HEADER HYDROLASE 18-SEP-13 4MSD TITLE CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEIN SST2 TITLE 2 T319I MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMSH-LIKE PROTEASE SST2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 245-435; COMPND 5 SYNONYM: SUPPRESSOR OF STE12 DELETION PROTEIN 2; COMPND 6 EC: 3.4.19.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 284812; SOURCE 5 STRAIN: 972/ATCC 24843; SOURCE 6 GENE: SST2, SPAC19B12.10; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS HELIX-BETA-HELIX SANDWICH, UBIQUITIN, DEUBIQUITINATION, ZINC KEYWDS 2 METALLOPROTEASE, AMSH, LYSINE 63-LINKED POLYUBIQUITIN, CYTOSOL, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.K.SHRESTHA,J.A.RONAU,C.DAS REVDAT 2 20-SEP-23 4MSD 1 REMARK SEQADV LINK REVDAT 1 18-JUN-14 4MSD 0 JRNL AUTH R.K.SHRESTHA,J.A.RONAU,C.W.DAVIES,R.G.GUENETTE,E.R.STRIETER, JRNL AUTH 2 L.N.PAUL,C.DAS JRNL TITL INSIGHTS INTO THE MECHANISM OF DEUBIQUITINATION BY JAMM JRNL TITL 2 DEUBIQUITINASES FROM COCRYSTAL STRUCTURES OF THE ENZYME WITH JRNL TITL 3 THE SUBSTRATE AND PRODUCT. JRNL REF BIOCHEMISTRY V. 53 3199 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24787148 JRNL DOI 10.1021/BI5003162 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 39791 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 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 33.6175 - 4.5750 1.00 2761 157 0.1566 0.2071 REMARK 3 2 4.5750 - 3.6327 1.00 2711 146 0.1517 0.1545 REMARK 3 3 3.6327 - 3.1739 1.00 2730 152 0.1904 0.1927 REMARK 3 4 3.1739 - 2.8839 1.00 2686 167 0.2028 0.2488 REMARK 3 5 2.8839 - 2.6773 1.00 2686 164 0.2079 0.2573 REMARK 3 6 2.6773 - 2.5195 1.00 2695 123 0.2091 0.2374 REMARK 3 7 2.5195 - 2.3933 1.00 2714 129 0.2030 0.2317 REMARK 3 8 2.3933 - 2.2892 1.00 2724 124 0.1985 0.2325 REMARK 3 9 2.2892 - 2.2011 1.00 2702 139 0.1937 0.2025 REMARK 3 10 2.2011 - 2.1251 1.00 2699 133 0.2059 0.2171 REMARK 3 11 2.1251 - 2.0587 1.00 2679 135 0.2121 0.2616 REMARK 3 12 2.0587 - 1.9998 1.00 2691 141 0.2258 0.2842 REMARK 3 13 1.9998 - 1.9472 1.00 2692 147 0.2422 0.2804 REMARK 3 14 1.9472 - 1.9000 0.98 2626 138 0.2614 0.3132 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 3029 REMARK 3 ANGLE : 1.122 4079 REMARK 3 CHIRALITY : 0.071 477 REMARK 3 PLANARITY : 0.005 507 REMARK 3 DIHEDRAL : 14.572 1124 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4MSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.56500 REMARK 200 R SYM FOR SHELL (I) : 0.56500 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4JXE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.03 M CITRIC ACID, 0.07 M BIS-TRIS REMARK 280 PROPANE, PH 7.6, 20% PEG 3350, BENZAMIDINE HYDROCHLORIDE