HEADER HYDROLASE 26-AUG-10 2XPH TITLE CRYSTAL STRUCTURE OF HUMAN SENP1 WITH THE BOUND COBALT 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) GOLD; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHISTEV30A KEYWDS HYDROLASE, CYSTEINE PROTEASE, THIOL PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR V.RIMSA,T.EADSFORTH,R.T.HAY,W.N.HUNTER REVDAT 4 20-DEC-23 2XPH 1 REMARK LINK REVDAT 3 11-APR-12 2XPH 1 JRNL REMARK VERSN HETSYN REVDAT 2 27-APR-11 2XPH 1 JRNL REMARK REVDAT 1 08-SEP-10 2XPH 0 JRNL AUTH V.RIMSA,T.EADSFORTH,R.T.HAY,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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 22537 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) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1217 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1663 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.4130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3790 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.24000 REMARK 3 B22 (A**2) : 1.24000 REMARK 3 B33 (A**2) : -1.87000 REMARK 3 B12 (A**2) : 0.62000 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): 0.409 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.317 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.235 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.805 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3880 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5245 ; 1.639 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 476 ; 6.696 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 201 ;39.419 ;23.980 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 680 ;19.878 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;17.659 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 549 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2983 ; 0.008 ; 0.020 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): 2285 ; 2.421 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3690 ; 4.233 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1595 ; 6.399 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1544 ; 8.495 ;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. RESIDUES 407-417 IN CHAIN A AND 407-418 IN CHAIN B REMARK 3 ARE DISORDERED. REMARK 4 REMARK 4 2XPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1290045119. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-10 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 : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97700 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23808 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: PDB ENTRY 2IYC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS FORMED FROM 1 TO 1 OF REMARK 280 RESERVOIR SOLUTION (1.8 M AMMONIUM SULFATE, 50 MM COCL2 AND 100 REMARK 280 MM MES PH 6.5) AND PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL REMARK 280 (PH 8.0), AND 50 MM NACL). 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 66.66267 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 133.32533 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 133.32533 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 66.66267 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 GLY A 407 REMARK 465 ALA A 408 REMARK 465 MET A 409 REMARK 465 ALA A 410 REMARK 465 ASP A 411 REMARK 465 ILE A 412 REMARK 465 GLY A 413 REMARK 465 SER A 414 REMARK 465 ASP A 415 REMARK 465 SER A 416 REMARK 465 GLU A 417 REMARK 465 GLY B 407 REMARK 465 ALA B 408 