PDB Short entry for 3IFW HEADER HYDROLASE/HYDROLASE INHIBITOR 26-JUL-09 3IFW TITLE CRYSTAL STRUCTURE OF THE S18Y VARIANT OF UBIQUITIN CARBOXY TERMINAL TITLE 2 HYDROLASE L1 BOUND TO UBIQUITIN VINYLMETHYLESTER. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UCH-L1, UBIQUITIN THIOESTERASE L1, NEURON CYTOPLASMIC COMPND 5 PROTEIN 9.5, PGP 9.5, PGP9.5; COMPND 6 EC: 3.4.19.12, 6.-.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UBIQUITIN; COMPND 11 CHAIN: B; COMPND 12 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: PGP9.5, UCHL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: RPS27A, UBA52, UBA80, UBB, UBC, UBCEP1, UBCEP2, UBIQ_HUMAN; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PTYB1 KEYWDS ENZYME-SUICIDE SUBSTRATE COMPLEX, CYTOPLASM, DISEASE MUTATION, KEYWDS 2 GLYCOPROTEIN, HYDROLASE, LIGASE, OXIDATION, POLYMORPHISM, PROTEASE, KEYWDS 3 THIOL PROTEASE, UBL CONJUGATION PATHWAY, ISOPEPTIDE BOND, NUCLEUS, KEYWDS 4 PHOSPHOPROTEIN, UBL CONJUGATION, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 5 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.DAS,D.BOUDREAUX,T.MAITI REVDAT 3 06-SEP-23 3IFW 1 REMARK REVDAT 2 13-OCT-21 3IFW 1 REMARK SEQADV LINK REVDAT 1 16-JUN-10 3IFW 0 JRNL AUTH D.A.BOUDREAUX,T.K.MAITI,C.W.DAVIES,C.DAS JRNL TITL UBIQUITIN VINYL METHYL ESTER BINDING ORIENTS THE MISALIGNED JRNL TITL 2 ACTIVE SITE OF THE UBIQUITIN HYDROLASE UCHL1 INTO PRODUCTIVE JRNL TITL 3 CONFORMATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 9117 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20439756 JRNL DOI 10.1073/PNAS.0910870107 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 10699 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 539 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 749 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2344 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.06000 REMARK 3 B12 (A**2) : 0.02000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.762 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.298 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.269 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.693 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2391 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3215 ; 0.896 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 296 ; 4.923 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;37.933 ;25.391 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 445 ;15.346 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;12.056 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 358 ; 0.054 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1794 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1016 ; 0.172 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1618 ; 0.291 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 95 ; 0.097 ; 0.200 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): 66 ; 0.186 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.087 ; 0.200 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): 1531 ; 0.162 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2382 ; 0.282 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 947 ; 0.507 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 833 ; 0.762 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 3IFW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0032 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11248 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.09400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : 0.60000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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 2ETL PDB ENTRY 1XD3, CHAIN B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M AMMONIUM SULFATE, 0.1M BICINE, REMARK 280 PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 43.65200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 25.20249 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 64.51467 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 43.65200 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 25.20249 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 64.51467 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 43.65200 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 25.20249 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 64.51467 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 43.65200 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 25.20249 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 64.51467 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 43.65200 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 25.20249 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 64.51467 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 43.65200 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 25.20249 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 64.51467 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 50.40499 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 129.02933 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 50.40499 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 129.02933 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 50.40499 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 129.02933 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 50.40499 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 129.02933 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 50.40499 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 129.02933 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 50.40499 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 129.02933 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 300 REMARK: THE BIOLOGICAL UNIT IS A HETERODIMER CONSIST OF CHAIN A AND REMARK 300 B IN THE ASYMMETRIC UNIT. 