PDB Short entry for 1UCH HEADER CYSTEINE PROTEASE 06-OCT-97 1UCH TITLE DEUBIQUITINATING ENZYME UCH-L3 (HUMAN) AT 1.8 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN C-TERMINAL HYDROLASE UCH-L3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UCH-L3,DUB; COMPND 5 EC: 3.1.2.15; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: B834 (DE3); SOURCE 6 TISSUE: HEMATOPOETIC; SOURCE 7 CELLULAR_LOCATION: CYTOPLASM; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 11 EXPRESSION_SYSTEM_VARIANT: GAL-MET- AUXOTROPH; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: B834 (DE3); SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PRSL3 KEYWDS CYSTEINE PROTEASE, DEUBIQUITINATING ENZYME, UBIQUITIN, C-TERMINAL KEYWDS 2 HYDROLASE, UBIQUITIN CONJUGATION EXPDTA X-RAY DIFFRACTION AUTHOR S.C.JOHNSTON,C.N.LARSEN,W.J.COOK,K.D.WILKINSON,C.P.HILL REVDAT 4 14-FEB-24 1UCH 1 REMARK REVDAT 3 24-FEB-09 1UCH 1 VERSN REVDAT 2 24-JUN-98 1UCH 1 COMPND REVDAT 1 28-JAN-98 1UCH 0 JRNL AUTH S.C.JOHNSTON,C.N.LARSEN,W.J.COOK,K.D.WILKINSON,C.P.HILL JRNL TITL CRYSTAL STRUCTURE OF A DEUBIQUITINATING ENZYME (HUMAN JRNL TITL 2 UCH-L3) AT 1.8 A RESOLUTION. JRNL REF EMBO J. V. 16 3787 1997 JRNL REFN ISSN 0261-4189 JRNL PMID 9233788 JRNL DOI 10.1093/EMBOJ/16.13.3787 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 21819 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 SET) : 0.232 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1056 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3296 REMARK 3 BIN R VALUE (WORKING SET) : 0.3580 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 164 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1660 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.40 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.28 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.980 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.170 ; 0.750 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.290 ; 1.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.730 ; 1.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.670 ; 1.250 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THERE IS A DISORDERED REGION BETWEEN RESIDUES 146 AND REMARK 3 167. REMARK 4 REMARK 4 1UCH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.080 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23334 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : 0.04000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000 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) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.19000 REMARK 200 R SYM FOR SHELL (I) : 0.19000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: X-PLOR 3.843 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN AT 12 MG/ML WAS CRYSTALLIZED REMARK 280 FROM 26%(W/W) PEG 4000, 200 MM SODIUM ACETATE, 100 MM PIPES PH REMARK 280 6.7 AND 10 MM DTT IN SITTING WELLS AT 4 DEGREES CELSIUS., VAPOR REMARK 280 DIFFUSION - SITTING DROP, TEMPERATURE 277K, VAPOR DIFFUSION, REMARK 280 SITTING DROP 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 24.30000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.70000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.70000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.30000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.45000 REMARK 290 SMTRY3 4 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: 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 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 1 REMARK 465 GLU A 2 REMARK 465 GLY A 3 REMARK 465 GLN A 4 REMARK 465 THR A 147 REMARK 465 HIS A 148 REMARK 465 GLU A 149 REMARK 465 THR A 150 REMARK 465 SER A 151 REMARK 465 ALA A 152 REMARK 465 HIS A 153 REMARK 465 GLU A 154 REMARK 465 GLY A 155 REMARK 465 GLN A 156 REMARK 465 THR A 157 REMARK 465 GLU A 158 REMARK 465 ALA A 159 REMARK 465 PRO A 160 REMARK 465 SER A 161 REMARK 465 ILE A 162 REMARK 465 ASP A 163 REMARK 465 GLU A 164 REMARK 465 LYS A 165 REMARK 465 VAL A 166 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 136 CD NE CZ NH1 NH2 REMARK 480 ARG A 145 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 199 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 62 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE RESIDUES. DBREF 1UCH A 1 230 UNP P15374 UBL3_HUMAN 1 230 SEQRES 1 A 230 MET GLU GLY GLN ARG TRP LEU PRO LEU GLU ALA ASN PRO SEQRES 2 A 230 GLU VAL THR ASN GLN PHE LEU LYS GLN LEU GLY LEU HIS SEQRES 3 A 230 PRO ASN TRP GLN PHE VAL ASP VAL TYR GLY MET ASP PRO SEQRES 4 A 230 GLU LEU LEU SER MET VAL PRO ARG PRO VAL CYS ALA VAL SEQRES 5 A 230 LEU LEU LEU PHE PRO ILE THR GLU LYS TYR GLU VAL PHE SEQRES 6 A 230 ARG THR GLU GLU GLU GLU LYS ILE LYS SER GLN GLY GLN SEQRES 7 A 230 ASP VAL THR SER SER VAL TYR PHE MET LYS GLN THR ILE SEQRES 8 A 230 SER ASN ALA CYS GLY THR ILE GLY LEU ILE HIS ALA ILE SEQRES 9 A 230 ALA ASN ASN LYS ASP LYS MET HIS PHE GLU SER GLY SER SEQRES 10 A 230 THR LEU LYS LYS PHE LEU GLU GLU SER VAL SER MET SER SEQRES 11 A 230 PRO GLU GLU ARG ALA ARG TYR LEU GLU ASN TYR ASP ALA SEQRES 12 A 230 ILE ARG VAL THR HIS GLU THR SER ALA HIS GLU GLY GLN SEQRES 13 A 230 THR GLU ALA PRO SER ILE ASP GLU LYS VAL ASP LEU HIS SEQRES 14 A 230 PHE ILE ALA LEU VAL HIS VAL ASP GLY HIS LEU TYR GLU SEQRES 15 A 230 LEU ASP GLY ARG LYS PRO PHE PRO ILE ASN HIS GLY GLU SEQRES 16 A 230 THR SER ASP GLU THR LEU LEU GLU ASP ALA ILE GLU VAL SEQRES 17 A 230 CYS LYS LYS PHE MET GLU ARG ASP PRO ASP GLU LEU ARG SEQRES 18 A 230 PHE ASN ALA ILE ALA LEU SER ALA ALA FORMUL 2 HOH *104(H2 O) HELIX 1 1 PRO A 13 GLN A 22 1 10 HELIX 2 2 PRO A 39 MET A 44 1 6 HELIX 3 3 GLU A 60 GLN A 76 1 17 HELIX 4 4 SER A 92 LYS A 110 5 19 HELIX 5 5 THR A 118 GLU A 125 1 8 HELIX 6 6 PRO A 131 ASN A 140 1 10 HELIX 7 7 LEU A 201 ASP A 216 1 16 SHEET 1 A 5 TRP A 29 VAL A 34 0 SHEET 2 A 5 ASN A 223 ALA A 229 -1 N SER A 228 O GLN A 30 SHEET 3 A 5 VAL A 49 PRO A 57 -1 N LEU A 55 O ASN A 223 SHEET 4 A 5 LEU A 168 VAL A 176 -1 N LEU A 173 O VAL A 52 SHEET 5 A 5 HIS A 179 LEU A 183 -1 N LEU A 183 O ALA A 172 CISPEP 1 ARG A 47 PRO A 48 0 -12.52 SITE 1 CAT 4 GLN A 89 CYS A 95 HIS A 169 ASP A 184 CRYST1 48.600 60.900 81.400 90.00 90.00 90.00 P 21 21 21 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 0.020576 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012285 0.00000