HEADER HYDROLASE 04-FEB-22 7R2E TITLE STRUCTURE OF HUMAN SENP7 WITH SUMO2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENTRIN-SPECIFIC PROTEASE 7; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SUMO-1-SPECIFIC PROTEASE 2,SENTRIN/SUMO-SPECIFIC PROTEASE COMPND 5 SENP7; COMPND 6 EC: 3.4.22.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SMALL UBIQUITIN-RELATED MODIFIER 3; COMPND 10 CHAIN: C, D; COMPND 11 SYNONYM: SUMO-3,SMT3 HOMOLOG 1,SUMO-2,UBIQUITIN-LIKE PROTEIN SMT3A, COMPND 12 SMT3A; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SENP7, KIAA1707, SSP2, SUSP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: SUMO3, SMT3A, SMT3H1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX SUMO HYDROLASE, SENP7, WITH A SUICIDE SUBSTRATE (SUMO-PA), KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.REVERTER,Y.LI REVDAT 3 07-FEB-24 7R2E 1 REMARK REVDAT 2 01-MAR-23 7R2E 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQADV SEQRES HELIX SHEET REVDAT 2 3 1 LINK ATOM REVDAT 1 07-DEC-22 7R2E 0 JRNL AUTH Y.LI,A.DE BOLOS,V.AMADOR,D.REVERTER JRNL TITL STRUCTURAL BASIS FOR THE SUMO2 ISOFORM SPECIFICITY OF SENP7. JRNL REF J.MOL.BIOL. V. 434 67875 2022 JRNL REFN ESSN 1089-8638 JRNL PMID 36334780 JRNL DOI 10.1016/J.JMB.2022.167875 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 74.9 REMARK 3 NUMBER OF REFLECTIONS : 51889 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2611 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 50.3600 - 4.6300 0.99 3512 161 0.1567 0.1800 REMARK 3 2 4.6300 - 3.6700 0.99 3432 185 0.1409 0.1832 REMARK 3 3 3.6700 - 3.2100 0.98 3463 147 0.1707 0.2304 REMARK 3 4 3.2100 - 2.9200 0.99 3454 155 0.1920 0.2531 REMARK 3 5 2.9200 - 2.7100 0.99 3398 212 0.2031 0.2457 REMARK 3 6 2.7100 - 2.5500 0.99 3412 215 0.2034 0.2413 REMARK 3 7 2.5500 - 2.4200 0.99 3437 187 0.1990 0.2437 REMARK 3 8 2.4200 - 2.3100 0.99 3440 174 0.1942 0.2646 REMARK 3 9 2.3100 - 2.2300 0.99 3435 156 0.2034 0.2508 REMARK 3 10 2.2300 - 2.1500 0.99 3394 184 0.2141 0.2643 REMARK 3 11 2.1500 - 2.0800 0.98 3431 202 0.2215 0.2794 REMARK 3 12 2.0800 - 2.0200 0.99 3389 171 0.2343 0.2738 REMARK 3 13 2.0200 - 1.9700 0.89 3087 181 0.2466 0.3023 REMARK 3 14 1.9700 - 1.9200 0.60 2049 93 0.2721 0.2842 REMARK 3 15 1.9200 - 1.8800 0.39 1339 79 0.2888 0.2829 REMARK 3 16 1.8800 - 1.8400 0.21 725 52 0.2845 0.3753 REMARK 3 17 1.8400 - 1.8000 0.14 482 32 0.3160 0.3690 REMARK 3 18 1.8000 - 1.7700 0.09 313 17 0.3712 0.3518 REMARK 3 19 1.7700 - 1.7400 0.03 86 8 0.3707 0.4168 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 9.1109 1.9122 22.9943 REMARK 3 T TENSOR REMARK 3 T11: 0.1541 T22: 0.2125 REMARK 3 T33: 0.1816 T12: 0.0111 REMARK 3 T13: -0.0054 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 0.2092 L22: 1.2846 REMARK 3 L33: 0.2379 L12: 0.2571 REMARK 3 L13: 0.0436 L23: 0.3440 REMARK 3 S TENSOR REMARK 3 S11: 0.0262 S12: -0.0425 S13: -0.0075 REMARK 3 S21: 0.1092 S22: 0.0034 S23: -0.0159 REMARK 3 S31: 0.0173 S32: 0.0136 S33: -0.0276 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7R2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120800. