HEADER HYDROLASE 14-JUL-06 2IYC TITLE SENP1 NATIVE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENTRIN-SPECIFIC PROTEASE 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC FRAGMENT, RESIDUES 419-643; COMPND 5 SYNONYM: SENP1, SENTRIN/SUMO-SPECIFIC PROTEASE SENP1; COMPND 6 EC: 3.4.22.-; COMPND 7 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 KEYWDS PROTEASE, HYDROLASE, THIOL PROTEASE, NUCLEAR PROTEIN, UBL KEYWDS 2 CONJUGATION PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR C.DONG,J.H.NAISMITH REVDAT 3 13-JUL-11 2IYC 1 VERSN REVDAT 2 24-FEB-09 2IYC 1 VERSN REVDAT 1 08-AUG-06 2IYC 0 JRNL AUTH C.DONG,J.H.NAISMITH JRNL TITL SENP1 NATIVE STRUCTURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.SHEN,C.DONG,H.LIU,J.H.NAISMITH,R.T.HAY REMARK 1 TITL THE STRUCTURE OF SENP1 SUMO-2 CO-COMPLEX SUGGESTS A REMARK 1 TITL 2 STRUCTURAL BASIS FOR DISCRIMINATION BETWEEN SUMO PARALOGUES REMARK 1 TITL 3 DURING PROCESSING REMARK 1 REF BIOCHEM.J. V. 397 279 2006 REMARK 1 REFN ISSN 0264-6021 REMARK 1 PMID 16553580 REMARK 1 DOI 10.1042/BJ20052030 REMARK 2 REMARK 2 RESOLUTION. 2.45 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21832 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.267 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) : 1557 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3782 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 90 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) : 28.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.08000 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): 0.422 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.280 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.229 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.526 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3868 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5202 ; 1.483 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 450 ; 6.240 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 198 ;39.163 ;24.242 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 746 ;19.043 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.565 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 552 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2902 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1801 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2628 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 179 ; 0.173 ; 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): 91 ; 0.382 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.355 ; 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): 2324 ; 0.576 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3660 ; 0.892 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1768 ; 1.672 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1542 ; 2.482 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 430 A 640 2 REMARK 3 1 B 430 B 640 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 844 ; 0.06 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 915 ; 0.53 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 844 ; 0.11 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 915 ; 0.77 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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): 28.0233 -9.6528 -6.2222 REMARK 3 T TENSOR REMARK 3 T11: -0.0796 T22: -0.3381 REMARK 3 T33: -0.2327 T12: -0.0314 REMARK 3 T13: 0.1534 T23: -0.0812 REMARK 3 L TENSOR REMARK 3 L11: 5.6773 L22: 2.9856 REMARK 3 L33: 4.1619 L12: 0.2597 REMARK 3 L13: -1.2397 L23: 0.1897 REMARK 3 S TENSOR REMARK 3 S11: 0.2845 S12: -0.3346 S13: 0.2642 REMARK 3 S21: 0.2679 S22: -0.0795 S23: 0.2677 REMARK 3 S31: -0.1451 S32: -0.0510 S33: -0.2049 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 419 B 644 REMARK 3 ORIGIN FOR THE GROUP (A): 36.6469 -16.9687 25.0269 REMARK 3 T TENSOR REMARK 3 T11: -0.0111 T22: -0.1598 REMARK 3 T33: -0.0813 T12: -0.1086 REMARK 3 T13: 0.1726 T23: 0.0456 REMARK 3 L TENSOR REMARK 3 L11: 5.6009 L22: 6.9026 REMARK 3 L33: 7.3873 L12: 4.0183 REMARK 3 L13: -2.0921 L23: -2.6928 REMARK 3 S TENSOR REMARK 3 S11: -0.2788 S12: -0.0475 S13: -0.6864 REMARK 3 S21: -0.5649 S22: -0.0426 S23: -1.1643 REMARK 3 S31: -0.2216 S32: 0.7850 S33: 0.3214 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: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS.THIS REPLACES PREVIOUS ENTRY WHICH WHICH HAD REMARK 3 SEQUENCE CONFLICTS. THE BOND DEVIATIONS FOR GLU AND HIS ARE REMARK 3 CAUSED BY DENSITY ON THE SYMMETRY POSITION. THIS SUCKS THE REMARK 3 SIDE CHAINS IN. A WATER HERE IS REJECTED BY ARWARP ETC. REMARK 4 REMARK 4 2IYC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUL-06. REMARK 100 THE PDBE ID CODE IS EBI-29389. 