PDB Short entry for 5K16 HEADER HYDROLASE 17-MAY-16 5K16 TITLE CRYSTAL STRUCTURE OF FREE UBIQUITIN-SPECIFIC PROTEASE 12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 12; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 16-370; COMPND 5 SYNONYM: DEUBIQUITINATING ENZYME 12,UBIQUITIN THIOESTERASE 12, COMPND 6 UBIQUITIN-HYDROLYZING ENZYME 1,UBIQUITIN-SPECIFIC-PROCESSING PROTEASE COMPND 7 12; COMPND 8 EC: 3.4.19.12; COMPND 9 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: USP12, UBH1, USP12L1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS DEUBIQUITINATION, DEUBIQUITNATING ENZYME, DUB, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.LI,A.D.D'ANDREA,N.ZHENG REVDAT 5 27-SEP-23 5K16 1 REMARK REVDAT 4 20-NOV-19 5K16 1 REMARK REVDAT 3 01-NOV-17 5K16 1 JRNL REMARK REVDAT 2 10-AUG-16 5K16 1 JRNL REVDAT 1 20-JUL-16 5K16 0 JRNL AUTH H.LI,K.S.LIM,H.KIM,T.R.HINDS,U.JO,H.MAO,C.E.WELLER,J.SUN, JRNL AUTH 2 C.CHATTERJEE,A.D.D'ANDREA,N.ZHENG JRNL TITL ALLOSTERIC ACTIVATION OF UBIQUITIN-SPECIFIC PROTEASES BY JRNL TITL 2 BETA-PROPELLER PROTEINS UAF1 AND WDR20. JRNL REF MOL.CELL V. 63 249 2016 JRNL REFN ISSN 1097-2765 JRNL PMID 27373336 JRNL DOI 10.1016/J.MOLCEL.2016.05.031 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1760 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 24515 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1256 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 42.4570 - 5.4028 1.00 2773 129 0.1751 0.2198 REMARK 3 2 5.4028 - 4.2897 1.00 2640 124 0.1532 0.1785 REMARK 3 3 4.2897 - 3.7478 1.00 2568 146 0.1712 0.2226 REMARK 3 4 3.7478 - 3.4053 1.00 2624 114 0.1920 0.2565 REMARK 3 5 3.4053 - 3.1613 1.00 2545 158 0.2108 0.2955 REMARK 3 6 3.1613 - 2.9750 1.00 2532 153 0.2176 0.2794 REMARK 3 7 2.9750 - 2.8260 1.00 2537 131 0.2413 0.2863 REMARK 3 8 2.8260 - 2.7030 1.00 2534 151 0.2523 0.3523 REMARK 3 9 2.7030 - 2.5990 0.99 2506 150 0.2759 0.3414 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.030 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 : 0.010 5255 REMARK 3 ANGLE : 1.232 7118 REMARK 3 CHIRALITY : 0.046 801 REMARK 3 PLANARITY : 0.005 914 REMARK 3 DIHEDRAL : 15.185 1859 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 5K16 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221563. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24515 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.599 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : 0.10500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.74000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 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: 3M99 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 18% PEG 3350, 0.2 M REMARK 280 LITHIUM SULFATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 