REMARK 280 (ADDITIVE), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 37.05850 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: 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 239 REMARK 465 PRO A 240 REMARK 465 LEU A 241 REMARK 465 GLY A 242 REMARK 465 SER A 243 REMARK 465 MET A 244 REMARK 465 ALA A 245 REMARK 465 GLY A 246 REMARK 465 THR A 247 REMARK 465 PHE A 248 REMARK 465 VAL A 434 REMARK 465 LYS A 435 REMARK 465 GLY B 239 REMARK 465 PRO B 240 REMARK 465 LEU B 241 REMARK 465 GLY B 242 REMARK 465 SER B 243 REMARK 465 MET B 244 REMARK 465 ALA B 245 REMARK 465 GLY B 246 REMARK 465 THR B 247 REMARK 465 PHE B 248 REMARK 465 VAL B 434 REMARK 465 LYS B 435 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 282 CG CD CE NZ REMARK 470 GLU A 327 CG CD OE1 OE2 REMARK 470 GLU B 327 CG CD OE1 OE2 REMARK 470 GLU B 389 CG CD OE1 OE2 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 HOH A 667 O HOH B 664 2656 1.98 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 ASP A 315 16.52 -142.34 REMARK 500 CYS A 317 62.18 -153.16 REMARK 500 ALA A 374 77.92 -119.45 REMARK 500 CYS B 317 56.09 -150.54 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 341 NE2 REMARK 620 2 HIS A 343 NE2 108.6 REMARK 620 3 ASP A 354 OD2 102.8 120.6 REMARK 620 4 HOH A 621 O 118.5 96.9 110.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 356 NE2 REMARK 620 2 CYS A 397 SG 119.4 REMARK 620 3 HIS A 404 NE2 110.8 99.3 REMARK 620 4 HIS A 406 NE2 113.4 107.3 104.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 341 NE2 REMARK 620 2 HIS B 343 NE2 106.3 REMARK 620 3 ASP B 354 OD2 103.9 114.1 REMARK 620 4 ASP B 354 OD1 82.9 167.5 54.6 REMARK 620 5 HOH B 624 O 115.2 101.2 116.2 81.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 356 NE2 REMARK 620 2 CYS B 397 SG 121.7 REMARK 620 3 HIS B 404 NE2 106.5 104.8 REMARK 620 4 HIS B 406 NE2 110.7 108.2 103.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTT A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 509 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RZU RELATED DB: PDB REMARK 900 STRUCTURE OF CATALYTIC DOMAIN, HUMAN PROTEIN AMSH REMARK 900 RELATED ID: 4JXE RELATED DB: PDB REMARK 900 STRUCTURE OF CATALYTIC DOMAIN, S.POMBE SSTE REMARK 900 RELATED ID: 4MS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE SST2 CATALYTIC DOMAIN REMARK 900 RELATED ID: 4MSJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S. POMBE AMSH-LIKE PROTEASE SST2 CATALYTIC REMARK 900 DOMAIN FROM P212121 SPACE GROUP REMARK 900 RELATED ID: 4MSM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEASE REMARK 900 SST2 E286A MUTANT BOUND TO UBIQUITIN REMARK 900 RELATED ID: 4MSQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEASE