HEADER HYDROLASE 14-SEP-10 2XRE TITLE DETECTION OF COBALT IN PREVIOUSLY UNASSIGNED HUMAN SENP1 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENTRIN-SPECIFIC PROTEASE 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC FRAGMENT, RESIDUES 415-644; COMPND 5 SYNONYM: SENTRIN/SUMO-SPECIFIC PROTEASE SENP1; COMPND 6 EC: 3.4.22.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: COBALT(II) ION, GLYCEROL SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PHISTEV30A KEYWDS HYDROLASE, CYSTEINE PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR V.RIMSA,T.EADSFORTH,R.T.HAY,W.N.HUNTER REVDAT 7 20-DEC-23 2XRE 1 REMARK LINK REVDAT 6 29-MAY-19 2XRE 1 REMARK REVDAT 5 20-NOV-13 2XRE 1 SOURCE REMARK REVDAT 4 03-OCT-12 2XRE 1 REMARK REVDAT 3 11-APR-12 2XRE 1 JRNL REMARK VERSN HETSYN REVDAT 2 27-APR-11 2XRE 1 JRNL REVDAT 1 06-OCT-10 2XRE 0 JRNL AUTH V.RIMSA,T.EADSFORTH,W.N.HUNTER JRNL TITL THE ROLE OF CO2+ IN THE CRYSTALLIZATION OF HUMAN SENP1 AND JRNL TITL 2 COMMENTS ON THE LIMITATIONS OF AUTOMATED REFINEMENT JRNL TITL 3 PROTOCOLS JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 67 442 2011 JRNL REFN ESSN 1744-3091 JRNL PMID 21505236 JRNL DOI 10.1107/S1744309111005835 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21829 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) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.317 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1136 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1555 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3705 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.03000 REMARK 3 B12 (A**2) : -0.01000 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): 0.479 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.337 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.270 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.596 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.874 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3990 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5379 ; 1.525 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 477 ; 6.304 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 201 ;40.532 ;23.980 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 728 ;20.308 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;14.202 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 558 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3026 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2316 ; 2.070 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3760 ; 3.716 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1674 ; 5.727 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1614 ; 7.856 ;10.000 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 : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2XRE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1290045373. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21832 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 45.