HEADER PROTEIN BINDING 19-SEP-25 9YCW TITLE CRYSTAL STRUCTURE OF USP16 ZNF-UBP DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 16; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 16,UBIQUITIN THIOESTERASE 16, COMPND 5 UBIQUITIN-PROCESSING PROTEASE UBP-M,UBIQUITIN-SPECIFIC-PROCESSING COMPND 6 PROTEASE 16; COMPND 7 EC: 3.4.19.12; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: NO DENSITY FOR GLYCINE ON THE N TERMINUS OF CHAINS A COMPND 10 AND B, MISSING DENSITY ON RESI D36 - K50 GP N TERM ORIGINATES FROM 3C COMPND 11 CLEAVAGE TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP16, MSTP039; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS USP16, DEUBIQUITINASE, DUB, PROTEASE, UBIQUITIN, HISTONE, NUCLEOSOME, KEYWDS 2 UBIQUITIN BINDING DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.A.ALEXANDROVICS,D.KOMANDER REVDAT 1 20-MAY-26 9YCW 0 JRNL AUTH J.A.ALEXANDROVICS,R.AGRATA,P.SCHENK,A.CERRA,U.NACHBUR, JRNL AUTH 2 J.J.BABON,D.KOMANDER JRNL TITL THE ZNF-UBP DOMAIN REGULATES USP16 ACTIVITY BY DISLODGING JRNL TITL 2 UBIQUITIN FROM THE ACTIVE SITE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 37004 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1963 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 41.5100 - 4.3400 0.93 2490 138 0.1114 0.1387 REMARK 3 2 4.3300 - 3.4400 0.93 2487 140 0.0960 0.1681 REMARK 3 3 3.4400 - 3.0100 0.95 2520 121 0.1224 0.1526 REMARK 3 4 3.0100 - 2.7300 0.93 2460 181 0.1341 0.1760 REMARK 3 5 2.7300 - 2.5400 0.94 2515 150 0.1417 0.1647 REMARK 3 6 2.5400 - 2.3900 0.94 2501 123 0.1504 0.1506 REMARK 3 7 2.3900 - 2.2700 0.95 2518 121 0.1504 0.1853 REMARK 3 8 2.2700 - 2.1700 0.94 2504 143 0.1570 0.2159 REMARK 3 9 2.1700 - 2.0900 0.94 2506 138 0.1656 0.1812 REMARK 3 10 2.0900 - 2.0100 0.94 2498 140 0.1732 0.2015 REMARK 3 11 2.0100 - 1.9500 0.95 2570 124 0.1858 0.2068 REMARK 3 12 1.9500 - 1.8900 0.95 2519 144 0.2053 0.2347 REMARK 3 13 1.8900 - 1.8500 0.95 2467 136 0.2336 0.2356 REMARK 3 14 1.8400 - 1.8000 0.94 2500 150 0.2341 0.2689 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.173 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.21 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: 0.3300 REMARK 3 OPERATOR: H,-H-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2674 REMARK 3 ANGLE : 0.696 3631 REMARK 3 CHIRALITY : 0.048 393 REMARK 3 PLANARITY : 0.007 465 REMARK 3 DIHEDRAL : 18.868 966 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 4 THROUGH 127) REMARK 3 ORIGIN FOR THE GROUP (A): 29.1393 25.6864 16.4867 REMARK 3 T TENSOR REMARK 3 T11: 0.1771 T22: 0.2185 REMARK 3 T33: 0.1888 T12: 0.0124 REMARK 3 T13: -0.0184 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 