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51898 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 93.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3EAY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM HEPES 7.0, 15 % W/V PEG REMARK 280 20,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 50.36500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 MET A 640 REMARK 465 GLY A 641 REMARK 465 SER A 642 REMARK 465 SER A 643 REMARK 465 HIS A 644 REMARK 465 HIS A 645 REMARK 465 HIS A 646 REMARK 465 HIS A 647 REMARK 465 HIS A 648 REMARK 465 HIS A 649 REMARK 465 SER A 650 REMARK 465 SER A 651 REMARK 465 GLY A 652 REMARK 465 LEU A 653 REMARK 465 VAL A 654 REMARK 465 PRO A 655 REMARK 465 ARG A 656 REMARK 465 GLY A 657 REMARK 465 SER A 658 REMARK 465 HIS A 659 REMARK 465 MET A 660 REMARK 465 ALA A 661 REMARK 465 SER A 662 REMARK 465 THR A 663 REMARK 465 SER A 664 REMARK 465 ASN A 665 REMARK 465 PRO A 666 REMARK 465 ASP A 667 REMARK 465 GLU A 668 REMARK 465 GLU A 669 REMARK 465 TRP A 670 REMARK 465 ARG A 671 REMARK 465 GLU A 672 REMARK 465 VAL A 673 REMARK 465 ARG A 674 REMARK 465 HIS A 675 REMARK 465 THR A 676 REMARK 465 GLY A 677 REMARK 465 LYS A 749 REMARK 465 GLU A 750 REMARK 465 ASN A 751 REMARK 465 ASN A 752 REMARK 465 LEU A 753 REMARK 465 THR A 754 REMARK 465 GLU A 755 REMARK 465 ASP A 756 REMARK 465 ASN A 757 REMARK 465 PRO A 758 REMARK 465 ASP A 812 REMARK 465 PHE A 813 REMARK 465 PRO A 814 REMARK 465 GLN A 815 REMARK 465 THR A 816 REMARK 465 VAL A 817 REMARK 465 SER A 818 REMARK 465 GLN A 819 REMARK 465 GLN A 820 REMARK 465 SER A 821 REMARK 465 GLN A 822 REMARK 465 ALA A 823 REMARK 465 GLN A 824 REMARK 465 GLN A 825 REMARK 465 SER A 826 REMARK 465 GLN A 827 REMARK 465 ASN A 828 REMARK 465 ASP A 829 REMARK 465 ASN A 830 REMARK 465 LYS A 831 REMARK 465 THR A 832 REMARK 465 ILE A 833 REMARK 465 ASP A 834 REMARK 465 ASN A 835 REMARK 465 ASP A 836 REMARK 465 LEU A 837 REMARK 465 ARG A 838 REMARK 465 THR A 839 REMARK 465 THR A 840 REMARK 465 SER A 841 REMARK 465 THR A 842 REMARK 465 LEU A 843 REMARK 465 SER A 844 REMARK 465 LEU A 845 REMARK 465 SER A 846 REMARK 465 ALA A 847 REMARK 465 GLU A 848 REMARK 465 ASP A 849 REMARK 465 SER A 850 REMARK 465 GLN A 851 REMARK 465 SER A 852 REMARK 465 THR A 853 REMARK 465 GLU A 854 REMARK 465 SER A 855 REMARK 465 ASN A 856 REMARK 465 MET A 857 REMARK 465 SER A 858 REMARK 465 VAL A 859 REMARK 465 PRO A 860 REMARK 465 LYS A 861 REMARK 465 