HEADER HYDROLASE 18-APR-06 2CKG TITLE THE STRUCTURE OF SENP1 SUMO-2 CO-COMPLEX SUGGESTS A STRUCTURAL BASIS TITLE 2 FOR DISCRIMINATION BETWEEN SUMO PARALOGUES DURING PROCESSING COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENTRIN-SPECIFIC PROTEASE 1; COMPND 3 CHAIN: A, B; COMPND 4 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 CONJUGATION KEYWDS 2 PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR C.DONG,J.H.NAISMITH REVDAT 6 13-DEC-23 2CKG 1 REMARK REVDAT 5 30-AUG-17 2CKG 1 REMARK REVDAT 4 13-JUL-11 2CKG 1 VERSN REVDAT 3 24-FEB-09 2CKG 1 VERSN REVDAT 2 20-DEC-06 2CKG 1 JRNL REVDAT 1 26-APR-06 2CKG 0 SPRSDE 26-APR-06 2CKG 2BZP JRNL AUTH L.N.SHEN,C.DONG,H.LIU,J.H.NAISMITH,R.T.HAY JRNL TITL THE STRUCTURE OF SENP1-SUMO-2 COMPLEX SUGGESTS A STRUCTURAL JRNL TITL 2 BASIS FOR DISCRIMINATION BETWEEN SUMO PARALOGUES DURING JRNL TITL 3 PROCESSING. JRNL REF BIOCHEM.J. V. 397 279 2006 JRNL REFN ISSN 0264-6021 JRNL PMID 16553580 JRNL 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,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) : 66.96 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.279 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) : 1561 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3764 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 76 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) : 66.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.70000 REMARK 3 B22 (A**2) : 1.70000 REMARK 3 B33 (A**2) : -2.55000 REMARK 3 B12 (A**2) : 0.85000 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): 0.406 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.284 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.237 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.670 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 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): 3850 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5178 ; 1.671 ; 1.939 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 448 ; 7.443 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;37.619 ;24.184 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 742 ;20.399 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;17.604 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 550 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2886 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1774 ; 0.237 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2599 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 164 ; 0.174 ; 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): 89 ; 0.372 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.401 ; 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): 2316 ; 0.687 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3644 ; 1.090 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1761 ; 1.907 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1534 ; 2.874 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 421 A 461 5 REMARK 3 1 B 421 B 461 5 REMARK 3 2 A 465 A 643 5 REMARK 3 2 B 465 B 643 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 880 ; 0.27 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 956 ; 0.61 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 880 ; 0.74 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 956 ; 1.80 ; 10.00 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 643 REMARK 3 ORIGIN FOR THE GROUP (A): 28.0380 -9.5741 -6.2653 REMARK 3 T TENSOR REMARK 3 T11: -0.0865 T22: -0.3253 REMARK 3 T33: -0.2211 T12: -0.0408 REMARK 3 T13: 0.1561 