4.3976 L22: 2.6745 REMARK 3 L33: 3.5276 L12: 0.8301 REMARK 3 L13: 0.5730 L23: 0.2431 REMARK 3 S TENSOR REMARK 3 S11: -0.1763 S12: -0.2689 S13: 0.1253 REMARK 3 S21: -0.1014 S22: 0.1903 S23: 0.2253 REMARK 3 S31: -0.0765 S32: -0.2237 S33: -0.0169 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 3 THROUGH 127) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5493 35.7346 33.2766 REMARK 3 T TENSOR REMARK 3 T11: 0.1791 T22: 0.1549 REMARK 3 T33: 0.1437 T12: 0.0182 REMARK 3 T13: -0.0119 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 1.0259 L22: 3.0669 REMARK 3 L33: 2.4714 L12: 0.3686 REMARK 3 L13: -0.1760 L23: -0.3089 REMARK 3 S TENSOR REMARK 3 S11: 0.0727 S12: 0.0380 S13: -0.0941 REMARK 3 S21: -0.1301 S22: -0.0420 S23: -0.0394 REMARK 3 S31: 0.2008 S32: 0.0812 S33: -0.0370 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 4 THROUGH 127) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9557 12.3979 2.6242 REMARK 3 T TENSOR REMARK 3 T11: 0.1588 T22: 0.1406 REMARK 3 T33: 0.1455 T12: 0.0107 REMARK 3 T13: 0.0026 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 2.0045 L22: 2.4616 REMARK 3 L33: 2.6010 L12: 1.1425 REMARK 3 L13: 0.2478 L23: -0.5746 REMARK 3 S TENSOR REMARK 3 S11: 0.0253 S12: -0.1048 S13: 0.0260 REMARK 3 S21: -0.0163 S22: -0.0419 S23: 0.0037 REMARK 3 S31: -0.0706 S32: 0.0057 S33: 0.0196 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 9YCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000300275. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MICRO-COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37022 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 41.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.66100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.81067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.62133 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 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 350 REMARK 350 BIOMOLECULE: 3 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: 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 GLY A 3 REMARK 465 ASP A 37 REMARK 465 ASN A 38 REMARK 465 LYS A 39 REMARK 465 VAL A 40 REMARK 465 LYS A 41 REMARK 465 ASP A 42 REMARK 465 LYS A 43 REMARK 465 ALA A 44 REMARK 465 GLU A 45 REMARK 465 GLU A 46 REMARK 465 GLU A 47 REMARK 465 THR A 48 REMARK 465 GLU A 49 REMARK 465 GLU A 50 REMARK 465 LYS A 51 REMARK 465 GLY B 3 REMARK 465 ASP B 37 REMARK 465 ASN B 38 REMARK 465 LYS B 39 REMARK 465 VAL B 40 REMARK 465 LYS B 41 REMARK 465 ASP B 42 REMARK 465 LYS B 43 REMARK 465 ALA B 44 REMARK 465 GLU B 45 REMARK 465 GLU B 46 REMARK 465 GLU B 47 REMARK 465 THR B 48 REMARK 465 GLU B 49 REMARK 465 GLU