26.19800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.09650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.81800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.09650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.19800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.81800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 300 REMARK: MONOMER AS DETERMINED BY SIZE-EXCLUSION CHROMATOGRAPHY 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 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 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 MET A 16 REMARK 465 GLY A 17 REMARK 465 ALA A 18 REMARK 465 ASN A 19 REMARK 465 ALA A 20 REMARK 465 PRO A 74 REMARK 465 ARG A 75 REMARK 465 GLY A 151 REMARK 465 ARG A 152 REMARK 465 LEU A 153 REMARK 465 PRO A 154 REMARK 465 ASN A 155 REMARK 465 GLY A 156 REMARK 465 ASN A 157 REMARK 465 ILE A 158 REMARK 465 ASP A 159 REMARK 465 ASN A 160 REMARK 465 GLU A 161 REMARK 465 ASN A 162 REMARK 465 ASN A 163 REMARK 465 ASN A 164 REMARK 465 SER A 165 REMARK 465 THR A 166 REMARK 465 LEU A 225 REMARK 465 CYS A 226 REMARK 465 SER A 227 REMARK 465 GLU A 228 REMARK 465 TYR A 229 REMARK 465 ASP A 353 REMARK 465 ILE A 354 REMARK 465 SER A 355 REMARK 465 MET B 16 REMARK 465 GLY B 17 REMARK 465 ALA B 18 REMARK 465 ASN B 150 REMARK 465 GLY B 151 REMARK 465 ARG B 152 REMARK 465 LEU B 153 REMARK 465 PRO B 154 REMARK 465 ASN B 155 REMARK 465 GLY B 156 REMARK 465 ASN B 157 REMARK 465 ILE B 158 REMARK 465 ASP B 159 REMARK 465 ASN B 160 REMARK 465 GLU B 161 REMARK 465 ASN B 162 REMARK 465 ASN B 163 REMARK 465 ASN B 164 REMARK 465 SER B 165 REMARK 465 THR B 166 REMARK 465 PRO B 167 REMARK 465 ASP B 168 REMARK 465 THR B 351 REMARK 465 SER B 352 REMARK 465 ASP B 353 REMARK 465 ILE B 354 REMARK 465 SER B 355 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 GLU A 24 CG CD OE1 OE2 REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 GLU A 30 CG CD OE1 OE2 REMARK 470 GLN A 31 CG CD OE1 NE2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 LYS A 77 CE NZ REMARK 470 LYS A 95 CG CD CE NZ REMARK 470 LYS A 96 CG CD CE NZ REMARK 470 LYS A 97 CG CD CE NZ REMARK 470 LYS A 104 CD CE NZ REMARK 470 LYS A 112 CD CE NZ REMARK 470 GLU A 142 CD OE1 OE2 REMARK 470 GLN A 146 CG CD OE1 NE2 REMARK 470 GLU A 147 CG CD OE1 OE2 REMARK 470 LYS A 148 CD CE NZ REMARK 470 GLN A 149 CG CD OE1 NE2 REMARK 470 ASP A 168 CG OD1 OD2 REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 GLU A 234 CG CD OE1 OE2 REMARK 470 SER A 238 OG REMARK 470 LYS A 239 CG CD CE NZ REMARK 470 GLU A 241 CG CD OE1 OE2 REMARK 470 LYS A 250 CG CD CE NZ REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 MET A 265 CG SD CE REMARK 470 ASP A 266 CG OD1 OD2 REMARK 470 GLN A 267 CG CD OE1 NE2 REMARK 