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2IYC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION WAS PERFORMED USING A REMARK 280 SITTING-DROP VAPOUR-DIFFUSION METHOD. CRYSTALS APPEARED FROM REMARK 280 EQUAL VOLUMES OF PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL, REMARK 280 PH 8.0, AND 50 MM NACL) AND RESERVOIR SOLUTION CONTAINING 100 MM REMARK 280 COCL2, 0.1M MES, PH 6.5, AND 1.8 M (NH4)2SO4., VAPOR DIFFUSION, REMARK 280 SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 66.88000 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 133.76000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 133.76000 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 66.88000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 35.99050 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -62.33737 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 66.88000 REMARK 350 REMARK 350 BIOMOLECULE: 3 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ASP A 415 REMARK 465 SER A 416 REMARK 465 GLU A 417 REMARK 465 ASP B 415 REMARK 465 SER B 416 REMARK 465 GLU B 417 REMARK 465 ASP B 418 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 GLU A 422 CG CD OE1 OE2 REMARK 470 LYS A 500 CG CD CE NZ REMARK 470 ARG A 511 CD NE CZ NH1 NH2 REMARK 470 LYS A 514 CB CG CD CE NZ REMARK 470 LYS A 568 CB CG CD CE NZ REMARK 470 LYS A 577 CD CE NZ REMARK 470 MET A 598 SD CE REMARK 470 GLN A 625 CD OE1 NE2 REMARK 470 ARG B 436 CB CG CD NE CZ NH1 NH2 REMARK 470 ASN B 437 CB CG OD1 ND2 REMARK 470 ASN B 439 CB CG OD1 ND2 REMARK 470 ASP B 441 CB CG OD1 OD2 REMARK 470 LYS B 485 CB CG CD CE NZ REMARK 470 SER B 571 CA CB OG REMARK 470 LYS B 574 CB CG CD CE NZ REMARK 470 LYS B 575 CB CG CD CE NZ REMARK 470 ARG B 576 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 577 CD CE NZ REMARK 470 LYS B 590 CG CD CE NZ REMARK 470 GLN B 625 CG CD OE1 NE2 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 OE1 GLU B 430 CO CO B 1651 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 430 CO CO B 1651 3654 1.61 REMARK 500 OE1 GLU A 430 OE1 GLU B 430 3654 2.11 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 SER B 482 N SER B 482 CA -0.152 REMARK 500 LYS B 483 CG LYS B 483 CD 0.287 REMARK 500 ARG B 576 C ARG B 576 O -0.190 REMARK 500 LYS B 590 C LYS B 590 O -0.202 REMARK 500 SER B 591 CA SER B 591 CB -0.127 REMARK 500 SER B 591 CB SER B 591 OG 0.107 REMARK 500 GLN B 592 C GLN B 592 O -0.183 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 GLU B 419 CA - C - O ANGL. DEV. = -34.9 DEGREES REMARK 500 GLU B 419 CA - C - N ANGL. DEV. = 31.5 DEGREES REMARK 500 SER B 482 N - CA - CB ANGL. DEV. = 10.7 DEGREES REMARK 500 LYS B 483 CB - CG - CD ANGL. DEV. = -24.6 DEGREES REMARK 500 LYS B 483 CG - CD - CE ANGL. DEV. = -55.0 DEGREES REMARK 500 LYS B 590 O - C - N ANGL. DEV. = -11.3 DEGREES REMARK 500 SER B 591 CB - CA - C ANGL. DEV. = 12.0 DEGREES REMARK 500 SER B 591 CA - CB - OG ANGL. DEV. = 25.0 DEGREES REMARK 500 SER B 591 O - C - N ANGL. DEV. = -19.6 DEGREES REMARK 500 GLN B 592 CB - CA - C ANGL. DEV. = 28.1 DEGREES REMARK 500 GLN B 592 CA - C - N ANGL. DEV. = -26.2 DEGREES REMARK 500 GLN B 592 O - C - N ANGL. DEV. = 26.4 DEGREES REMARK 500 GLU B 593 C - N - CA ANGL. DEV. = -26.6 DEGREES REMARK 500 ILE B 638 CA - C - O ANGL. DEV. = -14.4 DEGREES REMARK 500 ILE B 638 CA - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 ILE B 638 CA - C - N ANGL. DEV. = 16.1 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 GLU A 419 41.32 73.43 REMARK 500 ASN A 439 99.00 -55.53 REMARK 500 PHE A 448 25.43 44.78 REMARK 500 ARG A 449 7.17 87.06 REMARK 500 HIS A 462 -113.94 34.74 REMARK 500 ALA A 504 -4.92 -141.83 REMARK 500 ASN A 556 65.47 -159.45 REMARK 500 GLU B 446 115.83 -168.21 REMARK 500 ARG B 449 8.29 49.85 REMARK 500 ARG B 449 6.99 51.21 REMARK 500 ASN B 545 159.17 179.15 REMARK 500 ASN B 556 80.30 -159.11 REMARK 500 LYS B 574 -60.04 -100.68 REMARK 500 THR B 581 50.22 -110.54 REMARK 500 SER B 588 99.40 -66.56 REMARK 500 MET B 598 -34.69 -135.46 REMARK 500 ASP B 617 -22.07 90.75 REMARK 500 ASP B 617 -23.00 90.75 REMARK 500 ILE B 620 89.19 -67.96 REMARK 500 ASN B 621 58.58 -109.