B 50 REMARK 465 LYS B 51 REMARK 465 ASN C 38 REMARK 465 LYS C 39 REMARK 465 VAL C 40 REMARK 465 LYS C 41 REMARK 465 ASP C 42 REMARK 465 LYS C 43 REMARK 465 ALA C 44 REMARK 465 GLU C 45 REMARK 465 GLU C 46 REMARK 465 GLU C 47 REMARK 465 THR C 48 REMARK 465 GLU C 49 REMARK 465 GLU C 50 REMARK 465 LYS C 51 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 12 CG CD CE NZ REMARK 470 GLU A 15 CG CD OE1 OE2 REMARK 470 GLN A 16 CG CD OE1 NE2 REMARK 470 LYS A 20 CG CD CE NZ REMARK 470 LYS A 35 CG CD CE NZ REMARK 470 LYS B 12 CG CD CE NZ REMARK 470 GLU B 15 CG CD OE1 OE2 REMARK 470 LYS B 35 CG CD CE NZ REMARK 470 GLN B 70 CG CD OE1 NE2 REMARK 470 ARG C 11 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 15 CG CD OE1 OE2 REMARK 470 ASN C 68 CG OD1 ND2 REMARK 470 GLN C 70 CG CD OE1 NE2 REMARK 470 ILE C 127 CG1 CG2 CD1 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 A 363 O HOH A 390 2.03 REMARK 500 O ILE B 127 O HOH B 301 2.03 REMARK 500 O HOH A 395 O HOH A 400 2.11 REMARK 500 O HOH C 334 O HOH C 364 2.12 REMARK 500 O HOH C 348 O HOH C 372 2.14 REMARK 500 O HOH A 337 O HOH A 365 2.15 REMARK 500 OD1 ASN B 104 O HOH B 302 2.16 REMARK 500 O HOH C 337 O HOH C 342 2.16 REMARK 500 O HOH B 332 O HOH B 359 2.17 REMARK 500 OH TYR A 100 O1 GOL A 204 2.19 REMARK 500 O ARG B 8 O HOH B 303 2.19 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 ASN A 18 101.51 -163.42 REMARK 500 ASN B 18 42.55 -160.78 REMARK 500 LEU B 23 78.69 -101.67 REMARK 500 HIS B 86 70.58 -112.48 REMARK 500 GLN C 16 -128.08 56.38 REMARK 500 ASN C 68 22.34 -76.13 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 7 SG REMARK 620 2 HIS A 9 ND1 106.3 REMARK 620 3 CYS A 99 SG 111.9 103.2 REMARK 620 4 CYS A 102 SG 114.0 104.2 115.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 31 SG REMARK 620 2 CYS A 34 SG 116.0 REMARK 620 3 CYS A 65 SG 114.4 114.0 REMARK 620 4 HIS A 73 ND1 103.6 104.6 102.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 57 SG REMARK 620 2 CYS A 60 SG 113.1 REMARK 620 3 HIS A 77 NE2 112.8 99.3 REMARK 620 4 HIS A 86 ND1 107.9 112.5 111.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 7 SG REMARK 620 2 HIS B 9 ND1 110.8 REMARK 620 3 CYS B 99 SG 110.9 96.3 REMARK 620 4 CYS B 102 SG 110.1 113.5 114.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 31 SG REMARK 620 2 CYS B 34 SG 113.2 REMARK 620 3 CYS B 65 SG 123.0 114.2 REMARK 620 4 HIS B 73 ND1 91.4 101.0 108.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 57 SG REMARK 620 2 CYS B 60 SG 114.7 REMARK 620 3 HIS B 77 NE2 113.6 97.6 REMARK 620 4 HIS B 86 ND1 105.1 115.1 111.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 7 SG REMARK 620 2 HIS C 9 ND1 109.9 REMARK 620 3 CYS C 99 SG 110.5 99.6 REMARK 620 4 CYS C 102 SG 114.2 106.8 114.