REMARK 465 MET B 409 REMARK 465 ALA B 410 REMARK 465 ASP B 411 REMARK 465 ILE B 412 REMARK 465 GLY B 413 REMARK 465 SER B 414 REMARK 465 ASP B 415 REMARK 465 SER B 416 REMARK 465 GLU B 417 REMARK 465 ASP B 418 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 GLU A 422 CG CD OE1 OE2 REMARK 480 ASN A 439 CB CG OD1 ND2 REMARK 480 GLU A 442 CB CG CD OE1 OE2 REMARK 480 LYS A 455 CG CD CE NZ REMARK 480 LYS A 502 CD CE NZ REMARK 480 LYS A 510 CB CG CD CE NZ REMARK 480 ARG A 511 CB CG CD NE CZ NH1 NH2 REMARK 480 LYS A 514 CB CG CD CE NZ REMARK 480 LYS A 515 CD CE NZ REMARK 480 GLU A 558 CG CD OE1 OE2 REMARK 480 GLN A 565 CG CD OE1 NE2 REMARK 480 LYS A 568 CB CG CD CE NZ REMARK 480 ILE A 572 CB CG1 CG2 CD1 REMARK 480 LYS A 574 CB CG CD CE NZ REMARK 480 LYS A 589 CG CD CE NZ REMARK 480 LYS A 590 CB CG CD CE NZ REMARK 480 MET A 598 CG SD CE REMARK 480 LYS A 609 CG CD CE NZ REMARK 480 ARG B 436 CB CG CD NE CZ NH1 NH2 REMARK 480 ASP B 441 CB CG OD1 OD2 REMARK 480 LYS B 485 CB CG CD CE NZ REMARK 480 LYS B 500 CG CD CE NZ REMARK 480 LYS B 510 CG CD CE NZ REMARK 480 LYS B 514 C O CG CD CE NZ REMARK 480 LYS B 515 CG CD CE NZ REMARK 480 LYS B 543 CB CG CD CE NZ REMARK 480 LYS B 544 CB CG CD CE NZ REMARK 480 GLU B 558 CB CG CD OE1 OE2 REMARK 480 ASN B 582 CG OD1 ND2 REMARK 480 LYS B 590 CB CG CD CE NZ REMARK 480 LYS B 616 CE NZ 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 O ARG B 641 N LYS B 642 1.78 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 OE1 GLU B 430 3664 2.08 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 A 502 CG LYS A 502 CD -0.255 REMARK 500 ARG A 511 CA ARG A 511 CB -0.146 REMARK 500 LYS A 514 CA LYS A 514 CB -0.345 REMARK 500 LYS A 515 CD LYS A 515 CE -0.458 REMARK 500 LYS A 515 CE LYS A 515 NZ -0.168 REMARK 500 ASP B 441 CA ASP B 441 CB -0.262 REMARK 500 LYS B 485 CA LYS B 485 CB -0.220 REMARK 500 LYS B 510 CB LYS B 510 CG -0.176 REMARK 500 ARG B 641 N ARG B 641 CA 0.124 REMARK 500 ARG B 641 N ARG B 641 CA 0.127 REMARK 500 ARG B 641 C LYS B 642 N -0.262 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 A 422 CA - CB - CG ANGL. DEV. = 20.3 DEGREES REMARK 500 LYS A 502 CB - CG - CD ANGL. DEV. = 27.2 DEGREES REMARK 500 ARG A 511 N - CA - CB ANGL. DEV. = 11.4 DEGREES REMARK 500 LYS A 514 N - CA - CB ANGL. DEV. = 22.0 DEGREES REMARK 500 LYS A 515 CG - CD - CE ANGL. DEV. = 33.6 DEGREES REMARK 500 ILE A 572 CB - CA - C ANGL. DEV. = 15.5 DEGREES REMARK 500 ASP B 441 N - CA - CB ANGL. DEV. = 12.4 DEGREES REMARK 500 LYS B 485 N - CA - CB ANGL. DEV. = -25.2 DEGREES REMARK 500 LYS B 485 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 LYS B 510 CA - CB - CG ANGL. DEV. = 17.8 DEGREES REMARK 500 ARG B 641 CB - CA - C ANGL. DEV. = 18.7 DEGREES REMARK 500 ARG B 641 CB - CA - C ANGL. DEV. = 18.2 DEGREES REMARK 500 ARG B 641 CA - C - O ANGL. DEV. = -33.2 DEGREES REMARK 500 ARG B 641 CA - C - O ANGL. DEV. = -33.3 DEGREES REMARK 500 ARG B 641 CA - C - N ANGL. DEV. = 37.9 DEGREES REMARK 500 ARG B 641 CA - C - N ANGL. DEV. = 38.0 DEGREES REMARK 500 ARG B 641 O - C - N ANGL. DEV. = -21.8 DEGREES REMARK 500 LYS B 642 C - N - CA ANGL. DEV. = 21.5 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 PRO A 421 118.81 -39.69 REMARK 500 GLN A 440 37.90 -71.56 REMARK 500 GLU A 446 114.40 -162.78 REMARK 500 HIS A 462 -128.13 47.40 REMARK 500 ASN A 464 177.66 -56.26 REMARK 500 LYS A 500 30.06 -91.46 REMARK 500 LEU A 501 -59.05 -127.93 REMARK 500 ASN A 556 51.99 -156.04 REMARK 500 ASN A 557 -26.41 -39.82 REMARK 500 LYS