470 LEU A 268 CG CD1 CD2 REMARK 470 HIS A 269 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 342 CG CD OE1 NE2 REMARK 470 SER A 352 OG REMARK 470 LYS A 356 CG CD CE NZ REMARK 470 ASN A 357 CG OD1 ND2 REMARK 470 ASP A 370 CG OD1 OD2 REMARK 470 LYS B 25 CG CD CE NZ REMARK 470 GLU B 26 CG CD OE1 OE2 REMARK 470 GLU B 30 CG CD OE1 OE2 REMARK 470 SER B 72 OG REMARK 470 ARG B 75 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 LYS B 77 CG CD CE NZ REMARK 470 GLU B 78 CG CD OE1 OE2 REMARK 470 SER B 79 OG REMARK 470 LYS B 95 CG CD CE NZ REMARK 470 LYS B 104 CG CD CE NZ REMARK 470 LYS B 105 CG CD CE NZ REMARK 470 GLU B 115 CG CD OE1 OE2 REMARK 470 GLU B 142 CD OE1 OE2 REMARK 470 ARG B 144 CD NE CZ NH1 NH2 REMARK 470 LYS B 145 CG CD CE NZ REMARK 470 GLN B 146 CG CD OE1 NE2 REMARK 470 GLU B 147 CG CD OE1 OE2 REMARK 470 LYS B 148 CG CD CE NZ REMARK 470 GLN B 149 CG CD OE1 NE2 REMARK 470 GLU B 183 CG CD OE1 OE2 REMARK 470 GLN B 208 CG CD OE1 NE2 REMARK 470 SER B 220 OG REMARK 470 GLU B 223 CG CD OE1 OE2 REMARK 470 GLU B 228 CG CD OE1 OE2 REMARK 470 LYS B 247 CD CE NZ REMARK 470 LYS B 250 CG CD CE NZ REMARK 470 LYS B 263 CG CD CE NZ REMARK 470 GLN B 267 CG CD OE1 NE2 REMARK 470 LEU B 268 CG CD1 CD2 REMARK 470 SER B 290 OG REMARK 470 ASN B 314 CG OD1 ND2 REMARK 470 LYS B 356 CG CD CE NZ REMARK 470 SER B 358 OG 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 OE2 GLU A 207 OH TYR B 276 2.13 REMARK 500 OE1 GLU B 24 O HOH B 501 2.14 REMARK 500 OG1 THR A 188 OE1 GLN A 240 2.17 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 SER A 324 C HIS A 325 N 0.138 REMARK 500 ASP B 333 C ASP B 334 N 0.178 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 PRO B 74 CB - CA - C ANGL. DEV. = -17.4 DEGREES REMARK 500 PRO B 74 N - CA - C ANGL. DEV. = 21.7 DEGREES REMARK 500 PRO B 313 C - N - CD ANGL. DEV. = 12.7 DEGREES REMARK 500 ASN B 314 CB - CA - C ANGL. DEV. = 15.9 DEGREES REMARK 500 ARG B 315 O - C - N ANGL. DEV. = -11.2 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 GLN A 94 138.78 -39.31 REMARK 500 PRO A 103 48.47 -80.17 REMARK 500 GLU A 142 -3.21 -55.93 REMARK 500 GLN A 149 65.84 64.34 REMARK 500 PRO A 169 123.41 -34.95 REMARK 500 ASN A 209 71.55 50.00 REMARK 500 ARG A 237 4.58 56.63 REMARK 500 ASP A 292 106.42 -52.78 REMARK 500 HIS A 325 -118.25 41.95 REMARK 500 ASP A 333 -120.25 47.09 REMARK 500 THR B 210 -154.08 -110.90 REMARK 500 SER B 220 18.39 -144.12 REMARK 500 TYR B 229 118.75 -32.81 REMARK 500 SER B 311 -72.69 -106.19 REMARK 500 HIS B 325 -116.41 57.32 REMARK 500 ASP B 333 -105.90 41.38 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 PRO A 296 ASP A 297 -144.93 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 186 SG REMARK 620 2 CYS A 189 SG 111.5 REMARK 620 3 CYS A 233 SG 100.2 130.9 REMARK 620 4 CYS A 236 SG 96.3 103.9 108.