HEADER HYDROLASE/HYDROLASE ACTIVATOR 11-JUL-06 2IY0 TITLE SENP1 (MUTANT) SUMO1 RANGAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENTRIN-SPECIFIC PROTEASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL FRAGMENT, RESIDUES 419-643; COMPND 5 SYNONYM: SENP1, SENTRIN/SUMO-SPECIFIC PROTEASE SENP1; COMPND 6 EC: 3.4.22.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 1; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: SUMO-1, UBIQUITIN-LIKE PROTEIN SMT3C, SMT3 HOMOLOG 3, COMPND 13 UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1, UBIQUITIN-LIKE PROTEIN UBL1, COMPND 14 GAP-MODIFYING PROTEIN 1, GMP1, SENTRIN, SUMO1; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: RAN GTPASE-ACTIVATING PROTEIN 1; COMPND 18 CHAIN: C; COMPND 19 FRAGMENT: C-TERMINUS, RESIDUES 432-587; COMPND 20 SYNONYM: RANGAP; COMPND 21 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; 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 HYDROLASE-HYDROLASE ACTIVATOR COMPLEX, HYDROLASE-ACTIVATOR COMPLEX, KEYWDS 2 PROTEASE, HYDROLASE, UBIQUITIN, THIOL PROTEASE, LEUCINE- RICH KEYWDS 3 REPEAT, UBL CONJUGATION PATHWAY, PROTEIN PROTEIN COMPLEX, GTPASE KEYWDS 4 ACTIVATION, HYDROLASE-ACTIVATOR COMPLEX UBL CONJUGATION, NUCLEAR KEYWDS 5 PROTEIN, PHOSPHORYLATION EXPDTA X-RAY DIFFRACTION AUTHOR L.SHEN,C.DONG,J.H.NAISMITH REVDAT 5 28-JUN-17 2IY0 1 REMARK REVDAT 4 13-JUL-11 2IY0 1 VERSN REVDAT 3 24-FEB-09 2IY0 1 VERSN REVDAT 2 20-DEC-06 2IY0 1 JRNL REVDAT 1 07-AUG-06 2IY0 0 JRNL AUTH L.SHEN,M.H.TATHAM,C.DONG,A.ZAGORSKA,J.H.NAISMITH,R.T.HAY JRNL TITL SUMO PROTEASE SENP1 INDUCES ISOMERIZATION OF THE SCISSILE JRNL TITL 2 PEPTIDE BOND. JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 1069 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 17099698 JRNL DOI 10.1038/NSMB1172 REMARK 2 REMARK 2 RESOLUTION. 2.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13161 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 691 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) : 2.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 941 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3709 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.08000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.418 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.336 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 36.217 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.872 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3785 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5099 ; 1.177 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 6.202 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;38.597 ;24.602 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 720 ;16.860 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;15.061 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 566 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2801 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1786 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2600 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 133 ; 0.157 ; 0.200 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): 44 ; 0.229 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.170 ; 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): 2343 ; 0.317 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3707 ; 0.566 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1607 ; 0.784 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1392 ; 1.269 