PDB Short entry for 1CMX HEADER HYDROLASE 12-MAY-99 1CMX TITLE STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL TITLE 2 HYDROLASES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (UBIQUITIN YUH1-UBAL); COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: ALL; COMPND 5 EC: 3.1.2.15; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: UBIQUITIN C-TERMINUS MODIFIED TO AN ALDEHYDE; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROTEIN (UBIQUITIN YUH1-UBAL); COMPND 10 CHAIN: B, D; COMPND 11 FRAGMENT: ALL; COMPND 12 EC: 3.1.2.15; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: UBIQUITIN C-TERMINUS MODIFIED TO AN ALDEHYDE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 4 OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF PLASMID P- SOURCE 5 1A2/TRPYUH1-1 OF SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). THE SOURCE 6 EXPRESSION SYSTEM WAS ESCHERICHIA COLI, STRAIN MM294, PLASMID P- SOURCE 7 1A2/TRPYUH1-1.; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 11 OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF PLASMID P- SOURCE 12 1A2/TRPYUH1-1 OF SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). THE SOURCE 13 EXPRESSION SYSTEM WAS ESCHERICHIA COLI, STRAIN MM294, PLASMID P- SOURCE 14 1A2/TRPYUH1-1. KEYWDS UBIQUITIN HYDROLASE, UBIQUITIN, DEUBIQUITINATING ENZYME, CYSTEINE KEYWDS 2 PROTEASE, ENZYME SPECIFICITY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.C.JOHNSTON,S.M.RIDDLE,R.E.COHEN,C.P.HILL REVDAT 3 27-DEC-23 1CMX 1 LINK REVDAT 2 24-FEB-09 1CMX 1 VERSN REVDAT 1 27-JUL-99 1CMX 0 JRNL AUTH S.C.JOHNSTON,S.M.RIDDLE,R.E.COHEN,C.P.HILL JRNL TITL STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL JRNL TITL 2 HYDROLASES. JRNL REF EMBO J. V. 18 3877 1999 JRNL REFN ISSN 0261-4189 JRNL PMID 10406793 JRNL DOI 10.1093/EMBOJ/18.14.3877 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.C.JOHNSTON,C.N.LARSEN,W.J.COOK,K.D.WILKINSON,C.P.HILL REMARK 1 TITL CRYSTAL STRUCTURE OF A DEUBIQUITINATING ENZYME (HUMAN REMARK 1 TITL 2 UCH-L3) AT 1.8 A RESOLUTION REMARK 1 REF EMBO J. V. 16 3787 1997 REMARK 1 REFN ISSN 0261-4189 REMARK 1 DOI 10.1093/EMBOJ/16.13.3787 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 26106 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) : 0.248 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1262 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2995 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE : 0.4300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 174 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4067 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.00 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.790 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.870 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) : 4.071 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.929 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.456 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.480 ; 2.500 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_UBAL.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX_UBAL.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CMX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000001055. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 : NULL 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 : 26106 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 6000 0.1 M SODIUM ACETATE PH REMARK 280 4.4, PH 4.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+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 1.000000 0.000000 0.000000 99.65000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.53295 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.26667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 99.65000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 57.53295 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 12.26667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 99.65000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 57.53295 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 12.26667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 115.06591 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 24.53333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 115.06591 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 24.53333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 115.06591 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 24.53333 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 400 REMARK 400 COMPOUND REMARK 400 TER REMARK 400 GLY: MODIFIED TO ALDEHYDE REMARK 400 GLY: MODIFIED TO ALDEHYDE 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 SER A 2 REMARK 465 GLY A 3 REMARK 465 GLU A 4 REMARK 465 ASN A 5 REMARK 465 GLU A 63 REMARK 465 ASP A 64 REMARK 465 ARG A 65 REMARK 465 LYS A 66 REMARK 465 SER A 67 REMARK 465 SER A 68 REMARK 465 THR A 69 REMARK 465 SER A 70 REMARK 465 GLN A 71 REMARK 465 GLN A 72 REMARK 465 ILE A 73 REMARK 465 THR A 74 REMARK 465 SER A 75 REMARK 465 SER A 76 REMARK 465 TYR A 77 REMARK 465 TRP A 235 REMARK 465 MET C 401 REMARK 465 SER C 402 REMARK 465 GLY C 403 REMARK 465 GLU C 404 REMARK 465 ASN C 405 REMARK 465 ARG C 406 REMARK 465 ILE C 461 REMARK 465 ASN C 462 REMARK 465 GLU C 463 REMARK 465 ASP C 464 REMARK 465 ARG C 465 REMARK 465 LYS C 466 REMARK 465 SER C 467 REMARK 465 SER C 468 REMARK 465 THR C 469 REMARK 465 SER C 470 REMARK 465 GLN C 471 REMARK 465 GLN C 472 REMARK 465 ILE C 473 REMARK 465 THR C 474 REMARK 465 SER C 475 REMARK 465 SER C 476 REMARK 465 TYR C 477 REMARK 465 ASP C 478 REMARK 465 TRP C 635 REMARK 465 MET D 701 REMARK 465 GLN D 702 REMARK 465 ILE D 703 REMARK 465 PHE D 704 REMARK 465 VAL D 705 REMARK 465 LYS D 711 REMARK 465 THR D 712 REMARK 465 ILE D 713 REMARK 465 THR D 714 REMARK 465 LEU D 715 REMARK 465 GLU D 716 REMARK 465 VAL D 717 REMARK 465 GLU D 718 REMARK 465 PRO D 719 REMARK 465 SER D 720 REMARK 465 ASP D 721 REMARK 465 THR D 722 REMARK 465 ILE D 723 REMARK 465 GLU D 724 REMARK 465 ASN D 725 REMARK 465 VAL D 726 REMARK 465 LYS D 727 REMARK 465 ALA D 728 REMARK 465 LYS D 729 REMARK 465 ILE D 730 REMARK 465 GLN D 731 REMARK 465 ASP D 732 REMARK 465 LYS D 733 REMARK 465 GLU D 734 REMARK 465 GLY D 735 REMARK 465 ILE D 736 REMARK 465 PRO D 737 REMARK 465 PRO D 738 REMARK 465 ASP D 739 REMARK 465 ILE D 744 REMARK 465 PHE D 745 REMARK 465 ALA D 746 REMARK 465 GLY D 747 REMARK 465 LYS D 748 REMARK 465 GLN D 749 