T23: -0.0814 REMARK 3 L TENSOR REMARK 3 L11: 4.1068 L22: 2.8963 REMARK 3 L33: 3.9658 L12: 0.5045 REMARK 3 L13: -1.0053 L23: 0.1674 REMARK 3 S TENSOR REMARK 3 S11: 0.2985 S12: -0.3270 S13: 0.1660 REMARK 3 S21: 0.3099 S22: -0.0939 S23: 0.2966 REMARK 3 S31: -0.0963 S32: -0.0579 S33: -0.2046 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 643 REMARK 3 ORIGIN FOR THE GROUP (A): 36.5878 -16.8856 25.0660 REMARK 3 T TENSOR REMARK 3 T11: -0.0180 T22: -0.1455 REMARK 3 T33: -0.0705 T12: -0.0984 REMARK 3 T13: 0.1821 T23: 0.0438 REMARK 3 L TENSOR REMARK 3 L11: 4.5281 L22: 6.6344 REMARK 3 L33: 6.6177 L12: 3.5238 REMARK 3 L13: -1.6469 L23: -2.3988 REMARK 3 S TENSOR REMARK 3 S11: -0.3246 S12: -0.0497 S13: -0.8081 REMARK 3 S21: -0.6142 S22: -0.0409 S23: -1.1696 REMARK 3 S31: -0.1182 S32: 0.7565 S33: 0.3655 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CKG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-APR-06. REMARK 100 THE DEPOSITION ID IS D_1290028501. 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 : 4.50 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 : ACSD 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) : 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) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000 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 : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.43200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 2BKQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.50 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 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: PQS 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: PQS 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 400 REMARK 400 COMPOUND REMARK 400 DEGRADES UBL1 AND SMT3H2 CONJUGATES AND RELEASES THE REMARK 400 MONOMERS 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 639 1.94 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 1.26 REMARK 500 NE2 HIS A 639 OE1 GLU B 430 3654 2.03 REMARK 500 O HOH B 2004 O HOH B 2009 6555 2.13 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 0.169 REMARK 500 GLU A 430 CD GLU A 430 OE2 0.075 REMARK 500 GLU B 425 CG GLU B 425 CD 0.112 REMARK 500 GLU B 430 CB GLU B 430 CG 0.191 REMARK 500 GLU B 430 CD GLU B 430 OE1 0.072 REMARK 500 ARG B 561 NE ARG B 561 CZ 0.103 REMARK 500 ARG B 561 CZ ARG B 561 NH1 0.111 REMARK 500 GLN B 585 CD GLN B 585 OE1 0.220 REMARK 500 GLN B 585 CD GLN B 585 NE2 0.338 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. = 15.4 DEGREES REMARK 500 ARG B 561 NE - CZ - NH1 ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG B 561 NE - CZ - NH2 ANGL. DEV. = -8.7 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 GLU A 426 -91.31 80.37 REMARK 500 ASN A 439 101.13 -59.71 REMARK 500 ARG A 449 2.11 85.52 REMARK 500 HIS A 462 -122.22 35.25 REMARK 500 LYS A 483 -25.95 87.79 REMARK 500 ASN A 556 59.58 -143.37 REMARK 500 ASN A 557 -63.76 -23.60 REMARK 500 LYS A 590 -169.96 -78.90 REMARK 500 SER A 591 63.38 -61.06 REMARK 500 PHE B 435 72.02 -113.81 REMARK 500 GLN B 440 -15.41 -48.60 REMARK 500 HIS B 462 -138.30 46.65 REMARK 500 LEU B 463 44.72 -98.45 REMARK 500 LYS B 483 -33.98 106.40 REMARK 500 LYS B 515 -18.94 77.11 REMARK 500 LYS B 574 -62.85 -95.87 REMARK 500 SER B 591 50.92 -65.70 REMARK 500 GLN B 592 60.09 -119.21 REMARK 500 ASN B 598 103.08 67.68 REMARK 500 ASP B 616 -11.13 71.41 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 A 425 GLU A 426 48.61 REMARK 500 ASN B 461 HIS B 462 149.79 REMARK 500 GLN B 596 MET B 597 142.