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 419 A 644 REMARK 3 ORIGIN FOR THE GROUP (A): 7.3030 -27.0000 -12.8670 REMARK 3 T TENSOR REMARK 3 T11: -0.0260 T22: -0.1210 REMARK 3 T33: -0.0478 T12: -0.0584 REMARK 3 T13: 0.0581 T23: -0.0570 REMARK 3 L TENSOR REMARK 3 L11: 5.2408 L22: 3.5926 REMARK 3 L33: 3.5812 L12: 0.9072 REMARK 3 L13: -0.9203 L23: 0.4149 REMARK 3 S TENSOR REMARK 3 S11: 0.0141 S12: -0.1334 S13: -0.0516 REMARK 3 S21: 0.0591 S22: -0.2410 S23: 0.5109 REMARK 3 S31: 0.1196 S32: -0.2660 S33: 0.2269 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 22 B 97 REMARK 3 ORIGIN FOR THE GROUP (A): -7.3700 -7.7160 -16.3860 REMARK 3 T TENSOR REMARK 3 T11: 0.3817 T22: 0.2289 REMARK 3 T33: 0.9055 T12: 0.2025 REMARK 3 T13: -0.0927 T23: -0.0947 REMARK 3 L TENSOR REMARK 3 L11: 12.0769 L22: 7.7839 REMARK 3 L33: 4.7567 L12: -2.5061 REMARK 3 L13: 3.9075 L23: -1.9697 REMARK 3 S TENSOR REMARK 3 S11: -0.2038 S12: 0.2487 S13: 1.6353 REMARK 3 S21: -0.1961 S22: 0.0963 S23: 1.9103 REMARK 3 S31: -0.7554 S32: -0.8472 S33: 0.1075 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 432 C 587 REMARK 3 ORIGIN FOR THE GROUP (A): 19.5610 -1.2750 9.7140 REMARK 3 T TENSOR REMARK 3 T11: 0.0042 T22: -0.0235 REMARK 3 T33: -0.1143 T12: -0.0412 REMARK 3 T13: -0.0128 T23: -0.0572 REMARK 3 L TENSOR REMARK 3 L11: 5.2171 L22: 6.4915 REMARK 3 L33: 2.8417 L12: -2.9773 REMARK 3 L13: 0.1885 L23: -0.1949 REMARK 3 S TENSOR REMARK 3 S11: -0.1783 S12: -0.2913 S13: 0.0331 REMARK 3 S21: -0.1294 S22: 0.3180 S23: -0.1943 REMARK 3 S31: 0.1761 S32: -0.0658 S33: -0.1397 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2IY0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1290029364. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13161 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.770 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 74.02200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.69000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.69000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 111.03300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.69000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.69000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.01100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.69000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.69000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 111.03300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.69000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.69000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.01100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 74.02200 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 602 TO ALA 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 GLU B 20 REMARK 465 TYR B 21 REMARK 465 HIS B 98 REMARK 465 SER B 99 REMARK 465 THR B 100 REMARK 465 VAL B 101 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 GLY B 97 NZ LYS C 524 1.33 REMARK 500 OE2 GLU A 430 NE2 HIS A 640 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS B 46 CE LYS B 46 NZ 0.265 REMARK 500 GLU B 49 CD GLU B 49 OE1 0.077 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 PHE A 420 95.97 20.74 REMARK 500 HIS A 462 -129.18 44.25 REMARK 500 SER A 482 1.23 -68.57 REMARK 500 SER A 551 3.44 -69.59 REMARK 500 ASN A 557 -23.44 -17.61 REMARK 500 SER A 601 -14.24 -140.44 REMARK 500 ILE A 620 97.86 -65.79 REMARK 500 ASP B 30 29.22 -76.31 REMARK 500 SER B 31 78.38 47.46 REMARK 500 LYS B 37 66.48 -111.81 REMARK 500 MET B 40 -37.44 -35.96 REMARK 500 ASN B 60 22.16 -79.37 REMARK 500 GLU B 67 62.19 26.94 REMARK 500 GLU B 85 -41.77 -170.16 REMARK 500 GLN B 92 148.10 -28.33 REMARK 500 ASP C 433 -151.71 -74.14 REMARK 500 VAL C 434 -57.89 70.70 REMARK 500 ASP C 462 86.78 -66.80 REMARK 500 GLU C 483 117.53 -177.05 REMARK 500 LYS C 530 -9.76 -57.82 REMARK 500 ALA C 531 94.03 31.39 REMARK 500 THR C 564 -91.38 -77.91 REMARK 500 LYS C 565 111.04 -8.94 REMARK 500 PRO C 566 69.30 -49.