SER A 982 REMARK 465 SER A 983 REMARK 465 SER A 984 REMARK 465 MET B 640 REMARK 465 GLY B 641 REMARK 465 SER B 642 REMARK 465 SER B 643 REMARK 465 HIS B 644 REMARK 465 HIS B 645 REMARK 465 HIS B 646 REMARK 465 HIS B 647 REMARK 465 HIS B 648 REMARK 465 HIS B 649 REMARK 465 SER B 650 REMARK 465 SER B 651 REMARK 465 GLY B 652 REMARK 465 LEU B 653 REMARK 465 VAL B 654 REMARK 465 PRO B 655 REMARK 465 ARG B 656 REMARK 465 GLY B 657 REMARK 465 SER B 658 REMARK 465 HIS B 659 REMARK 465 MET B 660 REMARK 465 ALA B 661 REMARK 465 SER B 662 REMARK 465 THR B 663 REMARK 465 SER B 664 REMARK 465 ASN B 665 REMARK 465 PRO B 666 REMARK 465 ASP B 667 REMARK 465 GLU B 668 REMARK 465 GLU B 669 REMARK 465 TRP B 670 REMARK 465 ARG B 671 REMARK 465 GLU B 672 REMARK 465 VAL B 673 REMARK 465 ARG B 674 REMARK 465 HIS B 675 REMARK 465 THR B 676 REMARK 465 GLY B 677 REMARK 465 LEU B 678 REMARK 465 LYS B 749 REMARK 465 GLU B 750 REMARK 465 ASN B 751 REMARK 465 ASN B 752 REMARK 465 LEU B 753 REMARK 465 THR B 754 REMARK 465 GLU B 755 REMARK 465 ASP B 756 REMARK 465 ASN B 757 REMARK 465 ASP B 812 REMARK 465 PHE B 813 REMARK 465 PRO B 814 REMARK 465 GLN B 815 REMARK 465 THR B 816 REMARK 465 VAL B 817 REMARK 465 SER B 818 REMARK 465 GLN B 819 REMARK 465 GLN B 820 REMARK 465 SER B 821 REMARK 465 GLN B 822 REMARK 465 ALA B 823 REMARK 465 GLN B 824 REMARK 465 GLN B 825 REMARK 465 SER B 826 REMARK 465 GLN B 827 REMARK 465 ASN B 828 REMARK 465 ASP B 829 REMARK 465 ASN B 830 REMARK 465 LYS B 831 REMARK 465 THR B 832 REMARK 465 ILE B 833 REMARK 465 ASP B 834 REMARK 465 ASN B 835 REMARK 465 ASP B 836 REMARK 465 LEU B 837 REMARK 465 ARG B 838 REMARK 465 THR B 839 REMARK 465 THR B 840 REMARK 465 SER B 841 REMARK 465 THR B 842 REMARK 465 LEU B 843 REMARK 465 SER B 844 REMARK 465 LEU B 845 REMARK 465 SER B 846 REMARK 465 ALA B 847 REMARK 465 GLU B 848 REMARK 465 ASP B 849 REMARK 465 SER B 850 REMARK 465 GLN B 851 REMARK 465 SER B 852 REMARK 465 THR B 853 REMARK 465 GLU B 854 REMARK 465 SER B 855 REMARK 465 ASN B 856 REMARK 465 MET B 857 REMARK 465 SER B 858 REMARK 465 VAL B 859 REMARK 465 PRO B 860 REMARK 465 LYS B 861 REMARK 465 LYS B 862 REMARK 465 SER B 982 REMARK 465 SER B 983 REMARK 465 SER B 984 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 HOH B 1104 O HOH B 1224 1.93 REMARK 500 SG CYS B 926 C1 AYE B 1001 2.05 REMARK 500 O HOH B 1226 O HOH B 1237 2.13 REMARK 500 O GLN D 57 O HOH D 201 2.16 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 O ASP B 729 NZ LYS B 876 1455 1.83 REMARK 500 O HOH B 1190 O HOH B 1219 1455 2.00 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 PRO B 956 N PRO B 956 CA 0.208 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 ASN A 909 CB - CA - C ANGL. DEV. = -12.2 DEGREES REMARK 500 PRO B 956 C - N - CA ANGL. DEV. = 