HEADER HYDROLASE 21-APR-15 4ZFR TITLE CATALYTIC DOMAIN OF SST2 F403A MUTANT BOUND TO UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMSH-LIKE PROTEASE SST2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 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; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UBIQUITIN; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 77-152; COMPND 13 ENGINEERED: 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: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX-6-P1; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: UBB; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: ROSETTA; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX-6-P1 KEYWDS HELIX- BETA- HELIX SANDWICH, UBIQUITIN, ZINC METALLOPROTEASE, KEYWDS 2 CYTOSOL, ENDOSOME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.K.SHRESTHA REVDAT 5 27-SEP-23 4ZFR 1 LINK REVDAT 4 04-DEC-19 4ZFR 1 REMARK REVDAT 3 20-SEP-17 4ZFR 1 REMARK REVDAT 2 23-AUG-17 4ZFR 1 REMARK REVDAT 1 14-OCT-15 4ZFR 0 JRNL AUTH R.K.SHRESTHA JRNL TITL STRUCTURE OF CATALYTIC DOMAIN OF SST2 F403A MUTANT BOUND TO JRNL TITL 2 UBIQUITIN AT 1.7 ANGSTROMS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26060 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1382 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) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1939 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2019 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.120 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.593 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2073 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2045 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2812 ; 1.896 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4715 ; 0.881 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 261 ; 7.455 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;30.534 ;24.762 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 364 ;14.363 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;14.620 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 334 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2311 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 444 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1047 ; 2.209 ; 2.346 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1046 ; 2.208 ; 2.345 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1307 ; 2.897 ; 3.509 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1308 ; 2.896 ; 3.510 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1026 ; 2.838 ; 2.617 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1026 ; 2.837 ; 2.617 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1506 ; 4.075 ; 3.802 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2167 ; 5.849 ;18.344 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2168 ; 5.849 ;18.353 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 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 249 A 433 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4280 1.5400 17.3760 REMARK 3 T TENSOR REMARK 3 T11: 0.2211 T22: 0.0268 REMARK 3 T33: 0.0976 T12: -0.0224 REMARK 3 T13: 0.1177 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 1.3242 L22: 3.8626 REMARK 3 L33: 2.0001 L12: 0.2492 REMARK 3 L13: 0.1086 L23: 0.1226 REMARK 3 S TENSOR REMARK 3 S11: -0.1152 S12: 0.0940 S13: -0.0310 REMARK 3 S21: 0.2188 S22: -0.0324 S23: -0.1791 REMARK 3 S31: 0.1066 S32: 0.1446 S33: 0.1476 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4ZFR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26060 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.719 REMARK 200 RESOLUTION RANGE LOW (A) : 53.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : 0.04700 REMARK 200 FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.56100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.320 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: 4K1R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM CITRATE TRIBASIC REMARK 280 DIEHYDRATE, 0.1M HEPES SODIUM, 20% V/V 2-PROPANOL, PH 7.5, VAPOR REMARK 280 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 29.08700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL 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 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 -4 REMARK 465 PRO B -3 REMARK 465 LEU B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 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 267 CG CD CE NZ REMARK 470 LEU A 268 CG CD1 CD2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 LYS A 282 CG CD CE NZ REMARK 470 LYS A 283 CG CD CE NZ REMARK 470 GLU A 407 CG CD OE1 OE2 REMARK 470 ARG A 421 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LYS B 63 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASN B 60 NE2 GLN B 62 2.11 REMARK 500 O HOH A 623 O HOH A 624 2.18 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 NE2 GLN A 392 OE1 GLN B 62 2555 1.79 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 ARG A 296 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ASP A 321 79.25 -153.72 REMARK 500 LYS B 63 116.70 -36.99 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 GLY A 401 LEU A 402 -49.64 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 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 341 NE2 REMARK 620 2 HIS A 343 NE2 100.5 REMARK 620 3 ASP A 354 OD2 105.8 131.4 REMARK 620 4 GLY B 76 OXT 124.0 105.6 92.5 REMARK 620 N 1 2 3 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 356 NE2 REMARK 620 2 CYS A 397 SG 120.5 REMARK 620 3 HIS A 404 NE2 107.1 106.2 REMARK 620 4 HIS A 406 NE2 106.6 112.2 102.6 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 B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4K1R RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF SST2 BOUND TO UBIQUITIN REMARK 900 RELATED ID: 4MSQ RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF SST2 BOUND TO UBIQUITIN REMARK 900 RELATED ID: 4MSM RELATED DB: PDB REMARK 900 CATALYTIC MUTANT OF SST2 E286A BOUND TO UBIQUITIN REMARK 900 RELATED ID: 2ZNV RELATED DB: PDB REMARK 900 AMSH-LP E292A BOUND TO LYS63-LINKED UBIQUITIN DIMER REMARK 900 RELATED ID: 4ZFT RELATED DB: PDB DBREF 4ZFR A 245 435 UNP Q9P371 SST2_SCHPO 245 435 DBREF 4ZFR B 1 76 UNP P0CG47 UBB_HUMAN 77 152 SEQADV 4ZFR GLY A 239 UNP Q9P371 EXPRESSION TAG SEQADV 4ZFR PRO A 240 UNP Q9P371 EXPRESSION TAG SEQADV 4ZFR LEU A 241 UNP Q9P371 EXPRESSION TAG SEQADV 4ZFR GLY A 242 UNP Q9P371 EXPRESSION TAG SEQADV 4ZFR SER A 243 UNP Q9P371 EXPRESSION TAG SEQADV 4ZFR MET A 244 UNP Q9P371 EXPRESSION TAG SEQADV 4ZFR ALA A 403 UNP Q9P371 PHE 403 ENGINEERED MUTATION SEQADV 4ZFR GLY B -4 UNP P0CG47 EXPRESSION TAG SEQADV 4ZFR PRO B -3 UNP P0CG47 EXPRESSION TAG SEQADV 4ZFR LEU B -2 UNP P0CG47 EXPRESSION TAG SEQADV 4ZFR GLY B -1 UNP P0CG47 EXPRESSION TAG SEQADV 4ZFR SER B 0 UNP P0CG47 EXPRESSION TAG 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 THR 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 ALA 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 81 GLY PRO LEU GLY SER MET GLN ILE PHE VAL LYS THR LEU SEQRES 2 B 81 THR GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP SEQRES 3 B 81 THR ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU SEQRES 4 B 81 GLY ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY SEQRES 5 B 81 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN SEQRES 6 B 81 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU SEQRES 7 B 81 ARG GLY GLY HET ZN A 501 1 HET ZN A 502 1 HET EDO A 503 4 HET EDO B 101 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 5 EDO 2(C2 H6 O2) FORMUL 7 HOH *43(H2 O) HELIX 1 AA1 LEU A 268 VAL A 277 1 10 HELIX 2 AA2 VAL A 277 LYS A 283 1 7 HELIX 3 AA3 ASP A 321 HIS A 332 1 12 HELIX 4 AA4 SER A 351 LEU A 365 1 15 HELIX 5 AA5 PRO A 375 ASN A 378 5 4 HELIX 6 AA6 PRO A 388 CYS A 397 1 10 HELIX 7 AA7 THR B 22 GLY B 35 1 14 HELIX 8 AA8 PRO B 37 ASP B 39 5 3 HELIX 9 AA9 LEU B 56 ASN B 60 5 5 SHEET 1 AA1 2 ALA A 252 TYR A 253 0 SHEET 2 AA1 2 PRO A 259 LEU A 260 -1 O LEU A 260 N ALA A 252 SHEET 1 AA2 8 TYR A 411 MET A 413 0 SHEET 2 AA2 8 THR A 379 LEU A 385 -1 N ARG A 384 O THR A 412 SHEET 3 AA2 8 ILE A 369 ALA A 374 -1 N VAL A 372 O GLY A 381 SHEET 4 AA2 8 LEU A 335 THR A 342 1 N TRP A 339 O ILE A 371 SHEET 5 AA2 8 CYS A 288 ARG A 296 -1 N LEU A 291 O LEU A 337 SHEET 6 AA2 8 ALA A 299 ILE A 307 -1 O VAL A 306 N ILE A 290 SHEET 7 AA2 8 ILE A 263 PRO A 266 1 N TYR A 264 O PHE A 300 SHEET 8 AA2 8 VAL A 420 ILE A 423 1 O ARG A 421 N ILE A 263 SHEET 1 AA3 7 TYR A 411 MET A 413 0 SHEET 2 AA3 7 THR A 379 LEU A 385 -1 N ARG A 384 O THR A 412 SHEET 3 AA3 7 ILE A 369 ALA A 374 -1 N VAL A 372 O GLY A 381 SHEET 4 AA3 7 LEU A 335 THR A 342 1 N TRP A 339 O ILE A 371 SHEET 5 AA3 7 CYS A 288 ARG A 296 -1 N LEU A 291 O LEU A 337 SHEET 6 AA3 7 ALA A 299 ILE A 307 -1 O VAL A 306 N ILE A 290 SHEET 7 AA3 7 GLN A 428 ASP A 431 1 O VAL A 430 N ILE A 307 SHEET 1 AA4 3 GLN A 310 ALA A 312 0 SHEET 2 AA4 3 CYS A 317 THR A 319 -1 O GLY A 318 N GLU A 311 SHEET 3 AA4 3 ARG B 74 GLY B 75 -1 O GLY B 75 N CYS A 317 SHEET 1 AA5 5 THR B 12 GLU B 16 0 SHEET 2 AA5 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 AA5 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 AA5 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA5 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK NE2 HIS A 341 ZN ZN A 502 1555 1555 2.13 LINK NE2 HIS A 343 ZN ZN A 502 1555 1555 1.77 LINK OD2 ASP A 354 ZN ZN A 502 1555 1555 1.83 LINK NE2 HIS A 356 ZN ZN A 501 1555 1555 2.11 LINK SG CYS A 397 ZN ZN A 501 1555 1555 2.32 LINK NE2 HIS A 404 ZN ZN A 501 1555 1555 2.21 LINK NE2 HIS A 406 ZN ZN A 501 1555 1555 1.84 LINK ZN ZN A 502 OXT GLY B 76 1555 1555 2.18 CISPEP 1 ASP A 387 PRO A 388 0 18.65 CISPEP 2 GLN A 416 PRO A 417 0 2.04 SITE 1 AC1 4 HIS A 356 CYS A 397 HIS A 404 HIS A 406 SITE 1 AC2 4 HIS A 341 HIS A 343 ASP A 354 GLY B 76 SITE 1 AC3 5 GLY A 381 ILE A 382 MET A 413 VAL A 414 SITE 2 AC3 5 GLN A 416 SITE 1 AC4 6 HOH A 606 THR B 7 LEU B 8 LEU B 69 SITE 2 AC4 6 VAL B 70 LEU B 71 CRYST1 42.139 58.174 56.442 90.00 109.30 90.00 P 1 21 1 2 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 0.023731 0.000000 0.008312 0.00000 SCALE2 0.000000 0.017190 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018773 0.00000