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 186 SG REMARK 620 2 CYS B 189 SG 100.9 REMARK 620 3 CYS B 233 SG 110.4 116.0 REMARK 620 4 CYS B 236 SG 103.0 107.7 116.9 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5K1C RELATED DB: PDB REMARK 900 RELATED ID: 5K1A RELATED DB: PDB REMARK 900 RELATED ID: 5K1B RELATED DB: PDB REMARK 900 RELATED ID: 5K19 RELATED DB: PDB DBREF 5K16 A 16 370 UNP O75317 UBP12_HUMAN 16 370 DBREF 5K16 B 16 370 UNP O75317 UBP12_HUMAN 16 370 SEQRES 1 A 355 MET GLY ALA ASN ALA SER ALA LEU GLU LYS GLU ILE GLY SEQRES 2 A 355 PRO GLU GLN PHE PRO VAL ASN GLU HIS TYR PHE GLY LEU SEQRES 3 A 355 VAL ASN PHE GLY ASN THR CYS TYR CYS ASN SER VAL LEU SEQRES 4 A 355 GLN ALA LEU TYR PHE CYS ARG PRO PHE ARG GLU LYS VAL SEQRES 5 A 355 LEU ALA TYR LYS SER GLN PRO ARG LYS LYS GLU SER LEU SEQRES 6 A 355 LEU THR CYS LEU ALA ASP LEU PHE HIS SER ILE ALA THR SEQRES 7 A 355 GLN LYS LYS LYS VAL GLY VAL ILE PRO PRO LYS LYS PHE SEQRES 8 A 355 ILE THR ARG LEU ARG LYS GLU ASN GLU LEU PHE ASP ASN SEQRES 9 A 355 TYR MET GLN GLN ASP ALA HIS GLU PHE LEU ASN TYR LEU SEQRES 10 A 355 LEU ASN THR ILE ALA ASP ILE LEU GLN GLU GLU ARG LYS SEQRES 11 A 355 GLN GLU LYS GLN ASN GLY ARG LEU PRO ASN GLY ASN ILE SEQRES 12 A 355 ASP ASN GLU ASN ASN ASN SER THR PRO ASP PRO THR TRP SEQRES 13 A 355 VAL HIS GLU ILE PHE GLN GLY THR LEU THR ASN GLU THR SEQRES 14 A 355 ARG CYS LEU THR CYS GLU THR ILE SER SER LYS ASP GLU SEQRES 15 A 355 ASP PHE LEU ASP LEU SER VAL ASP VAL GLU GLN ASN THR SEQRES 16 A 355 SER ILE THR HIS CYS LEU ARG GLY PHE SER ASN THR GLU SEQRES 17 A 355 THR LEU CYS SER GLU TYR LYS TYR TYR CYS GLU GLU CYS SEQRES 18 A 355 ARG SER LYS GLN GLU ALA HIS LYS ARG MET LYS VAL LYS SEQRES 19 A 355 LYS LEU PRO MET ILE LEU ALA LEU HIS LEU LYS ARG PHE SEQRES 20 A 355 LYS TYR MET ASP GLN LEU HIS ARG TYR THR LYS LEU SER SEQRES 21 A 355 TYR ARG VAL VAL PHE PRO LEU GLU LEU ARG LEU PHE ASN SEQRES 22 A 355 THR SER GLY ASP ALA THR ASN PRO ASP ARG MET TYR ASP SEQRES 23 A 355 LEU VAL ALA VAL VAL VAL HIS CYS GLY SER GLY PRO ASN SEQRES 24 A 355 ARG GLY HIS TYR ILE ALA ILE VAL LYS SER HIS ASP PHE SEQRES 25 A 355 TRP LEU LEU PHE ASP ASP ASP ILE VAL GLU LYS ILE ASP SEQRES 26 A 355 ALA GLN ALA ILE GLU GLU PHE TYR GLY LEU THR SER ASP SEQRES 27 A 355 ILE SER LYS ASN SER GLU SER GLY TYR ILE LEU PHE TYR SEQRES 28 A 355 GLN SER ARG ASP SEQRES 1 B 355 MET GLY ALA ASN ALA SER ALA LEU GLU LYS GLU ILE GLY SEQRES 2 B 355 PRO GLU GLN PHE PRO VAL ASN GLU HIS TYR PHE GLY LEU SEQRES 3 B 355 VAL ASN PHE GLY ASN THR CYS TYR CYS ASN SER VAL LEU SEQRES 4 B 355 GLN ALA LEU TYR PHE CYS ARG PRO PHE ARG GLU LYS VAL SEQRES 5 B 355 LEU ALA TYR LYS SER GLN PRO ARG LYS LYS GLU SER LEU SEQRES 6 B 355 LEU THR CYS LEU ALA ASP LEU PHE HIS