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 31 SG REMARK 620 2 CYS C 34 SG 115.0 REMARK 620 3 CYS C 65 SG 115.3 116.1 REMARK 620 4 HIS C 73 ND1 101.0 102.6 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 57 SG REMARK 620 2 CYS C 60 SG 113.8 REMARK 620 3 HIS C 77 NE2 112.6 99.8 REMARK 620 4 HIS C 86 ND1 107.6 115.9 107.0 REMARK 620 N 1 2 3 DBREF 9YCW A 5 127 UNP Q9Y5T5 UBP16_HUMAN 22 144 DBREF 9YCW B 5 127 UNP Q9Y5T5 UBP16_HUMAN 22 144 DBREF 9YCW C 5 127 UNP Q9Y5T5 UBP16_HUMAN 22 144 SEQADV 9YCW GLY A 3 UNP Q9Y5T5 EXPRESSION TAG SEQADV 9YCW PRO A 4 UNP Q9Y5T5 EXPRESSION TAG SEQADV 9YCW GLY B 3 UNP Q9Y5T5 EXPRESSION TAG SEQADV 9YCW PRO B 4 UNP Q9Y5T5 EXPRESSION TAG SEQADV 9YCW GLY C 3 UNP Q9Y5T5 EXPRESSION TAG SEQADV 9YCW PRO C 4 UNP Q9Y5T5 EXPRESSION TAG SEQRES 1 A 125 GLY PRO PRO VAL CYS ARG HIS ILE ARG LYS GLY LEU GLU SEQRES 2 A 125 GLN GLY ASN LEU LYS LYS ALA LEU VAL ASN VAL GLU TRP SEQRES 3 A 125 ASN ILE CYS GLN ASP CYS LYS THR ASP ASN LYS VAL LYS SEQRES 4 A 125 ASP LYS ALA GLU GLU GLU THR GLU GLU LYS PRO SER VAL SEQRES 5 A 125 TRP LEU CYS LEU LYS CYS GLY HIS GLN GLY CYS GLY ARG SEQRES 6 A 125 ASN SER GLN GLU GLN HIS ALA LEU LYS HIS TYR LEU THR SEQRES 7 A 125 PRO ARG SER GLU PRO HIS CYS LEU VAL LEU SER LEU ASP SEQRES 8 A 125 ASN TRP SER VAL TRP CYS TYR VAL CYS ASP ASN GLU VAL SEQRES 9 A 125 GLN TYR CYS SER SER ASN GLN LEU GLY GLN VAL VAL ASP SEQRES 10 A 125 TYR VAL ARG LYS GLN ALA SER ILE SEQRES 1 B 125 GLY PRO PRO VAL CYS ARG HIS ILE ARG LYS GLY LEU GLU SEQRES 2 B 125 GLN GLY ASN LEU LYS LYS ALA LEU VAL ASN VAL GLU TRP SEQRES 3 B 125 ASN ILE CYS GLN ASP CYS LYS THR ASP ASN LYS VAL LYS SEQRES 4 B 125 ASP LYS ALA GLU GLU GLU THR GLU GLU LYS PRO SER VAL SEQRES 5 B 125 TRP LEU CYS LEU LYS CYS GLY HIS GLN GLY CYS GLY ARG SEQRES 6 B 125 ASN SER GLN GLU GLN HIS ALA LEU LYS HIS TYR LEU THR SEQRES 7 B 125 PRO ARG SER GLU PRO HIS CYS LEU VAL LEU SER LEU ASP SEQRES 8 B 125 ASN TRP SER VAL TRP CYS TYR VAL CYS ASP ASN GLU VAL SEQRES 9 B 125 GLN TYR CYS SER SER ASN GLN LEU GLY GLN VAL VAL ASP SEQRES 10 B 125 TYR VAL ARG LYS GLN ALA SER ILE SEQRES 1 C 125 GLY PRO PRO VAL CYS ARG HIS ILE ARG LYS GLY LEU GLU SEQRES 2 C 125 GLN GLY ASN LEU LYS LYS ALA LEU VAL ASN VAL GLU TRP SEQRES 3 C 125 ASN ILE CYS GLN ASP CYS LYS THR ASP ASN LYS VAL LYS SEQRES 4 C 125 ASP LYS ALA GLU GLU GLU THR GLU GLU LYS PRO SER VAL SEQRES 5 C 125 TRP LEU CYS LEU LYS CYS GLY HIS GLN GLY CYS GLY ARG SEQRES 6 C 125 ASN SER GLN GLU GLN HIS ALA LEU LYS HIS TYR LEU THR SEQRES 7 C 125 PRO ARG SER GLU PRO HIS CYS LEU VAL LEU SER LEU ASP SEQRES 8 C 125 ASN TRP SER VAL TRP CYS TYR VAL CYS ASP ASN