15.6 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 SER A 739 151.32 -49.94 REMARK 500 LEU A 875 -123.51 -128.61 REMARK 500 MET A 910 76.12 -154.44 REMARK 500 ASN A 922 -163.46 -123.29 REMARK 500 LEU B 875 -122.34 -131.55 REMARK 500 MET B 910 65.22 -154.32 REMARK 500 REMARK 500 REMARK: NULL DBREF 7R2E A 663 984 UNP Q9BQF6 SENP7_HUMAN 729 1050 DBREF 7R2E B 663 984 UNP Q9BQF6 SENP7_HUMAN 729 1050 DBREF 7R2E C 17 92 UNP P55854 SUMO3_HUMAN 16 91 DBREF 7R2E D 17 92 UNP P55854 SUMO3_HUMAN 16 91 SEQADV 7R2E MET A 640 UNP Q9BQF6 INITIATING METHIONINE SEQADV 7R2E GLY A 641 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER A 642 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER A 643 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS A 644 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS A 645 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS A 646 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS A 647 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS A 648 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS A 649 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER A 650 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER A 651 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E GLY A 652 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E LEU A 653 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E VAL A 654 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E PRO A 655 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E ARG A 656 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E GLY A 657 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER A 658 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS A 659 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E MET A 660 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E ALA A 661 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER A 662 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E MET B 640 UNP Q9BQF6 INITIATING METHIONINE SEQADV 7R2E GLY B 641 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER B 642 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER B 643 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS B 644 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS B 645 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS B 646 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS B 647 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS B 648 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS B 649 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER B 650 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER B 651 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E GLY B 652 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E LEU B 653 