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS B 574 -10.58 REMARK 500 SER B 591 26.13 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 CO B1651 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 430 OE2 REMARK 620 2 HIS A 640 NE2 99.0 REMARK 620 3 GLU B 430 OE2 171.8 83.2 REMARK 620 4 HIS B 640 NE2 77.6 127.0 94.8 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 GOL A 1645 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1646 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1647 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1648 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1645 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1646 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1647 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1648 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1649 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1650 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 1651 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IYD RELATED DB: PDB REMARK 900 SENP1 COVALENT COMPLEX WITH SUMO-2 REMARK 900 RELATED ID: 2IYC RELATED DB: PDB REMARK 900 SENP1 NATIVE STRUCTURE REMARK 900 RELATED ID: 2IY1 RELATED DB: PDB REMARK 900 SENP1 (MUTANT) FULL LENGTH SUMO1 REMARK 900 RELATED ID: 2IY0 RELATED DB: PDB REMARK 900 SENP1 (MUTANT) SUMO1 RANGAP 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: 2XPH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SENP1 WITH THE BOUND COBALT REMARK 900 RELATED ID: 2G4D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SENP1 MUTANT ( C603S) IN COMPLEXWITH REMARK 900 SUMO-1 REMARK 900 RELATED ID: 2CKH RELATED DB: PDB REMARK 900 SENP1-SUMO2 COMPLEX DBREF 2XRE A 415 644 UNP Q9P0U3 SENP1_HUMAN 415 644 DBREF 2XRE B 415 644 UNP Q9P0U3 SENP1_HUMAN 415 644 SEQRES 1 A 230 ASP SER GLU ASP GLU PHE PRO GLU ILE THR GLU GLU MET SEQRES 2 A 230 GLU LYS GLU ILE LYS ASN VAL PHE ARG ASN GLY ASN GLN SEQRES 3 A 230 ASP GLU VAL LEU SER GLU ALA PHE ARG LEU THR ILE THR SEQRES 4 A 230 ARG LYS ASP ILE GLN THR LEU ASN HIS LEU ASN TRP LEU SEQRES 5 A 230 ASN ASP GLU ILE ILE ASN PHE TYR MET ASN MET LEU MET SEQRES 6 A 230 GLU ARG SER LYS GLU LYS GLY LEU PRO SER VAL HIS ALA SEQRES 7 A 230 PHE ASN THR PHE PHE PHE THR LYS LEU LYS THR ALA GLY SEQRES 8 A 230 TYR GLN ALA VAL LYS ARG TRP THR LYS LYS VAL ASP VAL SEQRES 9 A 230 PHE SER VAL ASP ILE LEU LEU VAL PRO ILE HIS LEU GLY SEQRES 10 A 230 VAL HIS TRP CYS LEU ALA VAL VAL ASP PHE ARG LYS LYS SEQRES 11 A 230 ASN ILE THR TYR TYR ASP SER MET GLY GLY ILE ASN ASN SEQRES 12 A 230 GLU ALA CYS ARG ILE LEU LEU GLN TYR LEU LYS GLN GLU SEQRES 13 A 230 SER ILE ASP LYS LYS ARG LYS GLU PHE ASP THR ASN GLY SEQRES 14 A 230 TRP GLN LEU PHE SER LYS LYS SER GLN GLU ILE PRO GLN SEQRES 15 A 230 GLN MET ASN GLY SER ASP CYS GLY MET PHE ALA CYS LYS SEQRES 16 A 230 TYR ALA ASP CYS ILE THR LYS ASP ARG PRO ILE ASN PHE SEQRES 17 A 230 THR GLN GLN HIS MET PRO TYR PHE ARG LYS ARG MET VAL SEQRES 18 A 230 TRP GLU ILE LEU HIS ARG LYS LEU LEU SEQRES 1 B 230 ASP SER GLU ASP GLU PHE PRO GLU ILE THR GLU GLU MET SEQRES 2 B 230 GLU LYS GLU ILE LYS ASN VAL PHE ARG ASN GLY ASN GLN SEQRES 3 B 230 ASP GLU VAL LEU SER GLU ALA PHE ARG LEU THR ILE THR SEQRES 4 B 230 ARG LYS ASP ILE GLN THR LEU ASN HIS LEU ASN TRP LEU SEQRES 5 B 230 ASN ASP GLU ILE ILE ASN PHE TYR MET ASN MET LEU MET SEQRES 6 B 230 GLU ARG SER LYS GLU LYS GLY LEU PRO SER VAL HIS ALA SEQRES 7 B 230 PHE