS A -50 REMARK 465 HIS A -49 REMARK 465 HIS A -48 REMARK 465 HIS A -47 REMARK 465 HIS A -46 REMARK 465 SER A -45 REMARK 465 SER A -44 REMARK 465 GLY A -43 REMARK 465 LEU A -42 REMARK 465 VAL A -41 REMARK 465 PRO A -40 REMARK 465 ARG A -39 REMARK 465 GLY A -38 REMARK 465 SER A -37 REMARK 465 GLY A -36 REMARK 465 MET A -35 REMARK 465 LYS A -34 REMARK 465 GLU A -33 REMARK 465 THR A -32 REMARK 465 ALA A -31 REMARK 465 ALA A -30 REMARK 465 ALA A -29 REMARK 465 LYS A -28 REMARK 465 PHE A -27 REMARK 465 GLU A -26 REMARK 465 ARG A -25 REMARK 465 GLN A -24 REMARK 465 HIS A -23 REMARK 465 MET A -22 REMARK 465 ASP A -21 REMARK 465 SER A -20 REMARK 465 PRO A -19 REMARK 465 ASP A -18 REMARK 465 LEU A -17 REMARK 465 GLY A -16 REMARK 465 THR A -15 REMARK 465 ASP A -14 REMARK 465 ASP A -13 REMARK 465 ASP A -12 REMARK 465 ASP A -11 REMARK 465 LYS A -10 REMARK 465 ALA A -9 REMARK 465 MET A -8 REMARK 465 ALA A -7 REMARK 465 ASP A -6 REMARK 465 ILE A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 GLU A -2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A -1 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 24 CE NZ REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 LYS A 72 CE NZ REMARK 470 LYS A 78 NZ REMARK 470 GLU A 121 CD OE1 OE2 REMARK 470 VAL A 157 CG1 CG2 REMARK 470 LYS A 164 CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LEU A 39 CA CB CG CD1 CD2 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 ND2 ASN A 200 O HOH A 461 2.03 REMARK 500 OH TYR A 56 O HOH A 465 2.15 REMARK 500 OD1 ASN A 132 NE2 GLN A 136 2.15 REMARK 500 O HOH A 406 O HOH A 450 2.19 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 LYS A 97 -99.91 -123.33 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 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 0 O REMARK 620 2 HOH A 379 O 159.6 REMARK 620 3 HOH A 416 O 100.7 99.6 REMARK 620 4 HOH A 489 O 96.5 86.1 75.9 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 CA A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BEP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME E2-25 KDA REMARK 900 RELATED ID: 2BF9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AVIAN PANCREATIC POLYPEPTIDE REMARK 900 RELATED ID: 1YLA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME E2-25 KDA REMARK 900 RELATED ID: 1JBB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UBIQUITIN-CONJUGATING ENZYME UBC13 DBREF 3E46 A 1 200 UNP P61086 UBE2K_HUMAN 1 200 SEQADV 3E46 MET A -52 UNP P61086 EXPRESSION TAG SEQADV 3E46 HIS A -51 UNP P61086 EXPRESSION TAG SEQADV 3E46 HIS A -50 UNP P61086 EXPRESSION TAG SEQADV 3E46 HIS A -49 UNP P61086 EXPRESSION TAG SEQADV 3E46 HIS A -48 UNP P61086 EXPRESSION TAG SEQADV 3E46 HIS A -47 UNP P61086 EXPRESSION TAG SEQADV 3E46 HIS A -46 UNP P61086 EXPRESSION TAG SEQADV 3E46 SER A -45 UNP P61086 EXPRESSION TAG SEQADV 3E46 SER A -44 UNP P61086 EXPRESSION TAG SEQADV 3E46 GLY A -43 UNP P61086 EXPRESSION TAG SEQADV 3E46 LEU A -42 UNP P61086 EXPRESSION TAG SEQADV 3E46 VAL A -41 UNP P61086 EXPRESSION TAG SEQADV 3E46 PRO A -40 UNP P61086 EXPRESSION TAG SEQADV 3E46 ARG A -39 UNP P61086 EXPRESSION TAG SEQADV 3E46 GLY A -38 UNP P61086 EXPRESSION TAG SEQADV 3E46 SER A -37 UNP P61086 EXPRESSION TAG SEQADV 3E46 GLY A -36 UNP P61086 EXPRESSION TAG SEQADV 3E46 MET A -35 UNP P61086 EXPRESSION TAG SEQADV 3E46 LYS A -34 UNP P61086 EXPRESSION TAG SEQADV 3E46 GLU A -33 UNP P61086 EXPRESSION TAG SEQADV 3E46 THR A -32 UNP P61086 EXPRESSION TAG SEQADV 3E46 ALA A -31 UNP P61086 EXPRESSION TAG SEQADV 3E46 ALA A -30 UNP P61086 EXPRESSION TAG SEQADV 3E46 ALA A -29 UNP P61086 EXPRESSION TAG SEQADV 3E46 LYS A -28 UNP P61086 EXPRESSION TAG SEQADV 3E46 PHE A -27 UNP P61086 EXPRESSION TAG SEQADV 3E46 GLU A -26 