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: 2660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 225 LIES ON A SPECIAL POSITION. 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 -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 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 SG CYS A 90 CB GVE B 76 1.80 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 LEU A 70 39.27 -77.55 REMARK 500 LYS A 71 -70.88 -36.35 REMARK 500 ASP A 155 -60.36 -27.69 REMARK 500 ASP A 156 -104.19 59.74 REMARK 500 LYS A 157 -74.29 -65.01 REMARK 500 VAL A 158 107.21 -43.21 REMARK 500 GLU A 208 66.87 -104.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GVE B 76 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ETL RELATED DB: PDB REMARK 900 STRUCTURE OF WILD TYPE UCHL1 DBREF 3IFW A 1 223 UNP P09936 UCHL1_HUMAN 1 223 DBREF 3IFW B 1 75 UNP P62988 UBIQ_HUMAN 1 75 SEQADV 3IFW GLY A -4 UNP P09936 EXPRESSION TAG SEQADV 3IFW PRO A -3 UNP P09936 EXPRESSION TAG SEQADV 3IFW LEU A -2 UNP P09936 EXPRESSION TAG SEQADV 3IFW GLY A -1 UNP P09936 EXPRESSION TAG SEQADV 3IFW SER A 0 UNP P09936 EXPRESSION TAG SEQADV 3IFW TYR A 18 UNP P09936 SER 18 ENGINEERED MUTATION SEQRES 1 A 228 GLY PRO LEU GLY SER MET GLN LEU LYS PRO MET GLU ILE SEQRES 2 A 228 ASN PRO GLU MET LEU ASN LYS VAL LEU TYR ARG LEU GLY SEQRES 3 A 228 VAL ALA GLY GLN TRP ARG PHE VAL ASP VAL LEU GLY LEU SEQRES 4 A 228 GLU GLU GLU SER LEU GLY SER VAL PRO ALA PRO ALA CYS SEQRES 5 A 228 ALA LEU LEU LEU LEU PHE PRO LEU THR ALA GLN HIS GLU SEQRES 6 A 228 ASN PHE ARG LYS LYS GLN ILE GLU GLU LEU LYS GLY GLN SEQRES 7 A 228 GLU VAL SER PRO LYS VAL TYR PHE MET LYS GLN THR ILE SEQRES 8 A 228 GLY ASN SER CYS GLY THR ILE GLY LEU ILE HIS ALA VAL SEQRES 9 A 228 ALA ASN ASN GLN ASP LYS LEU GLY PHE GLU ASP GLY SER SEQRES 10 A 228 VAL LEU LYS GLN PHE LEU SER GLU THR GLU LYS MET SER SEQRES 11 A 228 PRO GLU ASP ARG ALA LYS CYS PHE GLU LYS ASN GLU ALA SEQRES 12 A 228 ILE GLN ALA ALA HIS ASP ALA VAL ALA GLN GLU GLY GLN SEQRES 13 A 228 CYS ARG VAL ASP ASP LYS VAL ASN PHE HIS PHE ILE LEU SEQRES 14 A 228 PHE ASN ASN VAL ASP GLY HIS LEU TYR GLU LEU ASP GLY SEQRES 15 A 228 ARG MET PRO PHE PRO VAL ASN HIS GLY ALA SER SER GLU SEQRES 16 A 228 ASP THR LEU LEU LYS ASP ALA ALA LYS VAL CYS ARG GLU SEQRES 17 A 228 PHE THR GLU ARG GLU GLN GLY GLU VAL ARG PHE SER ALA SEQRES 18 A 228 VAL ALA LEU CYS LYS ALA ALA SEQRES 1 B 75 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 75 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 75 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 75 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 75 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 75 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY HET GVE B 76 8 HETNAM GVE METHYL 4-AMINOBUTANOATE FORMUL 3 GVE C5 H11 N O2 FORMUL 4 HOH *51(H2 O) HELIX 1 1 ASN A 9 LEU A 20 1 12 HELIX 2 2 GLU A 35 GLY A 40 1 6 HELIX 3 3 THR A 56 GLU A 68 1 13 HELIX 4 4 SER A 89 ASN A 101 1 13 HELIX 5 5 SER A 112 THR A 121 1 10 HELIX 6 6 SER A 125 LYS A 135 1 11 HELIX 7 7 ASN A 136 GLN A 148 1 13 HELIX 8 8 THR A 192 GLU A 208 1 17 HELIX 9 9 THR B 22 GLY B 35 1 14 HELIX 10 10 PRO B 37 ASP B 39 5 3 HELIX 11 11 LEU B 56 ASN B 60 5 5 SHEET 1 A 2 MET A 6 GLU A 7 0 SHEET 2 A 2 ARG B 74 GLY B 75 -1 O GLY B 75 N MET A 6 SHEET 1 B 2 VAL A 22 ALA A 23 0 SHEET 2 B 2 GLY A 107 PHE A 108 -1 O GLY A 107 N ALA A 23 SHEET 1 C 6 TRP A 26 ASP A 30 0 SHEET 2 C 6 SER A 215 LYS A 221 -1 O ALA A 218 N VAL A 29 SHEET 3 C 6 ALA A 46 PRO A 54 -1 N LEU A 52 O SER A 215 SHEET 4 C 6 PHE A 160 VAL A 168 -1 O PHE A 165 N LEU A 49 SHEET 5 C 6 HIS A 171 LEU A 175 -1 O LEU A 175 N LEU A 164 SHEET 6 C 6 VAL A 183 ALA A 187 -1 O HIS A 185 N LEU A 172 SHEET 1 D 5 THR B 12 GLU B 16 0 SHEET 2 D 5 GLN B 2 THR B 7 -1 N VAL B 5 O ILE B 13 SHEET 3 D 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 D 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 D 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK C GLY B 75 N GVE B 76 1555 1555 1.33 CISPEP 1 ALA A 44 PRO A 45 0 1.79 SITE 1 AC1 6 LEU A 55 GLN A 84 ASN A 88 CYS A 90 SITE 2 AC1 6 PHE A 160 GLY B 75 CRYST1 87.304 87.304 193.544 90.00 90.00 120.00 H 3 2 18 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 0.011454 0.006613 0.000000 0.00000 SCALE2 0.000000 0.013226 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005167 0.00000