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E VAL B 654 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E PRO B 655 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E ARG B 656 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E GLY B 657 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER B 658 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E HIS B 659 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E MET B 660 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E ALA B 661 UNP Q9BQF6 EXPRESSION TAG SEQADV 7R2E SER B 662 UNP Q9BQF6 EXPRESSION TAG SEQRES 1 A 345 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 345 LEU VAL PRO ARG GLY SER HIS MET ALA SER THR SER ASN SEQRES 3 A 345 PRO ASP GLU GLU TRP ARG GLU VAL ARG HIS THR GLY LEU SEQRES 4 A 345 VAL GLN LYS LEU ILE VAL TYR PRO PRO PRO PRO THR LYS SEQRES 5 A 345 GLY GLY LEU GLY VAL THR ASN GLU ASP LEU GLU CYS LEU SEQRES 6 A 345 GLU GLU GLY GLU PHE LEU ASN ASP VAL ILE ILE ASP PHE SEQRES 7 A 345 TYR LEU LYS TYR LEU ILE LEU GLU LYS ALA SER ASP GLU SEQRES 8 A 345 LEU VAL GLU ARG SER HIS ILE PHE SER SER PHE PHE TYR SEQRES 9 A 345 LYS CYS LEU THR ARG LYS GLU ASN ASN LEU THR GLU ASP SEQRES 10 A 345 ASN PRO ASN LEU SER MET ALA GLN ARG ARG HIS LYS ARG SEQRES 11 A 345 VAL ARG THR TRP THR ARG HIS ILE ASN ILE PHE ASN LYS SEQRES 12 A 345 ASP TYR ILE PHE VAL PRO VAL ASN GLU SER SER HIS TRP SEQRES 13 A 345 TYR LEU ALA VAL ILE CYS PHE PRO TRP LEU GLU GLU ALA SEQRES 14 A 345 VAL TYR GLU ASP PHE PRO GLN THR VAL SER GLN GLN SER SEQRES 15 A 345 GLN ALA GLN GLN SER GLN ASN ASP ASN LYS THR ILE ASP SEQRES 16 A 345 ASN ASP LEU ARG THR THR SER THR LEU SER LEU SER ALA SEQRES 17 A 345 GLU ASP SER GLN SER THR GLU SER ASN MET SER VAL PRO SEQRES 18 A 345 LYS LYS MET CYS LYS ARG PRO CYS ILE LEU ILE LEU ASP SEQRES 19 A 345 SER LEU LYS ALA ALA SER VAL GLN ASN THR VAL GLN ASN SEQRES 20 A 345 LEU ARG GLU TYR LEU GLU VAL GLU TRP GLU VAL LYS LEU SEQRES 21 A 345 LYS THR HIS ARG GLN PHE SER LYS THR ASN MET VAL ASP SEQRES 22 A 345 LEU CYS PRO LYS VAL PRO LYS GLN ASP ASN SER SER ASP SEQRES 23 A 345 CYS GLY VAL TYR LEU LEU GLN TYR VAL GLU SER PHE PHE SEQRES 24 A 345 LYS ASP PRO ILE VAL ASN PHE GLU LEU PRO ILE HIS LEU SEQRES 25 A 345 GLU LYS TRP PHE PRO ARG HIS VAL ILE LYS THR LYS ARG SEQRES 26 A 345 GLU ASP ILE ARG GLU LEU ILE LEU LYS LEU HIS LEU GLN SEQRES 27 A 345 GLN GLN LYS GLY SER SER SER SEQRES 1 B 345 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 345 LEU VAL PRO ARG GLY SER HIS MET ALA SER THR SER ASN SEQRES 3 B 345 PRO ASP GLU GLU TRP ARG GLU VAL ARG HIS THR GLY LEU SEQRES 4 B 345 VAL GLN LYS LEU ILE VAL TYR PRO PRO PRO PRO THR LYS SEQRES 5 B 345 GLY GLY LEU GLY VAL THR ASN GLU ASP LEU GLU CYS LEU SEQRES 6 B 345 GLU GLU GLY GLU PHE LEU ASN ASP VAL ILE ILE ASP