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN B 585 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CKH RELATED DB: PDB REMARK 900 SENP1-SUMO2 COMPLEX DBREF 2CKG A 419 643 UNP Q9P0U3 SENP1_HUMAN 419 643 DBREF 2CKG B 419 643 UNP Q9P0U3 SENP1_HUMAN 419 643 SEQRES 1 A 225 GLU PHE PRO GLU ILE THR GLU GLU MET GLU LYS GLU ILE SEQRES 2 A 225 LYS ASN VAL PHE ARG ASN GLY ASN GLN ASP GLU VAL LEU SEQRES 3 A 225 SER GLU ALA PHE ARG LEU THR ILE THR ARG LYS ASP ILE SEQRES 4 A 225 GLN THR LEU ASN HIS LEU ASN TRP LEU ASN ASP GLU ILE SEQRES 5 A 225 ILE ASN PHE TYR MET ASN MET LEU MET GLU ARG SER LYS SEQRES 6 A 225 GLU LYS GLY LEU PRO SER VAL HIS ALA PHE ASN THR PHE SEQRES 7 A 225 PHE PHE THR LYS LEU LYS THR ALA GLY TYR GLN ALA VAL SEQRES 8 A 225 LYS ARG TRP THR LYS LYS VAL ASP VAL PHE SER VAL ASP SEQRES 9 A 225 ILE LEU LEU VAL PRO ILE HIS LEU GLY VAL HIS TRP CYS SEQRES 10 A 225 LEU ALA VAL VAL ASP PHE ARG LYS LYS ASN ILE THR TYR SEQRES 11 A 225 TYR ASP SER MET GLY GLY ILE ASN ASN GLU ALA CYS ARG SEQRES 12 A 225 ILE LEU LEU GLN TYR LEU LYS GLN GLU SER ILE ASP LYS SEQRES 13 A 225 LYS ARG LYS GLU PHE ASP THR ASN GLY TRP GLN LEU PHE SEQRES 14 A 225 SER LYS LYS SER GLN ILE PRO GLN GLN MET ASN GLY SER SEQRES 15 A 225 ASP CYS GLY MET PHE ALA CYS LYS TYR ALA ASP CYS ILE SEQRES 16 A 225 THR LYS ASP ARG PRO ILE ASN PHE THR GLN GLN HIS MET SEQRES 17 A 225 PRO TYR PHE ARG LYS ARG MET VAL TRP GLU ILE LEU HIS SEQRES 18 A 225 ARG LYS LEU LEU SEQRES 1 B 225 GLU PHE PRO GLU ILE THR GLU GLU MET GLU LYS GLU ILE SEQRES 2 B 225 LYS ASN VAL PHE ARG ASN GLY ASN GLN ASP GLU VAL LEU SEQRES 3 B 225 SER GLU ALA PHE ARG LEU THR ILE THR ARG LYS ASP ILE SEQRES 4 B 225 GLN THR LEU ASN HIS LEU ASN TRP LEU ASN ASP GLU ILE SEQRES 5 B 225 ILE ASN PHE TYR MET ASN MET LEU MET GLU ARG SER LYS SEQRES 6 B 225 GLU LYS GLY LEU PRO SER VAL HIS ALA PHE ASN THR PHE SEQRES 7 B 225 PHE PHE THR LYS LEU LYS THR ALA GLY TYR GLN ALA VAL SEQRES 8 B 225 LYS ARG TRP THR LYS LYS VAL ASP VAL PHE SER VAL ASP SEQRES 9 B 225 ILE LEU LEU VAL PRO ILE HIS LEU GLY VAL HIS TRP CYS SEQRES 10 B 225 LEU ALA VAL VAL ASP PHE ARG LYS LYS ASN ILE THR TYR SEQRES 11 B 225 TYR ASP SER MET GLY GLY ILE ASN ASN GLU ALA CYS ARG SEQRES 12 B 225 ILE LEU LEU GLN TYR LEU LYS GLN GLU SER ILE ASP LYS SEQRES 13 B 225 LYS ARG LYS GLU PHE ASP THR ASN GLY TRP GLN LEU PHE SEQRES 14 B 225 SER LYS LYS SER GLN ILE PRO GLN GLN MET ASN GLY SER SEQRES 15 B 225 ASP CYS GLY MET PHE ALA CYS LYS TYR ALA ASP CYS ILE SEQRES 16 B 225 THR LYS ASP ARG PRO ILE ASN PHE THR GLN GLN HIS MET SEQRES 17 B 225 PRO TYR PHE ARG LYS ARG MET VAL TRP GLU ILE LEU HIS SEQRES 18 B 225 ARG LYS LEU LEU FORMUL 3 HOH *76(H2 O) HELIX 1 1 GLU A 426 ARG A 436 1 11 HELIX 2 2 ARG A 454 GLN A 458 1 5 HELIX 3 3 THR A 459 ASN A 461 5 3 HELIX 4 4 ASN A 467 SER A 482 1 16 HELIX 5 5 THR A 495 GLY A 505 1 11 HELIX 6 6 GLY A 505 LYS A 510 1 6 HELIX 7 7 ARG A 511 LYS A 514 5 4 HELIX 8 8 ASP A 517 VAL A 521 5 5 HELIX 9 9 ASN A 556 ARG A 576 1 21 HELIX 10 10 ASP A 601 LYS A 615 1 15 HELIX 11 11 THR A 622 GLN A 624 5 3 HELIX 12 12 HIS A 625 ARG A 640 1 16 HELIX 13 13 THR B 424 ASN B 433 1 10 HELIX 14 14 ARG B 454 GLN B 458 1 5 HELIX 15 15 THR B 459 ASN B 461 5 3 HELIX 16 16 ASN B 467 SER B 482 1 16 HELIX 17 17 THR B 495 GLY B 505 1 11 HELIX 18 18 TYR B 506 LYS B 514 5 9 HELIX 19 19 ASP B 517 VAL B 521 5 5 HELIX 20 20 ASN B 556 LYS B 574 1 19 HELIX 21 21 ASN B 598 SER B 600 5 3 HELIX 22 22 ASP B 601 LYS B 615 1 15 HELIX 23 23 THR B 622 GLN B 624 5 3 HELIX 24 24 HIS B 625 ARG B 640 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