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU B 79 LEU B 80 148.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CKG RELATED DB: PDB REMARK 900 THE STRUCTURE OF SENP1 SUMO-2 CO-COMPLEX SUGGESTS A STRUCTURAL REMARK 900 BASIS FOR DISCRIMINATION BETWEEN SUMO PARALOGUES DURING PROCESSING REMARK 900 RELATED ID: 2CKH RELATED DB: PDB REMARK 900 SENP1-SUMO2 COMPLEX REMARK 900 RELATED ID: 1A5R RELATED DB: PDB REMARK 900 STRUCTURE DETERMINATION OF THE SMALL UBIQUITIN -RELATED MODIFIER REMARK 900 SUMO-1, NMR, 10 STRUCTURES REMARK 900 RELATED ID: 1TGZ RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH SUMO-1 REMARK 900 RELATED ID: 1WYW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SUMO1-CONJUGATED THYMINE DNAGLYCOSYLASE REMARK 900 RELATED ID: 1Y8R RELATED DB: PDB REMARK 900 SUMO E1 ACTIVATING ENZYME SAE1-SAE2-SUMO1- MG-ATP COMPLEX REMARK 900 RELATED ID: 1Z5S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A COMPLEX BETWEEN UBC9, SUMO-1,RANGAP1 AND REMARK 900 NUP358/RANBP2 REMARK 900 RELATED ID: 2ASQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF SUMO-1 IN COMPLEX WITH A SUMO-BINDINGMOTIF REMARK 900 (SBM) REMARK 900 RELATED ID: 2BF8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SUMO MODIFIED UBIQUITIN CONJUGATING ENZYME E2- REMARK 900 25K REMARK 900 RELATED ID: 2GRN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN RANGAP1-UBC9 REMARK 900 RELATED ID: 2GRO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN RANGAP1-UBC9-N85Q REMARK 900 RELATED ID: 2GRP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN RANGAP1-UBC9-Y87A REMARK 900 RELATED ID: 2GRQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN RANGAP1-UBC9- D127A REMARK 900 RELATED ID: 2GRR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN RANGAP1-UBC9- D127S REMARK 900 RELATED ID: 2IY1 RELATED DB: PDB REMARK 900 SENP1 (MUTANT) FULL LENGTH SUMO1 REMARK 900 RELATED ID: 2IYC RELATED DB: PDB REMARK 900 SENP1 NATIVE STRUCTURE REMARK 900 RELATED ID: 2IYD RELATED DB: PDB REMARK 900 SENP1 COVALENT COMPLEX WITH SUMO-2 DBREF 2IY0 A 419 592 UNP Q9P0U3 SENP1_HUMAN 419 592 DBREF 2IY0 A 593 593 PDB 2IY0 2IY0 593 593 DBREF 2IY0 A 594 644 UNP Q9P0U3 SENP1_HUMAN 593 643 DBREF 2IY0 B 20 101 UNP P63165 SUMO1_HUMAN 20 101 DBREF 2IY0 C 432 587 UNP P46060 RGP1_HUMAN 432 587 SEQADV 2IY0 ALA A 603 UNP Q9P0U3 CYS 602 ENGINEERED MUTATION SEQRES 1 A 226 GLU PHE PRO GLU ILE THR GLU GLU MET GLU LYS GLU ILE SEQRES 2 A 226 LYS ASN VAL PHE ARG ASN GLY ASN GLN ASP GLU VAL LEU SEQRES 3 A 226 SER GLU ALA PHE ARG LEU THR ILE THR ARG LYS ASP ILE SEQRES 4 A 226 GLN THR LEU ASN HIS LEU ASN TRP LEU ASN ASP GLU ILE SEQRES 5 A 226 ILE ASN PHE TYR MET ASN MET LEU MET GLU ARG SER LYS SEQRES 6 A 226 GLU LYS GLY LEU PRO SER VAL HIS ALA PHE ASN THR PHE SEQRES 7 A 226 PHE PHE THR LYS LEU LYS THR ALA GLY TYR GLN ALA VAL SEQRES 8 A 226 LYS ARG TRP THR LYS LYS VAL ASP VAL PHE SER VAL ASP SEQRES 9 A 226 ILE LEU LEU VAL PRO ILE HIS LEU GLY VAL HIS TRP CYS SEQRES 10 A 226 LEU ALA VAL VAL ASP PHE ARG LYS LYS ASN ILE THR TYR SEQRES 11 A 226 TYR ASP SER MET GLY GLY ILE ASN ASN GLU ALA CYS ARG