A 574 -53.96 114.83 REMARK 500 ARG A 576 -4.93 63.42 REMARK 500 SER A 591 -30.52 94.01 REMARK 500 GLU A 593 -73.70 72.12 REMARK 500 ASP A 602 21.73 -74.27 REMARK 500 ALA B 447 154.93 176.14 REMARK 500 LYS B 483 40.01 -67.37 REMARK 500 LYS B 502 -70.68 -64.28 REMARK 500 THR B 513 51.30 -118.17 REMARK 500 ASN B 556 70.98 -161.41 REMARK 500 LYS B 574 -61.15 -108.02 REMARK 500 ARG B 576 -28.05 66.04 REMARK 500 THR B 581 41.68 -107.18 REMARK 500 ASP B 617 18.26 52.52 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 ARG B 641 -60.55 REMARK 500 ARG B 641 -60.73 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 B1646 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 430 OE1 REMARK 620 2 GLU A 430 OE2 56.8 REMARK 620 3 HIS A 640 NE2 114.5 95.4 REMARK 620 4 GLU B 430 OE2 126.2 176.1 85.4 REMARK 620 5 GLU B 430 OE1 72.3 129.1 104.5 54.0 REMARK 620 6 HIS B 640 NE2 127.3 92.2 109.5 83.9 122.5 REMARK 620 N 1 2 3 4 5 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 A 1649 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1645 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 1646 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: 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: 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: 2G4D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SENP1 MUTANT (C603S) IN COMPLEXWITH SUMO- REMARK 900 1 REMARK 900 RELATED ID: 2CKH RELATED DB: PDB REMARK 900 SENP1-SUMO2 COMPLEX REMARK 900 RELATED ID: 2XRE RELATED DB: PDB REMARK 900 DETECTION OF COBALT IN PREVIOUSLY UNASSIGNED HUMAN SENP1 STRUCTURE DBREF 2XPH A 415 644 UNP Q9P0U3 SENP1_HUMAN 415 644 DBREF 2XPH B 415 644 UNP Q9P0U3 SENP1_HUMAN 415 644 SEQADV 2XPH GLY A 407 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH ALA A 408 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH MET A 409 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH ALA A 410 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH ASP A 411 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH ILE A 412 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH GLY A 413 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH SER A 414 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH GLY B 407 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH ALA B 408 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH MET B 409 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH ALA B 410 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH ASP B 411 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH ILE B 412 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH GLY B 413 UNP Q9P0U3 EXPRESSION TAG SEQADV 2XPH SER B 414 UNP Q9P0U3 EXPRESSION TAG SEQRES 1 A 238 GLY ALA MET ALA ASP ILE GLY SER ASP SER GLU ASP GLU SEQRES 2 A 238 PHE PRO GLU ILE THR GLU GLU MET GLU LYS GLU ILE LYS SEQRES 3 A 238 ASN VAL PHE ARG ASN GLY ASN GLN ASP GLU VAL LEU SER SEQRES 4 A 238 GLU ALA PHE ARG LEU THR ILE THR ARG LYS ASP ILE GLN SEQRES 5 A 238 THR LEU ASN HIS LEU ASN TRP LEU ASN ASP GLU ILE ILE SEQRES 6 A 238 ASN PHE TYR MET ASN MET LEU MET GLU ARG SER LYS GLU SEQRES 7 A 238 LYS GLY LEU PRO SER VAL HIS ALA PHE ASN THR PHE PHE SEQRES 8 A 238 PHE THR LYS LEU LYS THR ALA GLY TYR GLN ALA VAL LYS SEQRES 9 A 238 ARG TRP THR LYS LYS VAL ASP VAL PHE SER VAL ASP ILE SEQRES 10 A 238 LEU LEU VAL PRO ILE HIS LEU GLY VAL HIS TRP CYS LEU SEQRES 11 A 238 ALA VAL VAL ASP PHE ARG LYS LYS ASN ILE THR TYR TYR SEQRES 12 A 238 ASP SER MET GLY GLY ILE ASN ASN GLU ALA