SER ILE ALA THR SEQRES 7 B 355 GLN LYS LYS LYS VAL GLY VAL ILE PRO PRO LYS LYS PHE SEQRES 8 B 355 ILE THR ARG LEU ARG LYS GLU ASN GLU LEU PHE ASP ASN SEQRES 9 B 355 TYR MET GLN GLN ASP ALA HIS GLU PHE LEU ASN TYR LEU SEQRES 10 B 355 LEU ASN THR ILE ALA ASP ILE LEU GLN GLU GLU ARG LYS SEQRES 11 B 355 GLN GLU LYS GLN ASN GLY ARG LEU PRO ASN GLY ASN ILE SEQRES 12 B 355 ASP ASN GLU ASN ASN ASN SER THR PRO ASP PRO THR TRP SEQRES 13 B 355 VAL HIS GLU ILE PHE GLN GLY THR LEU THR ASN GLU THR SEQRES 14 B 355 ARG CYS LEU THR CYS GLU THR ILE SER SER LYS ASP GLU SEQRES 15 B 355 ASP PHE LEU ASP LEU SER VAL ASP VAL GLU GLN ASN THR SEQRES 16 B 355 SER ILE THR HIS CYS LEU ARG GLY PHE SER ASN THR GLU SEQRES 17 B 355 THR LEU CYS SER GLU TYR LYS TYR TYR CYS GLU GLU CYS SEQRES 18 B 355 ARG SER LYS GLN GLU ALA HIS LYS ARG MET LYS VAL LYS SEQRES 19 B 355 LYS LEU PRO MET ILE LEU ALA LEU HIS LEU LYS ARG PHE SEQRES 20 B 355 LYS TYR MET ASP GLN LEU HIS ARG TYR THR LYS LEU SER SEQRES 21 B 355 TYR ARG VAL VAL PHE PRO LEU GLU LEU ARG LEU PHE ASN SEQRES 22 B 355 THR SER GLY ASP ALA THR ASN PRO ASP ARG MET TYR ASP SEQRES 23 B 355 LEU VAL ALA VAL VAL VAL HIS CYS GLY SER GLY PRO ASN SEQRES 24 B 355 ARG GLY HIS TYR ILE ALA ILE VAL LYS SER HIS ASP PHE SEQRES 25 B 355 TRP LEU LEU PHE ASP ASP ASP ILE VAL GLU LYS ILE ASP SEQRES 26 B 355 ALA GLN ALA ILE GLU GLU PHE TYR GLY LEU THR SER ASP SEQRES 27 B 355 ILE SER LYS ASN SER GLU SER GLY TYR ILE LEU PHE TYR SEQRES 28 B 355 GLN SER ARG ASP HET ZN A 401 1 HET GOL A 402 6 HET ZN B 401 1 HET GOL B 402 6 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *56(H2 O) HELIX 1 AA1 SER A 21 GLY A 28 1 8 HELIX 2 AA2 THR A 47 PHE A 59 1 13 HELIX 3 AA3 CYS A 60 GLN A 73 1 14 HELIX 4 AA4 SER A 79 GLN A 94 1 16 HELIX 5 AA5 PRO A 103 ASN A 114 1 12 HELIX 6 AA6 GLU A 115 ASP A 118 5 4 HELIX 7 AA7 ASP A 124 LYS A 145 1 22 HELIX 8 AA8 THR A 170 GLN A 177 1 8 HELIX 9 AA9 ILE A 212 SER A 220 1 9 HELIX 10 AB1 ASP A 340 TYR A 348 5 9 HELIX 11 AB2 SER B 21 PHE B 32 1 12 HELIX 12 AB3 THR B 47 PHE B 59 1 13 HELIX 13 AB4 CYS B 60 GLN B 73 1 14 HELIX 14 AB5 SER B 79 THR B 93 1 15 HELIX 15 AB6 PRO B 103 ASN B 114 1 12 HELIX 16 AB7 GLU B 115 ASP B 118 5 4 HELIX 17 AB8 ASP B 124 GLN B 149 1 26 HELIX 18 AB9 THR B 170 GLN B 177 1 8 HELIX 19 AC1 SER B 211 ARG B 217 1 7 HELIX 20 AC2 ASP B 340 TYR B 348 5 9 SHEET 1 AA1 2 TYR A 38 LEU A 41 0 SHEET 2 AA1 2 VAL A 98 ILE A 101 1 O ILE A 101 N GLY A 40 SHEET 1 AA2 3 ASP A 196 PHE A 199 0 SHEET 2 AA2 3 GLY A 178 THR A 181 -1 N LEU A 180 O GLU A 197 SHEET 3 AA2 3 LYS A 247 LYS A 250 -1 O LYS A 247 N THR A 181 SHEET 1 AA3 2 THR A 184 CYS A 186 0 SHEET 2 AA3 2 ALA A 242 LYS A 244 -1 O HIS A 243 N ARG A 185 SHEET 1 AA4 5 LEU A 202 VAL A 204 0 SHEET 2 AA4 5 ILE A 254 LEU A 259 1 O HIS A 258 N LEU A 202 