ASN THR PHE PHE PHE THR LYS LEU LYS THR ALA GLY SEQRES 8 B 230 TYR GLN ALA VAL LYS ARG TRP THR LYS LYS VAL ASP VAL SEQRES 9 B 230 PHE SER VAL ASP ILE LEU LEU VAL PRO ILE HIS LEU GLY SEQRES 10 B 230 VAL HIS TRP CYS LEU ALA VAL VAL ASP PHE ARG LYS LYS SEQRES 11 B 230 ASN ILE THR TYR TYR ASP SER MET GLY GLY ILE ASN ASN SEQRES 12 B 230 GLU ALA CYS ARG ILE LEU LEU GLN TYR LEU LYS GLN GLU SEQRES 13 B 230 SER ILE ASP LYS LYS ARG LYS GLU PHE ASP THR ASN GLY SEQRES 14 B 230 TRP GLN LEU PHE SER LYS LYS SER GLN GLU ILE PRO GLN SEQRES 15 B 230 GLN MET ASN GLY SER ASP CYS GLY MET PHE ALA CYS LYS SEQRES 16 B 230 TYR ALA ASP CYS ILE THR LYS ASP ARG PRO ILE ASN PHE SEQRES 17 B 230 THR GLN GLN HIS MET PRO TYR PHE ARG LYS ARG MET VAL SEQRES 18 B 230 TRP GLU ILE LEU HIS ARG LYS LEU LEU HET GOL A1645 6 HET GOL A1646 6 HET GOL A1647 6 HET GOL A1648 6 HET GOL B1645 6 HET GOL B1646 6 HET GOL B1647 6 HET GOL B1648 6 HET GOL B1649 6 HET GOL B1650 6 HET CO B1651 1 HETNAM GOL GLYCEROL HETNAM CO COBALT (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 10(C3 H8 O3) FORMUL 13 CO CO 2+ FORMUL 14 HOH *61(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 ASN A 467 SER A 482 1 16 HELIX 4 4 PHE A 498 THR A 503 1 6 HELIX 5 5 GLY A 505 VAL A 509 5 5 HELIX 6 6 ASP A 517 VAL A 521 5 5 HELIX 7 7 ASN A 556 ARG A 576 1 21 HELIX 8 8 ASP A 602 LYS A 616 1 15 HELIX 9 9 THR A 623 GLN A 625 5 3 HELIX 10 10 HIS A 626 ARG A 641 1 16 HELIX 11 11 THR B 424 VAL B 434 1 11 HELIX 12 12 ARG B 454 THR B 459 1 6 HELIX 13 13 ASN B 467 LYS B 483 1 17 HELIX 14 14 THR B 495 GLY B 505 1 11 HELIX 15 15 TYR B 506 THR B 513 5 8 HELIX 16 16 ASP B 517 VAL B 521 5 5 HELIX 17 17 ASN B 556 GLU B 570 1 15 HELIX 18 18 ASN B 599 SER B 601 5 3 HELIX 19 19 ASP B 602 ASP B 617 1 16 HELIX 20 20 THR B 623 GLN B 625 5 3 HELIX 21 21 HIS B 626 ARG B 641 1 16 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 5 VAL A 490 ALA A 492 0 SHEET 2 AB 5 ILE A 523 LEU A 530 1 O ILE A 523 N HIS A 491 SHEET 3 AB 5 HIS A 533 ASP A 540 -1 O HIS A 533 N LEU A 530 SHEET 4 AB 5 ASN A 545 TYR A 549 -1 O ASN A 545 N ASP A 540 SHEET 5 AB 5 GLN A 585 SER A 588 1 O GLN A 585 N ILE A 546 SHEET 1 BA 2 VAL B 443 ALA B 447 0 SHEET 2 BA 2 LEU B 450 THR B 453 -1 O LEU B 450 N ALA B 447 SHEET 1 BB 5 VAL B 490 ALA B 492 0 SHEET 2 BB 5 ILE B 523 LEU B 530 1 O ILE B 523 N HIS B 491 SHEET 3 BB 5 HIS B 533 ASP B 540 -1 O HIS B 533 N LEU B 530 SHEET 4 BB 5 ASN B 545 TYR B 549 -1 O ASN B 545 N ASP B 540 SHEET 5 BB 5 LEU B 586 SER B 588 1 O PHE B 587 N TYR B 548 LINK OE2 GLU A 430 CO CO B1651 2545 1555 2.73 LINK NE2 HIS A 640 CO CO B1651 2545 1555 1.84 LINK OE2 GLU B 430 CO CO B1651 1555 1555 2.71 LINK NE2 HIS B 640 CO CO B1651 1555 1555 1.71 SITE 1 AC1 6 MET A 477 GLU A 480 ARG A 481 ARG A 641 SITE 2 AC1 6 LEU A 643 GLU B 422 SITE 1 AC2 4 GLY A 505 TYR A 506 GLN A 507 GLN A 569 SITE 1 AC3 3 LYS A 543 LYS A 589 GOL B1648 SITE 1 AC4 2 LYS A 616 ARG B 511 SITE 1 AC5 2 ILE A 555 TRP B 465 SITE 1 AC6 5 PHE B 420 PRO B 421 ARG B 618 PHE B 630 SITE 2 AC6 5 ARG B 633 SITE 1 AC7 3 LYS A 543 TYR B 506 GLN B 507 SITE 1 AC8 5 GOL A1647 LYS B 502 THR B 503 ALA B 504 SITE 2 AC8 5 GLY B 505 SITE 1 AC9 3 ALA B 447 PHE B 448 ARG B 641 SITE 1 BC1 4 LYS B 429 GLN B 458 ASN B 461 ASN B 464 SITE 1 BC2 4 GLU A 430 HIS A 640 GLU B 430 HIS B 640 CRYST1 71.981 71.981 200.640 90.00 90.00 120.00 P 31 2 1 12 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 0.013893 0.008021 0.000000 0.00000 SCALE2 0.000000 0.016042 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004984 0.00000