SEQRES 12 A 226 ILE LEU LEU GLN TYR LEU LYS GLN GLU SER ILE ASP LYS SEQRES 13 A 226 LYS ARG LYS GLU PHE ASP THR ASN GLY TRP GLN LEU PHE SEQRES 14 A 226 SER LYS LYS SER GLN GLU ILE PRO GLN GLN MET ASN GLY SEQRES 15 A 226 SER ASP ALA GLY MET PHE ALA CYS LYS TYR ALA ASP CYS SEQRES 16 A 226 ILE THR LYS ASP ARG PRO ILE ASN PHE THR GLN GLN HIS SEQRES 17 A 226 MET PRO TYR PHE ARG LYS ARG MET VAL TRP GLU ILE LEU SEQRES 18 A 226 HIS ARG LYS LEU LEU SEQRES 1 B 82 GLU TYR ILE LYS LEU LYS VAL ILE GLY GLN ASP SER SER SEQRES 2 B 82 GLU ILE HIS PHE LYS VAL LYS MET THR THR HIS LEU LYS SEQRES 3 B 82 LYS LEU LYS GLU SER TYR CYS GLN ARG GLN GLY VAL PRO SEQRES 4 B 82 MET ASN SER LEU ARG PHE LEU PHE GLU GLY GLN ARG ILE SEQRES 5 B 82 ALA ASP ASN HIS THR PRO LYS GLU LEU GLY MET GLU GLU SEQRES 6 B 82 GLU ASP VAL ILE GLU VAL TYR GLN GLU GLN THR GLY GLY SEQRES 7 B 82 HIS SER THR VAL SEQRES 1 C 156 ALA ASP VAL SER THR PHE LEU ALA PHE PRO SER PRO GLU SEQRES 2 C 156 LYS LEU LEU ARG LEU GLY PRO LYS SER SER VAL LEU ILE SEQRES 3 C 156 ALA GLN GLN THR ASP THR SER ASP PRO GLU LYS VAL VAL SEQRES 4 C 156 SER ALA PHE LEU LYS VAL SER SER VAL PHE LYS ASP GLU SEQRES 5 C 156 ALA THR VAL ARG MET ALA VAL GLN ASP ALA VAL ASP ALA SEQRES 6 C 156 LEU MET GLN LYS ALA PHE ASN SER SER SER PHE ASN SER SEQRES 7 C 156 ASN THR PHE LEU THR ARG LEU LEU VAL HIS MET GLY LEU SEQRES 8 C 156 LEU LYS SER GLU ASP LYS VAL LYS ALA ILE ALA ASN LEU SEQRES 9 C 156 TYR GLY PRO LEU MET ALA LEU ASN HIS MET VAL GLN GLN SEQRES 10 C 156 ASP TYR PHE PRO LYS ALA LEU ALA PRO LEU LEU LEU ALA SEQRES 11 C 156 PHE VAL THR LYS PRO ASN SER ALA LEU GLU SER CYS SER SEQRES 12 C 156 PHE ALA ARG HIS SER LEU LEU GLN THR LEU TYR LYS VAL FORMUL 4 HOH *6(H2 O) HELIX 1 1 THR A 424 ARG A 436 1 13 HELIX 2 2 ARG A 454 THR A 459 1 6 HELIX 3 3 ASP A 468 SER A 482 1 15 HELIX 4 4 PHE A 496 ALA A 504 1 9 HELIX 5 5 GLY A 505 VAL A 509 5 5 HELIX 6 6 VAL A 509 LYS A 514 5 6 HELIX 7 7 ASP A 517 VAL A 521 5 5 HELIX 8 8 GLU A 558 ARG A 576 1 19 HELIX 9 9 ASP A 602 LYS A 616 1 15 HELIX 10 10 THR A 623 GLN A 625 5 3 HELIX 11 11 HIS A 626 ARG A 641 1 16 HELIX 12 12 LEU B 44 GLY B 56 1 13 HELIX 13 13 PRO B 58 ASN B 60 5 3 HELIX 14 14 VAL C 434 PHE C 440 1 7 HELIX 15 15 SER C 442 LEU C 449 1 8 HELIX 16 16 LYS C 452 THR C 461 1 10 HELIX 17 17 ASP C 465 SER C 478 1 14 HELIX 18 18 GLU C 483 ASN C 503 1 21 HELIX 19 19 ASN C 508 MET C 520 1 13 HELIX 20 20 LEU C 535 VAL C 546 1 12 HELIX 21 21 ALA C 554 LYS C 565 1 12 HELIX 22 22 ASN C 567 SER C 572 1 6 HELIX 23 23 CYS C 573 VAL C 587 1 15 SHEET 1 AA 2 VAL A 443 ALA A 447 0 SHEET 2 AA 2 LEU A 450 THR A 453 -1 O LEU A 450 N ALA A 447 SHEET 1 AB 2 LEU A 466 ASN A 467 0 SHEET 2 AB 2 THR B 95 GLY B 96 -1 O GLY B 96 N LEU A 466 SHEET 1 AC 5 VAL A 490 ALA A 492 0 SHEET 2 AC 5 ILE A 523 LEU A 530 1 O ILE A 523 N HIS A 491 SHEET 3 AC 5 HIS A 533 ASP A 540 -1 O HIS A 533 N LEU A 530 SHEET 4 AC 5 ASN A 545 TYR A 549 -1 O ASN A 545 N ASP A 540 SHEET 5 AC 5 GLN A 585 SER A 588 1 O GLN A 585 N ILE A 546 SHEET 1 BA 5 HIS B 35 LYS B 37 0 SHEET 2 BA 5 LYS B 23 GLY B 28 -1 O LEU B 24 N PHE B 36 SHEET 3 BA 5 VAL B 87 GLN B 92 1 O ILE B 88 N ILE B 27 SHEET 4 BA 5 LEU B 62 PHE B 66 -1 O ARG B 63 N TYR B 91 SHEET 5 BA 5 GLN B 69 ARG B 70 -1 O GLN B 69 N PHE B 66 CRYST1 83.380 83.380 148.044 90.00 90.00 90.00 P 43 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 0.011993 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011993 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006755 0.00000 MASTER 445 0 0 23 14 0 0 6 0 0 0 37 END