SHEET 3 AA4 5 SER A 358 SER A 368 -1 O LEU A 364 N LEU A 257 SHEET 4 AA4 5 ASP A 297 GLY A 310 -1 N ASP A 301 O GLN A 367 SHEET 5 AA4 5 GLU A 283 PHE A 287 -1 N LEU A 286 O ARG A 298 SHEET 1 AA5 7 LEU A 202 VAL A 204 0 SHEET 2 AA5 7 ILE A 254 LEU A 259 1 O HIS A 258 N LEU A 202 SHEET 3 AA5 7 SER A 358 SER A 368 -1 O LEU A 364 N LEU A 257 SHEET 4 AA5 7 ASP A 297 GLY A 310 -1 N ASP A 301 O GLN A 367 SHEET 5 AA5 7 GLY A 316 SER A 324 -1 O HIS A 317 N CYS A 309 SHEET 6 AA5 7 PHE A 327 ASP A 332 -1 O LEU A 329 N VAL A 322 SHEET 7 AA5 7 ILE A 335 ILE A 339 -1 O GLU A 337 N LEU A 330 SHEET 1 AA6 2 THR A 210 SER A 211 0 SHEET 2 AA6 2 VAL A 278 VAL A 279 1 O VAL A 279 N THR A 210 SHEET 1 AA7 2 TYR A 231 TYR A 232 0 SHEET 2 AA7 2 LYS A 239 GLN A 240 -1 O GLN A 240 N TYR A 231 SHEET 1 AA8 2 PHE A 262 MET A 265 0 SHEET 2 AA8 2 ARG A 270 LYS A 273 -1 O THR A 272 N LYS A 263 SHEET 1 AA9 2 TYR B 38 LEU B 41 0 SHEET 2 AA9 2 VAL B 98 ILE B 101 1 O ILE B 101 N GLY B 40 SHEET 1 AB1 4 ILE B 192 PHE B 199 0 SHEET 2 AB1 4 GLY B 178 CYS B 186 -1 N GLY B 178 O PHE B 199 SHEET 3 AB1 4 SER B 238 LYS B 250 -1 O LYS B 247 N THR B 181 SHEET 4 AB1 4 LYS B 230 CYS B 233 -1 N TYR B 231 O GLN B 240 SHEET 1 AB2 5 LEU B 202 ASP B 205 0 SHEET 2 AB2 5 ILE B 254 LYS B 260 1 O HIS B 258 N VAL B 204 SHEET 3 AB2 5 SER B 358 SER B 368 -1 O TYR B 366 N LEU B 255 SHEET 4 AB2 5 ASP B 297 GLY B 310 -1 N ASP B 301 O GLN B 367 SHEET 5 AB2 5 GLU B 283 PHE B 287 -1 N LEU B 286 O ARG B 298 SHEET 1 AB3 7 LEU B 202 ASP B 205 0 SHEET 2 AB3 7 ILE B 254 LYS B 260 1 O HIS B 258 N VAL B 204 SHEET 3 AB3 7 SER B 358 SER B 368 -1 O TYR B 366 N LEU B 255 SHEET 4 AB3 7 ASP B 297 GLY B 310 -1 N ASP B 301 O GLN B 367 SHEET 5 AB3 7 HIS B 317 SER B 324 -1 O LYS B 323 N VAL B 303 SHEET 6 AB3 7 PHE B 327 ASP B 332 -1 O PHE B 331 N ALA B 320 SHEET 7 AB3 7 ILE B 335 ILE B 339 -1 O GLU B 337 N LEU B 330 SHEET 1 AB4 2 PHE B 262 MET B 265 0 SHEET 2 AB4 2 ARG B 270 LYS B 273 -1 O THR B 272 N LYS B 263 LINK SG CYS A 186 ZN ZN A 401 1555 1555 2.27 LINK SG CYS A 189 ZN ZN A 401 1555 1555 2.22 LINK SG CYS A 233 ZN ZN A 401 1555 1555 2.28 LINK SG CYS A 236 ZN ZN A 401 1555 1555 2.37 LINK SG CYS B 186 ZN ZN B 401 1555 1555 2.47 LINK SG CYS B 189 ZN ZN B 401 1555 1555 2.22 LINK SG CYS B 233 ZN ZN B 401 1555 1555 2.30 LINK SG CYS B 236 ZN ZN B 401 1555 1555 2.33 SITE 1 AC1 4 CYS A 186 CYS A 189 CYS A 233 CYS A 236 SITE 1 AC2 3 ILE A 192 SER A 193 SER A 194 SITE 1 AC3 4 CYS B 186 CYS B 189 CYS B 233 CYS B 236 SITE 1 AC4 3 ILE B 107 THR B 108 ARG B 111 CRYST1 52.396 109.636 134.193 90.00 90.00 90.00 P 21 21 21 8 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 0.019085 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009121 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007452 0.00000