REMARK 900 SST2 CATALYTIC DOMAIN BOUND TO UBIQUITIN DBREF 4MSD A 245 435 UNP Q9P371 SST2_SCHPO 245 435 DBREF 4MSD B 245 435 UNP Q9P371 SST2_SCHPO 245 435 SEQADV 4MSD GLY A 239 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD PRO A 240 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD LEU A 241 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD GLY A 242 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD SER A 243 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD MET A 244 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD ILE A 319 UNP Q9P371 THR 319 ENGINEERED MUTATION SEQADV 4MSD GLY B 239 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD PRO B 240 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD LEU B 241 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD GLY B 242 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD SER B 243 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD MET B 244 UNP Q9P371 EXPRESSION TAG SEQADV 4MSD ILE B 319 UNP Q9P371 THR 319 ENGINEERED MUTATION SEQRES 1 A 197 GLY PRO LEU GLY SER MET ALA GLY THR PHE LYS ILE HIS SEQRES 2 A 197 ALA TYR THR GLU GLY GLY LYS PRO LEU ARG THR ILE TYR SEQRES 3 A 197 LEU PRO LYS LEU LEU LYS LYS VAL PHE LEU ASP VAL VAL SEQRES 4 A 197 LYS PRO ASN THR LYS LYS ASN LEU GLU THR CYS GLY ILE SEQRES 5 A 197 LEU CYS GLY LYS LEU ARG GLN ASN ALA PHE PHE ILE THR SEQRES 6 A 197 HIS LEU VAL ILE PRO LEU GLN GLU ALA THR SER ASP THR SEQRES 7 A 197 CYS GLY ILE THR ASP GLU ALA SER LEU PHE GLU PHE GLN SEQRES 8 A 197 ASP LYS HIS ASN LEU LEU THR LEU GLY TRP ILE HIS THR SEQRES 9 A 197 HIS PRO THR GLN THR CYS PHE MET SER SER VAL ASP LEU SEQRES 10 A 197 HIS THR HIS CYS SER TYR GLN LEU MET LEU PRO GLU ALA SEQRES 11 A 197 ILE ALA ILE VAL MET ALA PRO SER LYS ASN THR SER GLY SEQRES 12 A 197 ILE PHE ARG LEU LEU ASP PRO GLU GLY LEU GLN THR ILE SEQRES 13 A 197 VAL LYS CYS ARG LYS PRO GLY LEU PHE HIS PRO HIS GLU SEQRES 14 A 197 GLY LYS VAL TYR THR MET VAL ALA GLN PRO GLY HIS VAL SEQRES 15 A 197 ARG GLU ILE ASN SER LYS LEU GLN VAL VAL ASP LEU ARG SEQRES 16 A 197 VAL LYS SEQRES 1 B 197 GLY PRO LEU GLY SER MET ALA GLY THR PHE LYS ILE HIS SEQRES 2 B 197 ALA TYR THR GLU GLY GLY LYS PRO LEU ARG THR ILE TYR SEQRES 3 B 197 LEU PRO LYS LEU LEU LYS LYS VAL PHE LEU ASP VAL VAL SEQRES 4 B 197 LYS PRO ASN THR LYS LYS ASN LEU GLU THR CYS GLY ILE SEQRES 5 B 197 LEU CYS GLY LYS LEU ARG GLN ASN ALA PHE PHE ILE THR SEQRES 6 B 197 HIS LEU VAL ILE PRO LEU GLN GLU ALA THR SER ASP THR SEQRES 7 B 197 CYS GLY ILE THR ASP GLU ALA SER LEU PHE GLU PHE GLN SEQRES 8 B 197 ASP LYS HIS ASN LEU LEU THR LEU GLY TRP ILE HIS THR SEQRES 9 B 197 HIS PRO THR GLN THR CYS PHE MET SER SER