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) : 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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21832 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 54.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 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 : 9.00 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA):2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 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 NE2 HIS B 640 2.04 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 OE2 GLU A 430 OE1 GLU B 430 3654 1.31 REMARK 500 NE2 HIS A 640 OE1 GLU B 430 3654 2.15 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 GLU A 430 CB GLU A 430 CG 0.155 REMARK 500 GLU A 430 CD GLU A 430 OE2 0.067 REMARK 500 GLU B 425 CG GLU B 425 CD 0.097 REMARK 500 GLU B 430 CB GLU B 430 CG 0.198 REMARK 500 ARG B 561 CZ ARG B 561 NH1 0.116 REMARK 500 SER B 571 CB SER B 571 OG 0.147 REMARK 500 SER B 588 CB SER B 588 OG 0.097 REMARK 500 GLN B 592 CD GLN B 592 NE2 0.162 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 430 CA - CB - CG ANGL. DEV. = 14.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 439 92.53 -32.70 REMARK 500 ARG A 449 -6.77 84.96 REMARK 500 HIS A 462 -126.16 36.22 REMARK 500 LEU A 463 54.79 -119.23 REMARK 500 LYS A 483 -31.01 95.37 REMARK 500 TRP A 512 -6.20 -59.40 REMARK 500 LYS A 515 3.34 58.64 REMARK 500 ASN B 439 94.34 -29.22 REMARK 500 HIS B 462 -141.13 50.56 REMARK 500 LEU B 463 55.10 -110.79 REMARK 500 LYS B 483 -30.97 96.45 REMARK 500 LYS B 515 -1.97 62.14 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 REMARK 900 SUGGESTS A STRUCTURAL BASIS FOR DISCRIMINATION REMARK 900 BETWEEN SUMO PARALOGUES DURING PROCESSING REMARK 900 RELATED ID: 2CKH RELATED DB: PDB REMARK 900 SENP1-SUMO2 COMPLEX REMARK 900 RELATED ID: 2IY0 RELATED DB: PDB REMARK 900 SENP1 (MUTANT) SUMO1 RANGAP REMARK 900 RELATED ID: 2IY1 RELATED DB: PDB REMARK 900 SENP1 (MUTANT) FULL LENGTH SUMO1 REMARK 900 RELATED ID: 2IYD RELATED DB: PDB REMARK 900 SENP1 COVALENT COMPLEX WITH SUMO-2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE EXTRA RESIDUE AT POSITION 593 IN CHAINS A AND B IS REMARK 999 A KNOWN CONFLICT IN UNIPROT AND IS DESCRIBED IN REMARK 999 PUBMED ID: 12477932. DBREF 2IYC A 419 592 UNP Q9P0U3 SENP1_HUMAN 419 592 DBREF 2IYC A 593 593 PDB 2IYC 2IYC 593 593 DBREF 2IYC A 594 644 UNP Q9P0U3 SENP1_HUMAN 593 643 DBREF 2IYC B 419 592 UNP Q9P0U3 SENP1_HUMAN 419 592 DBREF 2IYC B 593 593 PDB 2IYC 2IYC 593 593 DBREF 2IYC B 594 644 UNP Q9P0U3 SENP1_HUMAN 593 643 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 CYS 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 226 GLU PHE PRO GLU ILE THR GLU GLU MET GLU LYS GLU ILE SEQRES 2 B 226 LYS ASN VAL PHE ARG ASN GLY ASN GLN ASP GLU VAL LEU SEQRES 3 B 226 SER GLU ALA PHE ARG LEU THR ILE THR ARG LYS ASP ILE SEQRES 4 B 226 GLN THR LEU ASN HIS LEU ASN TRP LEU ASN ASP GLU ILE SEQRES 5 B 226 ILE ASN PHE TYR MET ASN MET LEU MET GLU ARG SER LYS SEQRES 6 B 226 GLU LYS GLY LEU PRO SER VAL HIS ALA PHE ASN THR PHE SEQRES 7 B 226 PHE PHE THR LYS LEU LYS THR ALA GLY TYR GLN ALA VAL SEQRES 8 B 226 LYS ARG TRP THR LYS LYS VAL ASP VAL PHE SER VAL ASP SEQRES 9 B 226 ILE LEU LEU VAL PRO ILE HIS LEU GLY VAL HIS TRP CYS SEQRES 10 B 226 LEU ALA VAL VAL ASP PHE ARG LYS LYS ASN ILE THR TYR SEQRES 11 B 226 TYR ASP SER MET GLY GLY ILE ASN ASN GLU ALA CYS ARG SEQRES 12 B 226 ILE LEU LEU GLN TYR LEU LYS GLN GLU SER ILE ASP LYS SEQRES 13 B 226 LYS ARG LYS GLU PHE ASP THR ASN GLY TRP GLN LEU PHE SEQRES 14 B 226 SER LYS LYS SER GLN GLU ILE PRO GLN GLN MET ASN GLY SEQRES 15 B 226 SER ASP CYS GLY MET PHE ALA CYS LYS TYR ALA ASP CYS SEQRES 16 B 226 ILE THR LYS ASP ARG PRO ILE ASN PHE THR GLN GLN HIS SEQRES 17 B 226 MET PRO TYR PHE ARG LYS ARG MET VAL TRP GLU ILE LEU SEQRES 18 B 226 HIS ARG LYS LEU LEU FORMUL 3 HOH *90(H2 O) HELIX 1 1 THR A 424 PHE A 435 1 12 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 THR A 495 GLY A 505 1 11 HELIX 5 5 TYR A 506 LYS A 514 5 9 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 THR B 459 1 6 HELIX 13 13 ASN B 467 SER B 482 1 16 HELIX 14 14 THR B 495 GLY B 505 1 11 HELIX 15 15 TYR B 506 LYS B 514 5 9 HELIX 16 16 ASP B 517 VAL B 521 5 5 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 LYS B 616 1 15 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 GLN B 585 SER B 588 1 O GLN B 585 N ILE B 546 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