PHE SEQRES 7 B 345 TYR LEU LYS TYR LEU ILE LEU GLU LYS ALA SER ASP GLU SEQRES 8 B 345 LEU VAL GLU ARG SER HIS ILE PHE SER SER PHE PHE TYR SEQRES 9 B 345 LYS CYS LEU THR ARG LYS GLU ASN ASN LEU THR GLU ASP SEQRES 10 B 345 ASN PRO ASN LEU SER MET ALA GLN ARG ARG HIS LYS ARG SEQRES 11 B 345 VAL ARG THR TRP THR ARG HIS ILE ASN ILE PHE ASN LYS SEQRES 12 B 345 ASP TYR ILE PHE VAL PRO VAL ASN GLU SER SER HIS TRP SEQRES 13 B 345 TYR LEU ALA VAL ILE CYS PHE PRO TRP LEU GLU GLU ALA SEQRES 14 B 345 VAL TYR GLU ASP PHE PRO GLN THR VAL SER GLN GLN SER SEQRES 15 B 345 GLN ALA GLN GLN SER GLN ASN ASP ASN LYS THR ILE ASP SEQRES 16 B 345 ASN ASP LEU ARG THR THR SER THR LEU SER LEU SER ALA SEQRES 17 B 345 GLU ASP SER GLN SER THR GLU SER ASN MET SER VAL PRO SEQRES 18 B 345 LYS LYS MET CYS LYS ARG PRO CYS ILE LEU ILE LEU ASP SEQRES 19 B 345 SER LEU LYS ALA ALA SER VAL GLN ASN THR VAL GLN ASN SEQRES 20 B 345 LEU ARG GLU TYR LEU GLU VAL GLU TRP GLU VAL LYS LEU SEQRES 21 B 345 LYS THR HIS ARG GLN PHE SER LYS THR ASN MET VAL ASP SEQRES 22 B 345 LEU CYS PRO LYS VAL PRO LYS GLN ASP ASN SER SER ASP SEQRES 23 B 345 CYS GLY VAL TYR LEU LEU GLN TYR VAL GLU SER PHE PHE SEQRES 24 B 345 LYS ASP PRO ILE VAL ASN PHE GLU LEU PRO ILE HIS LEU SEQRES 25 B 345 GLU LYS TRP PHE PRO ARG HIS VAL ILE LYS THR LYS ARG SEQRES 26 B 345 GLU ASP ILE ARG GLU LEU ILE LEU LYS LEU HIS LEU GLN SEQRES 27 B 345 GLN GLN LYS GLY SER SER SER SEQRES 1 C 76 HIS ILE ASN LEU LYS VAL ALA GLY GLN ASP GLY SER VAL SEQRES 2 C 76 VAL GLN PHE LYS ILE LYS ARG HIS THR PRO LEU SER LYS SEQRES 3 C 76 LEU MET LYS ALA TYR CYS GLU ARG GLN GLY LEU SER MET SEQRES 4 C 76 ARG GLN ILE ARG PHE ARG PHE ASP GLY GLN PRO ILE ASN SEQRES 5 C 76 GLU THR ASP THR PRO ALA GLN LEU GLU MET GLU ASP GLU SEQRES 6 C 76 ASP THR ILE ASP VAL PHE GLN GLN GLN THR GLY SEQRES 1 D 76 HIS ILE ASN LEU LYS VAL ALA GLY GLN ASP GLY SER VAL SEQRES 2 D 76 VAL GLN PHE LYS ILE LYS ARG HIS THR PRO LEU SER LYS SEQRES 3 D 76 LEU MET LYS ALA TYR CYS GLU ARG GLN GLY LEU SER MET SEQRES 4 D 76 ARG GLN ILE ARG PHE ARG PHE ASP GLY GLN PRO ILE ASN SEQRES 5 D 76 GLU THR ASP THR PRO ALA GLN LEU GLU MET GLU ASP GLU SEQRES 6 D 76 ASP THR ILE ASP VAL PHE GLN GLN GLN THR GLY HET AYE A1001 4 HET AYE B1001 4 HETNAM AYE PROP-2-EN-1-AMINE HETSYN AYE ALLYLAMINE FORMUL 5 AYE 2(C3 H7 N) FORMUL 7 HOH *325(H2 O) HELIX 1 AA1 ASN A 698 GLU A 702 1 5 HELIX 2 AA2 CYS A 703 GLU A 705 5 3 HELIX 3 AA3 ASP A 712 LYS A 726 1 15 HELIX 4 AA4 SER A 728 ARG A 734 1 7 HELIX 5 AA5 PHE A 741 THR A 747 1 7 HELIX 6 AA6 SER A 761 VAL A 770 1 10 HELIX 7 AA7 ARG A 771 ARG A 775 5 5 HELIX 8 AA8 ASN A 778 LYS A 782 5 5 HELIX 9 AA9 SER A 879 LYS A 900 1 22 HELIX 10 AB1 ASP A 925 ASP A 940 1 16 HELIX 11 AB2 PRO A 956 THR A 962 1 7 HELIX 12 AB3 THR A 962 GLY A 981 1 20 HELIX 13 AB4 ASN