VAL ASP LEU SEQRES 10 B 197 HIS THR HIS CYS SER TYR GLN LEU MET LEU PRO GLU ALA SEQRES 11 B 197 ILE ALA ILE VAL MET ALA PRO SER LYS ASN THR SER GLY SEQRES 12 B 197 ILE PHE ARG LEU LEU ASP PRO GLU GLY LEU GLN THR ILE SEQRES 13 B 197 VAL LYS CYS ARG LYS PRO GLY LEU PHE HIS PRO HIS GLU SEQRES 14 B 197 GLY LYS VAL TYR THR MET VAL ALA GLN PRO GLY HIS VAL SEQRES 15 B 197 ARG GLU ILE ASN SER LYS LEU GLN VAL VAL ASP LEU ARG SEQRES 16 B 197 VAL LYS HET ZN A 501 1 HET ZN A 502 1 HET EDO A 503 4 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HET EDO A 508 4 HET EDO A 509 4 HET DTT A 510 8 HET ZN B 501 1 HET ZN B 502 1 HET EDO B 503 4 HET EDO B 504 4 HET EDO B 505 4 HET EDO B 506 4 HET EDO B 507 4 HET EDO B 508 4 HET EDO B 509 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETSYN EDO ETHYLENE GLYCOL HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 3 ZN 4(ZN 2+) FORMUL 5 EDO 14(C2 H6 O2) FORMUL 12 DTT C4 H10 O2 S2 FORMUL 22 HOH *165(H2 O) HELIX 1 1 LEU A 268 LYS A 283 1 16 HELIX 2 2 ASP A 321 HIS A 332 1 12 HELIX 3 3 SER A 351 LEU A 365 1 15 HELIX 4 4 PRO A 375 ASN A 378 5 4 HELIX 5 5 PRO A 388 CYS A 397 1 10 HELIX 6 6 LEU B 268 LYS B 283 1 16 HELIX 7 7 ASP B 321 HIS B 332 1 12 HELIX 8 8 SER B 351 LEU B 365 1 15 HELIX 9 9 PRO B 388 CYS B 397 1 10 SHEET 1 A 2 ALA A 252 TYR A 253 0 SHEET 2 A 2 PRO A 259 LEU A 260 -1 O LEU A 260 N ALA A 252 SHEET 1 B 8 TYR A 411 MET A 413 0 SHEET 2 B 8 THR A 379 LEU A 385 -1 N ARG A 384 O THR A 412 SHEET 3 B 8 ILE A 369 ALA A 374 -1 N ALA A 374 O THR A 379 SHEET 4 B 8 LEU A 335 THR A 342 1 N TRP A 339 O ILE A 371 SHEET 5 B 8 CYS A 288 ARG A 296 -1 N LEU A 291 O LEU A 337 SHEET 6 B 8 ALA A 299 ILE A 307 -1 O VAL A 306 N ILE A 290 SHEET 7 B 8 ILE A 263 PRO A 266 1 N TYR A 264 O PHE A 300 SHEET 8 B 8 VAL A 420 ILE A 423 1 O ARG A 421 N LEU A 265 SHEET 1 C 7 TYR A 411 MET A 413 0 SHEET 2 C 7 THR A 379 LEU A 385 -1 N ARG A 384 O THR A 412 SHEET 3 C 7 ILE A 369 ALA A 374 -1 N ALA A 374 O THR A 379 SHEET 4 C 7 LEU A 335 THR A 342 1 N TRP A 339 O ILE A 371 SHEET 5 C 7 CYS A 288 ARG A 296 -1 N LEU A 291 O LEU A 337 SHEET 6 C 7 ALA A 299 ILE A 307 -1 O VAL A 306 N ILE A 290 SHEET 7 C 7 GLN A 428 ASP A 431 1 O VAL A 430 N ILE A 307 SHEET 1 D 2 ALA B 252 TYR B 253 0 SHEET 2 D 2 PRO B 259 LEU B 260 -1 O LEU B 260 N ALA B 252 SHEET 1 E 8 TYR B 411 MET B 413 0 SHEET 2 E 8 THR B 379 LEU B 385 -1 N ARG B 384 O THR B 412 SHEET 3 E 8 ILE B 369 ALA B 374 -1 N VAL B 372 O GLY B 381 SHEET 4 E 8 LEU B 335 THR B 342 1 N TRP B 339 O ILE B 371 SHEET 5 E 8 CYS B 288 ARG B 296 -1 N LEU B 291 O LEU B 337 SHEET 6 E 8 ALA B 299 ILE B 307 -1 O VAL B 306 N ILE B 290 SHEET 7 E 8 ILE B 263 PRO B 266 1 N TYR B 264 O PHE B 300 SHEET 8 E 8 