GLU VAL SEQRES 9 C 125 GLN TYR CYS SER SER ASN GLN LEU GLY GLN VAL VAL ASP SEQRES 10 C 125 TYR VAL ARG LYS GLN ALA SER ILE HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET GOL A 204 14 HET ZN B 201 1 HET ZN B 202 1 HET ZN B 203 1 HET GOL B 204 14 HET ZN C 201 1 HET ZN C 202 1 HET ZN C 203 1 HET GOL C 204 14 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 ZN 9(ZN 2+) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 16 HOH *252(H2 O) HELIX 1 AA1 HIS A 9 GLU A 15 1 7 HELIX 2 AA2 ASN A 18 LEU A 23 1 6 HELIX 3 AA3 GLN A 72 THR A 80 1 9 HELIX 4 AA4 ASN A 112 SER A 126 1 15 HELIX 5 AA5 HIS B 9 GLU B 15 1 7 HELIX 6 AA6 ASN B 18 LEU B 23 1 6 HELIX 7 AA7 CYS B 31 THR B 36 1 6 HELIX 8 AA8 GLN B 72 THR B 80 1 9 HELIX 9 AA9 ASN B 112 ILE B 127 1 16 HELIX 10 AB1 HIS C 9 GLU C 15 1 7 HELIX 11 AB2 ASN C 18 LEU C 23 1 6 HELIX 12 AB3 GLN C 72 THR C 80 1 9 HELIX 13 AB4 ASN C 112 ALA C 125 1 14 SHEET 1 AA1 5 GLN A 63 CYS A 65 0 SHEET 2 AA1 5 VAL A 54 CYS A 57 -1 N TRP A 55 O GLY A 64 SHEET 3 AA1 5 LEU A 88 SER A 91 -1 O LEU A 90 N LEU A 56 SHEET 4 AA1 5 VAL A 97 CYS A 99 -1 O TRP A 98 N VAL A 89 SHEET 5 AA1 5 ASN A 104 VAL A 106 -1 O VAL A 106 N VAL A 97 SHEET 1 AA2 5 GLN B 63 CYS B 65 0 SHEET 2 AA2 5 VAL B 54 CYS B 57 -1 N TRP B 55 O GLY B 64 SHEET 3 AA2 5 LEU B 88 SER B 91 -1 O LEU B 90 N LEU B 56 SHEET 4 AA2 5 VAL B 97 CYS B 99 -1 O TRP B 98 N VAL B 89 SHEET 5 AA2 5 ASN B 104 VAL B 106 -1 O VAL B 106 N VAL B 97 SHEET 1 AA3 5 GLN C 63 CYS C 65 0 SHEET 2 AA3 5 VAL C 54 CYS C 57 -1 N TRP C 55 O GLY C 64 SHEET 3 AA3 5 LEU C 88 SER C 91 -1 O LEU C 90 N LEU C 56 SHEET 4 AA3 5 VAL C 97 CYS C 99 -1 O TRP C 98 N VAL C 89 SHEET 5 AA3 5 ASN C 104 VAL C 106 -1 O VAL C 106 N VAL C 97 LINK SG CYS A 7 ZN ZN A 201 1555 1555 2.34 LINK ND1 HIS A 9 ZN ZN A 201 1555 1555 2.01 LINK SG CYS A 31 ZN ZN A 202 1555 1555 2.21 LINK SG CYS A 34 ZN ZN A 202 1555 1555 2.35 LINK SG CYS A 57 ZN ZN A 203 1555 1555 2.29 LINK SG CYS A 60 ZN ZN A 203 1555 1555 2.35 LINK SG CYS A 65 ZN ZN A 202 1555 1555 2.30 LINK ND1 HIS A 73 ZN ZN A 202 1555 1555 1.99 LINK NE2 HIS A 77 ZN ZN A 203 1555 1555 1.96 LINK ND1 HIS A 86 ZN ZN A 203 1555 1555 1.97 LINK SG CYS A 99 ZN ZN A 201 1555 1555 2.27 LINK SG CYS A 102 ZN ZN A 201 1555 1555 2.26 LINK SG CYS B 7 ZN ZN B 201 1555 1555 2.43 LINK ND1 HIS B 9 ZN ZN B 201 1555 1555 1.75 LINK SG CYS B 31 ZN ZN B 202 1555 1555 2.09 LINK SG CYS B 34 ZN ZN B 202 1555 1555 2.27 LINK SG CYS B 57 ZN ZN B 203 1555 1555 2.24 LINK SG CYS B 60 ZN ZN B 203 1555 1555 2.10 LINK SG CYS B 65 ZN ZN B 202 1555 1555 2.24 LINK ND1 HIS B 73 ZN ZN B 202 1555 1555 2.00 LINK NE2 HIS B 77 ZN ZN B 203 1555 1555 1.99 LINK ND1 HIS B 86 ZN ZN B 203 1555 1555 2.11 