CYS ARG ILE SEQRES 13 A 238 LEU LEU GLN TYR LEU LYS GLN GLU SER ILE ASP LYS LYS SEQRES 14 A 238 ARG LYS GLU PHE ASP THR ASN GLY TRP GLN LEU PHE SER SEQRES 15 A 238 LYS LYS SER GLN GLU ILE PRO GLN GLN MET ASN GLY SER SEQRES 16 A 238 ASP CYS GLY MET PHE ALA CYS LYS TYR ALA ASP CYS ILE SEQRES 17 A 238 THR LYS ASP ARG PRO ILE ASN PHE THR GLN GLN HIS MET SEQRES 18 A 238 PRO TYR PHE ARG LYS ARG MET VAL TRP GLU ILE LEU HIS SEQRES 19 A 238 ARG LYS LEU LEU SEQRES 1 B 238 GLY ALA MET ALA ASP ILE GLY SER ASP SER GLU ASP GLU SEQRES 2 B 238 PHE PRO GLU ILE THR GLU GLU MET GLU LYS GLU ILE LYS SEQRES 3 B 238 ASN VAL PHE ARG ASN GLY ASN GLN ASP GLU VAL LEU SER SEQRES 4 B 238 GLU ALA PHE ARG LEU THR ILE THR ARG LYS ASP ILE GLN SEQRES 5 B 238 THR LEU ASN HIS LEU ASN TRP LEU ASN ASP GLU ILE ILE SEQRES 6 B 238 ASN PHE TYR MET ASN MET LEU MET GLU ARG SER LYS GLU SEQRES 7 B 238 LYS GLY LEU PRO SER VAL HIS ALA PHE ASN THR PHE PHE SEQRES 8 B 238 PHE THR LYS LEU LYS THR ALA GLY TYR GLN ALA VAL LYS SEQRES 9 B 238 ARG TRP THR LYS LYS VAL ASP VAL PHE SER VAL ASP ILE SEQRES 10 B 238 LEU LEU VAL PRO ILE HIS LEU GLY VAL HIS TRP CYS LEU SEQRES 11 B 238 ALA VAL VAL ASP PHE ARG LYS LYS ASN ILE THR TYR TYR SEQRES 12 B 238 ASP SER MET GLY GLY ILE ASN ASN GLU ALA CYS ARG ILE SEQRES 13 B 238 LEU LEU GLN TYR LEU LYS GLN GLU SER ILE ASP LYS LYS SEQRES 14 B 238 ARG LYS GLU PHE ASP THR ASN GLY TRP GLN LEU PHE SER SEQRES 15 B 238 LYS LYS SER GLN GLU ILE PRO GLN GLN MET ASN GLY SER SEQRES 16 B 238 ASP CYS GLY MET PHE ALA CYS LYS TYR ALA ASP CYS ILE SEQRES 17 B 238 THR LYS ASP ARG PRO ILE ASN PHE THR GLN GLN HIS MET SEQRES 18 B 238 PRO TYR PHE ARG LYS ARG MET VAL TRP GLU ILE LEU HIS SEQRES 19 B 238 ARG LYS LEU LEU HET GOL A1645 6 HET GOL A1646 6 HET GOL A1647 6 HET GOL A1648 6 HET GOL A1649 6 HET GOL B1645 6 HET CO B1646 1 HETNAM GOL GLYCEROL HETNAM CO COBALT (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 6(C3 H8 O3) FORMUL 9 CO CO 2+ FORMUL 10 HOH *70(H2 O) HELIX 1 1 THR A 424 PHE A 435 1 12 HELIX 2 2 THR A 453 THR A 459 1 7 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 LYS A 510 1 6 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 PHE B 435 1 12 HELIX 12 12 ARG B 454 GLN B 458 1 5 HELIX 13 13 THR B 459 ASN B 461 5 3 HELIX 14 14 ASN B 467 SER B 482 1 16 HELIX 15 15 PHE B 496 GLY B 505 1 10 HELIX 16 16 TYR B 506 LYS B 514 5 9 HELIX 17 17 ASN B 556 ARG B 576 1 21 HELIX 18 18 ASN B 599 SER B 601 5 3 HELIX 19 19 ASP B 602 THR B 615 1 14 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 SER A 445 ALA A 447 0 SHEET 2 AA 2 LEU A 450 ILE A 452 -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 GLN B 585 SER B 588 1 O GLN B 585 N ILE B 546 LINK OE1 GLU A 430 CO CO B1646 2655 1555 1.75 LINK OE2 GLU A 430 CO CO B1646 2655 1555 2.58 LINK NE2 HIS A 640 CO CO B1646 2655 1555 1.83 LINK OE2 GLU B 430 CO CO B1646 1555 1555 2.68 LINK OE1 GLU B 430 CO CO B1646 1555 1555 1.77 LINK NE2 HIS B 640 CO CO B1646 1555 1555 2.21 SITE 1 AC1 2 ILE A 555 TRP B 465 SITE 1 AC2 2 LYS A 543 GLN B 569 SITE 1 AC3 1 LYS A 632 SITE 1 AC4 4 GLN A 440 TRP A 584 LEU A 586 HOH A2003 SITE 1 AC5 6 PRO A 421 LYS A 616 ASN A 621 PHE A 630 SITE 2 AC5 6 ARG A 633 HOH A2041 SITE 1 AC6 4 LYS B 429 GLN B 458 ASN B 461 ASN B 464 SITE 1 AC7 4 GLU A 430 HIS A 640 GLU B 430 HIS B 640 CRYST1 71.172 71.172 199.988 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 0.014050 0.008112 0.000000 0.00000 SCALE2 0.000000 0.016224 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005000 0.00000