VAL B 420 ILE B 423 1 O ARG B 421 N ILE B 263 SHEET 1 F 7 TYR B 411 MET B 413 0 SHEET 2 F 7 THR B 379 LEU B 385 -1 N ARG B 384 O THR B 412 SHEET 3 F 7 ILE B 369 ALA B 374 -1 N VAL B 372 O GLY B 381 SHEET 4 F 7 LEU B 335 THR B 342 1 N TRP B 339 O ILE B 371 SHEET 5 F 7 CYS B 288 ARG B 296 -1 N LEU B 291 O LEU B 337 SHEET 6 F 7 ALA B 299 ILE B 307 -1 O VAL B 306 N ILE B 290 SHEET 7 F 7 GLN B 428 ASP B 431 1 O VAL B 430 N ILE B 307 SHEET 1 G 2 GLN B 310 ALA B 312 0 SHEET 2 G 2 CYS B 317 ILE B 319 -1 O GLY B 318 N GLU B 311 LINK NE2 HIS A 341 ZN ZN A 501 1555 1555 2.10 LINK NE2 HIS A 343 ZN ZN A 501 1555 1555 2.04 LINK OD2 ASP A 354 ZN ZN A 501 1555 1555 1.98 LINK NE2 HIS A 356 ZN ZN A 502 1555 1555 2.03 LINK SG CYS A 397 ZN ZN A 502 1555 1555 2.35 LINK NE2 HIS A 404 ZN ZN A 502 1555 1555 1.97 LINK NE2 HIS A 406 ZN ZN A 502 1555 1555 1.88 LINK ZN ZN A 501 O HOH A 621 1555 1555 1.99 LINK NE2 HIS B 341 ZN ZN B 501 1555 1555 2.02 LINK NE2 HIS B 343 ZN ZN B 501 1555 1555 2.01 LINK OD2 ASP B 354 ZN ZN B 501 1555 1555 1.92 LINK OD1 ASP B 354 ZN ZN B 501 1555 1555 2.67 LINK NE2 HIS B 356 ZN ZN B 502 1555 1555 2.01 LINK SG CYS B 397 ZN ZN B 502 1555 1555 2.28 LINK NE2 HIS B 404 ZN ZN B 502 1555 1555 2.01 LINK NE2 HIS B 406 ZN ZN B 502 1555 1555 2.02 LINK ZN ZN B 501 O HOH B 624 1555 1555 1.88 CISPEP 1 ASP A 387 PRO A 388 0 9.83 CISPEP 2 GLN A 416 PRO A 417 0 -1.51 CISPEP 3 ASP B 387 PRO B 388 0 12.92 CISPEP 4 GLN B 416 PRO B 417 0 -3.34 CISPEP 5 PRO B 417 GLY B 418 0 -5.97 SITE 1 AC1 4 HIS A 341 HIS A 343 ASP A 354 HOH A 621 SITE 1 AC2 4 HIS A 356 CYS A 397 HIS A 404 HIS A 406 SITE 1 AC3 6 CYS A 317 GLY A 318 ILE A 319 THR A 357 SITE 2 AC3 6 TYR A 361 EDO A 509 SITE 1 AC4 4 LYS A 409 TYR A 411 MET A 413 EDO A 508 SITE 1 AC5 4 GLN A 346 EDO A 507 HOH A 603 HOH A 635 SITE 1 AC6 2 SER A 360 HOH A 647 SITE 1 AC7 5 PHE A 349 SER A 351 SER A 352 PHE A 403 SITE 2 AC7 5 EDO A 505 SITE 1 AC8 4 LYS A 409 THR A 412 MET A 413 EDO A 504 SITE 1 AC9 6 THR A 316 CYS A 317 VAL A 353 THR A 357 SITE 2 AC9 6 EDO A 503 HOH A 637 SITE 1 BC1 2 ARG A 296 HOH A 632 SITE 1 BC2 4 HIS B 341 HIS B 343 ASP B 354 HOH B 624 SITE 1 BC3 4 HIS B 356 CYS B 397 HIS B 404 HIS B 406 SITE 1 BC4 2 LYS B 409 TYR B 411 SITE 1 BC5 8 ASP B 315 HIS B 343 GLN B 346 PHE B 349 SITE 2 BC5 8 SER B 351 HOH B 603 HOH B 604 HOH B 642 SITE 1 BC6 5 CYS B 288 CYS B 317 GLY B 318 THR B 357 SITE 2 BC6 5 TYR B 361 SITE 1 BC7 1 PHE B 349 SITE 1 BC8 2 MET B 364 HOH B 611 SITE 1 BC9 1 ASP B 315 CRYST1 58.048 74.117 64.865 90.00 113.41 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 0.017227 0.000000 0.007457 0.00000 SCALE2 0.000000 0.013492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016799 0.00000