LINK SG CYS B 99 ZN ZN B 201 1555 1555 2.26 LINK SG CYS B 102 ZN ZN B 201 1555 1555 2.19 LINK SG CYS C 7 ZN ZN C 201 1555 1555 2.22 LINK ND1 HIS C 9 ZN ZN C 201 1555 1555 1.98 LINK SG CYS C 31 ZN ZN C 202 1555 1555 2.16 LINK SG CYS C 34 ZN ZN C 202 1555 1555 2.30 LINK SG CYS C 57 ZN ZN C 203 1555 1555 2.27 LINK SG CYS C 60 ZN ZN C 203 1555 1555 2.28 LINK SG CYS C 65 ZN ZN C 202 1555 1555 2.21 LINK ND1 HIS C 73 ZN ZN C 202 1555 1555 2.27 LINK NE2 HIS C 77 ZN ZN C 203 1555 1555 2.03 LINK ND1 HIS C 86 ZN ZN C 203 1555 1555 1.96 LINK SG CYS C 99 ZN ZN C 201 1555 1555 2.30 LINK SG CYS C 102 ZN ZN C 201 1555 1555 2.32 CRYST1 84.390 84.390 50.432 90.00 90.00 120.00 P 31 9 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 0.011850 0.006841 0.000000 0.00000 SCALE2 0.000000 0.013683 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019829 0.00000 CONECT 50 5045 CONECT 85 5045 CONECT 407 5046 CONECT 446 5046 CONECT 561 5047 CONECT 612 5047 CONECT 670 5046 CONECT 786 5046 CONECT 857 5047 CONECT 1003 5047 CONECT 1215 5045 CONECT 1262 5045 CONECT 1716 5062 CONECT 1751 5062 CONECT 2109 5063 CONECT 2148 5063 CONECT 2263 5064 CONECT 2314 5064 CONECT 2372 5063 CONECT 2478 5063 CONECT 2549 5064 CONECT 2695 5064 CONECT 2907 5062 CONECT 2954 5062 CONECT 3419 5079 CONECT 3454 5079 CONECT 3799 5080 CONECT 3838 5080 CONECT 3980 5081 CONECT 4031 5081 CONECT 4089 5080 CONECT 4188 5080 CONECT 4259 5081 CONECT 4405 5081 CONECT 4617 5079 CONECT 4664 5079 CONECT 5045 50 85 1215 1262 CONECT 5046 407 446 670 786 CONECT 5047 561 612 857 1003 CONECT 5048 5049 5050 5054 5055 CONECT 5049 5048 5056 CONECT 5050 5048 5051 5052 5057 CONECT 5051 5050 5058 CONECT 5052 5050 5053 5059 5060 CONECT 5053 5052 5061 CONECT 5054 5048 CONECT 5055 5048 CONECT 5056 5049 CONECT 5057 5050 CONECT 5058 5051 CONECT 5059 5052 CONECT 5060 5052 CONECT 5061 5053 CONECT 5062 1716 1751 2907 2954 CONECT 5063 2109 2148 2372 2478 CONECT 5064 2263 2314 2549 2695 CONECT 5065 5066 5067 5071 5072 CONECT 5066 5065 5073 CONECT 5067 5065 5068 5069 5074 CONECT 5068 5067 5075 CONECT 5069 5067 5070 5076 5077 CONECT 5070 5069 5078 CONECT 5071 5065 CONECT 5072 5065 CONECT 5073 5066 CONECT 5074 5067 CONECT 5075 5068 CONECT 5076 5069 CONECT 5077 5069 CONECT 5078 5070 CONECT 5079 3419 3454 4617 4664 CONECT 5080 3799 3838 4089 4188 CONECT 5081 3980 4031 4259 4405 CONECT 5082 5083 5084 5088 5089 CONECT 5083 5082 5090 CONECT 5084 5082 5085 5086 5091 CONECT 5085 5084 5092 CONECT 5086 5084 5087 5093 5094 CONECT 5087 5086 5095 CONECT 5088 5082 CONECT 5089 5082 CONECT 5090 5083 CONECT 5091 5084 CONECT 5092 5085 CONECT 5093 5086 CONECT 5094 5086 CONECT 5095 5087 MASTER 462 0 12 13 15 0 0 6 2851 3 87 30 END