B 698 GLU B 702 1 5 HELIX 14 AB5 CYS B 703 GLU B 705 5 3 HELIX 15 AB6 ASP B 712 LYS B 726 1 15 HELIX 16 AB7 SER B 728 ARG B 734 1 7 HELIX 17 AB8 PHE B 741 THR B 747 1 7 HELIX 18 AB9 SER B 761 VAL B 770 1 10 HELIX 19 AC1 ARG B 771 ARG B 775 5 5 HELIX 20 AC2 ASN B 778 LYS B 782 5 5 HELIX 21 AC3 SER B 879 LYS B 900 1 22 HELIX 22 AC4 ASP B 925 ASP B 940 1 16 HELIX 23 AC5 PRO B 956 THR B 962 1 7 HELIX 24 AC6 THR B 962 LYS B 980 1 19 HELIX 25 AC7 LEU C 40 GLN C 51 1 12 HELIX 26 AC8 LEU D 40 GLY D 52 1 13 HELIX 27 AC9 SER D 54 ARG D 56 5 3 HELIX 28 AD1 THR D 72 GLU D 77 1 6 SHEET 1 AA1 2 LYS A 681 TYR A 685 0 SHEET 2 AA1 2 LEU A 694 THR A 697 -1 O VAL A 696 N ILE A 683 SHEET 1 AA2 2 LEU A 710 ASN A 711 0 SHEET 2 AA2 2 THR D 91 GLY D 92 -1 O GLY D 92 N LEU A 710 SHEET 1 AA3 5 SER A 735 ILE A 737 0 SHEET 2 AA3 5 TYR A 784 ASN A 790 1 O PHE A 786 N HIS A 736 SHEET 3 AA3 5 TRP A 795 CYS A 801 -1 O ALA A 798 N VAL A 787 SHEET 4 AA3 5 CYS A 868 LEU A 872 -1 O LEU A 872 N LEU A 797 SHEET 5 AA3 5 VAL A 911 LEU A 913 1 O LEU A 913 N ILE A 871 SHEET 1 AA4 2 VAL A 809 TYR A 810 0 SHEET 2 AA4 2 CYS A 864 LYS A 865 -1 O LYS A 865 N VAL A 809 SHEET 1 AA5 2 LYS B 681 TYR B 685 0 SHEET 2 AA5 2 LEU B 694 THR B 697 -1 O LEU B 694 N TYR B 685 SHEET 1 AA6 2 LEU B 710 ASN B 711 0 SHEET 2 AA6 2 THR C 91 GLY C 92 -1 O GLY C 92 N LEU B 710 SHEET 1 AA7 5 SER B 735 ILE B 737 0 SHEET 2 AA7 5 TYR B 784 ASN B 790 1 O PHE B 786 N HIS B 736 SHEET 3 AA7 5 TRP B 795 CYS B 801 -1 O TYR B 796 N VAL B 789 SHEET 4 AA7 5 CYS B 868 LEU B 872 -1 O CYS B 868 N CYS B 801 SHEET 5 AA7 5 VAL B 911 LEU B 913 1 O LEU B 913 N ILE B 871 SHEET 1 AA8 5 VAL C 29 ILE C 34 0 SHEET 2 AA8 5 ILE C 18 ALA C 23 -1 N ILE C 18 O ILE C 34 SHEET 3 AA8 5 ASP C 82 GLN C 88 1 O ILE C 84 N LYS C 21 SHEET 4 AA8 5 ILE C 58 PHE C 62 -1 N ARG C 61 O ASP C 85 SHEET 5 AA8 5 GLN C 65 PRO C 66 -1 O GLN C 65 N PHE C 62 SHEET 1 AA9 5 VAL D 29 ILE D 34 0 SHEET 2 AA9 5 ILE D 18 ALA D 23 -1 N ILE D 18 O ILE D 34 SHEET 3 AA9 5 ASP D 82 GLN D 88 1 O ILE D 84 N LYS D 21 SHEET 4 AA9 5 ILE D 58 PHE D 62 -1 N ARG D 61 O ASP D 85 SHEET 5 AA9 5 GLN D 65 PRO D 66 -1 O GLN D 65 N PHE D 62 LINK SG CYS A 926 C2 AYE A1001 1555 1555 1.67 LINK N1 AYE A1001 C GLY D 92 1555 1555 1.43 LINK SG CYS B 926 C2 AYE B1001 1555 1555 1.66 LINK N1 AYE B1001 C GLY C 92 1555 1555 1.43 CISPEP 1 TYR A 685 PRO A 686 0 -7.61 CISPEP 2 PRO A 688 PRO A 689 0 8.16 CISPEP 3 LEU A 947 PRO A 948 0 -6.76 CISPEP 4 TYR B 685 PRO B 686 0 -3.00 CISPEP 5 PRO B 688 PRO B 689 0 7.83 CISPEP 6 LEU B 947 PRO B 948 0 -7.98 CRYST1 36.413 100.730 93.037 90.00 90.28 90.00 P 1 21 1 4 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 0.027463 0.000000 0.000133 0.00000 SCALE2 0.000000 0.009928 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010749 0.00000