UNP P61086 EXPRESSION TAG SEQADV 3E46 ARG A -25 UNP P61086 EXPRESSION TAG SEQADV 3E46 GLN A -24 UNP P61086 EXPRESSION TAG SEQADV 3E46 HIS A -23 UNP P61086 EXPRESSION TAG SEQADV 3E46 MET A -22 UNP P61086 EXPRESSION TAG SEQADV 3E46 ASP A -21 UNP P61086 EXPRESSION TAG SEQADV 3E46 SER A -20 UNP P61086 EXPRESSION TAG SEQADV 3E46 PRO A -19 UNP P61086 EXPRESSION TAG SEQADV 3E46 ASP A -18 UNP P61086 EXPRESSION TAG SEQADV 3E46 LEU A -17 UNP P61086 EXPRESSION TAG SEQADV 3E46 GLY A -16 UNP P61086 EXPRESSION TAG SEQADV 3E46 THR A -15 UNP P61086 EXPRESSION TAG SEQADV 3E46 ASP A -14 UNP P61086 EXPRESSION TAG SEQADV 3E46 ASP A -13 UNP P61086 EXPRESSION TAG SEQADV 3E46 ASP A -12 UNP P61086 EXPRESSION TAG SEQADV 3E46 ASP A -11 UNP P61086 EXPRESSION TAG SEQADV 3E46 LYS A -10 UNP P61086 EXPRESSION TAG SEQADV 3E46 ALA A -9 UNP P61086 EXPRESSION TAG SEQADV 3E46 MET A -8 UNP P61086 EXPRESSION TAG SEQADV 3E46 ALA A -7 UNP P61086 EXPRESSION TAG SEQADV 3E46 ASP A -6 UNP P61086 EXPRESSION TAG SEQADV 3E46 ILE A -5 UNP P61086 EXPRESSION TAG SEQADV 3E46 GLY A -4 UNP P61086 EXPRESSION TAG SEQADV 3E46 SER A -3 UNP P61086 EXPRESSION TAG SEQADV 3E46 GLU A -2 UNP P61086 EXPRESSION TAG SEQADV 3E46 PHE A -1 UNP P61086 EXPRESSION TAG SEQADV 3E46 ASP A 0 UNP P61086 EXPRESSION TAG SEQADV 3E46 ALA A 172 UNP P61086 MET 172 ENGINEERED MUTATION SEQRES 1 A 253 MET HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO SEQRES 2 A 253 ARG GLY SER GLY MET LYS GLU THR ALA ALA ALA LYS PHE SEQRES 3 A 253 GLU ARG GLN HIS MET ASP SER PRO ASP LEU GLY THR ASP SEQRES 4 A 253 ASP ASP ASP LYS ALA MET ALA ASP ILE GLY SER GLU PHE SEQRES 5 A 253 ASP MET ALA ASN ILE ALA VAL GLN ARG ILE LYS ARG GLU SEQRES 6 A 253 PHE LYS GLU VAL LEU LYS SER GLU GLU THR SER LYS ASN SEQRES 7 A 253 GLN ILE LYS VAL ASP LEU VAL ASP GLU ASN PHE THR GLU SEQRES 8 A 253 LEU ARG GLY GLU ILE ALA GLY PRO PRO ASP THR PRO TYR SEQRES 9 A 253 GLU GLY GLY ARG TYR GLN LEU GLU ILE LYS ILE PRO GLU SEQRES 10 A 253 THR TYR PRO PHE ASN PRO PRO LYS VAL ARG PHE ILE THR SEQRES 11 A 253 LYS ILE TRP HIS PRO ASN ILE SER SER VAL THR GLY ALA SEQRES 12 A 253 ILE CYS LEU ASP ILE LEU LYS ASP GLN TRP ALA ALA ALA SEQRES 13 A 253 MET THR LEU ARG THR VAL LEU LEU SER LEU GLN ALA LEU SEQRES 14 A 253 LEU ALA ALA ALA GLU PRO ASP ASP PRO GLN ASP ALA VAL SEQRES 15 A 253 VAL ALA ASN GLN TYR LYS GLN ASN PRO GLU MET PHE LYS SEQRES 16 A 253 GLN THR ALA ARG LEU TRP ALA HIS VAL TYR ALA GLY ALA SEQRES 17 A 253 PRO VAL SER SER PRO GLU TYR THR LYS LYS ILE GLU ASN SEQRES 18 A 253 LEU CYS ALA ALA GLY PHE ASP ARG ASN ALA VAL ILE VAL SEQRES 19 A 253 ALA LEU SER SER LYS SER TRP ASP VAL GLU THR ALA THR SEQRES 20 A 253 GLU LEU LEU LEU SER ASN HET CA A 301 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *207(H2 O) HELIX 1 1 ALA A 2 SER A 19 1 18 HELIX 2 2 SER A 19 LYS A 24 1 6 HELIX 3 3 LEU A 93 LYS A 97 5 5 HELIX 4 4 THR A 105 ALA A 119 1 15 HELIX 5 5 ASP A 127 ASN A 137 1 11 HELIX 6 6 ASN A 137 GLY A 154 1 18 HELIX 7 7 SER A 159 ALA A 172 1 14 HELIX 8 8 ASP A 175 LYS A 186 1 12 HELIX 9 9 ASP A 189 ASN A 200 1 12 SHEET 1 A 4 ILE A 27 LEU A 31 0 SHEET 2 A 4 GLU A 38 ALA A 44 -1 O ARG A 40 N ASP A 30 SHEET 3 A 4 ARG A 55 LYS A 61 -1 O ILE A 60 N LEU A 39 SHEET 4 A 4 LYS A 72 PHE A 75 -1 O LYS A 72 N LYS A 61 LINK O ASP A 0 CA CA A 301 1555 1555 2.21 LINK CA CA A 301 O HOH A 379 1555 1555 2.48 LINK CA CA A 301 O HOH A 416 1555 1555 2.12 LINK CA CA A 301 O HOH A 489 1555 1555 2.48 CISPEP 1 TYR A 66 PRO A 67 0 5.72 SITE 1 AC1 6 ASP A 0 GLU A 20 GLN A 99 HOH A 379 SITE 2 AC1 6 HOH A 416 HOH A 489 CRYST1 134.490 134.490 38.404 90.00 90.00 90.00 I 4 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 0.007435 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026039 0.00000