REMARK 465 LEU D 750 REMARK 465 GLU D 751 REMARK 465 ASP D 752 REMARK 465 GLY D 753 REMARK 465 ARG D 754 REMARK 465 THR D 755 REMARK 465 LEU D 756 REMARK 465 SER D 757 REMARK 465 ASP D 758 REMARK 465 TYR D 759 REMARK 465 ASN D 760 REMARK 465 ILE D 761 REMARK 465 GLN D 762 REMARK 465 LYS D 763 REMARK 465 GLU D 764 REMARK 465 SER D 765 REMARK 465 THR D 766 REMARK 465 LEU D 767 REMARK 465 HIS D 768 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 GLU A 16 CG CD OE1 OE2 REMARK 480 ARG A 128 CG CD NE CZ NH1 NH2 REMARK 480 GLU B 324 CG CD OE1 OE2 REMARK 480 ARG B 354 CG CD NE CZ NH1 NH2 REMARK 480 LYS C 483 CG CD CE NZ REMARK 480 ARG C 528 CG CD NE CZ NH1 NH2 REMARK 480 ASP C 535 CG OD1 OD2 REMARK 480 LYS C 543 CG CD CE NZ REMARK 480 ARG C 583 CB CG CD NE CZ NH1 NH2 REMARK 480 ARG D 742 CG CD NE CZ NH1 NH2 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 THR C 440 N - CA - CB ANGL. DEV. = 12.8 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 LEU A 39 69.27 -114.45 REMARK 500 THR A 40 59.21 144.89 REMARK 500 ILE A 61 58.86 -68.48 REMARK 500 ASN A 102 41.11 -140.42 REMARK 500 SER A 124 -76.18 -57.08 REMARK 500 ASN A 127 -1.38 -162.53 REMARK 500 THR A 151 -179.33 -65.61 REMARK 500 ALA A 159 -38.95 -39.05 REMARK 500 ASN A 164 -9.21 69.85 REMARK 500 GLU A 173 -95.28 -101.85 REMARK 500 THR A 197 31.27 -95.43 REMARK 500 ASP A 200 -161.78 -172.57 REMARK 500 ASN A 225 75.83 -69.88 REMARK 500 ASP B 352 -39.63 -39.29 REMARK 500 GLU B 364 -0.10 74.10 REMARK 500 LEU C 439 65.33 -113.46 REMARK 500 THR C 440 33.54 159.71 REMARK 500 SER C 510 172.56 -57.14 REMARK 500 SER C 524 -78.60 -54.97 REMARK 500 ASN C 527 3.76 -170.61 REMARK 500 ASP C 531 -157.96 -78.36 REMARK 500 SER C 554 -168.44 -120.76 REMARK 500 ASN C 564 -6.19 72.66 REMARK 500 ASP C 622 18.63 58.25 REMARK 500 ARG D 742 111.26 -161.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: CYSTEINE PROTEASE DBREF 1CMX A 1 235 UNP P35127 UBL1_YEAST 1 235 DBREF 1CMX B 301 376 UNP P02248 UBIQ_HUMANX 1 75 DBREF 1CMX C 401 635 UNP P35127 UBL1_YEAST 1 235 DBREF 1CMX D 701 776 UNP P02248 UBIQ_HUMANX 1 75 SEQRES 1 A 235 MET SER GLY GLU ASN ARG ALA VAL VAL PRO ILE GLU SER SEQRES 2 A 235 ASN PRO GLU VAL PHE THR ASN PHE ALA HIS LYS LEU GLY SEQRES 3 A 235 LEU LYS ASN GLU TRP ALA TYR PHE ASP ILE TYR SER LEU SEQRES 4 A 235 THR GLU PRO GLU LEU LEU ALA PHE LEU PRO ARG PRO VAL SEQRES 5 A 235 LYS ALA ILE VAL LEU LEU PHE PRO ILE ASN GLU ASP ARG SEQRES 6 A 235 LYS SER SER THR SER GLN GLN ILE THR SER SER TYR ASP SEQRES 7 A 235 VAL ILE TRP PHE LYS GLN SER VAL LYS ASN ALA CYS GLY SEQRES 8 A 235 LEU TYR ALA ILE LEU HIS SER LEU SER ASN ASN GLN SER SEQRES 9 A 235 LEU LEU GLU PRO GLY SER ASP LEU ASP ASN PHE LEU LYS SEQRES 10 A 235 SER GLN SER ASP THR SER SER SER LYS ASN ARG PHE ASP SEQRES 11 A 235 ASP VAL THR THR ASP GLN PHE VAL LEU ASN VAL ILE LYS SEQRES 12 A 235 GLU ASN VAL GLN THR PHE SER THR GLY GLN SER GLU ALA SEQRES 13 A 235 PRO GLU ALA THR ALA ASP THR ASN LEU HIS TYR ILE THR SEQRES 14 A 235 TYR VAL GLU GLU ASN GLY GLY ILE PHE GLU LEU ASP GLY SEQRES 15 A 235 ARG ASN LEU SER GLY PRO LEU TYR LEU GLY LYS SER ASP SEQRES 16 A 235 PRO THR ALA THR ASP LEU ILE GLU GLN GLU LEU VAL ARG SEQRES 17 A 235 VAL ARG VAL ALA SER TYR MET GLU ASN ALA ASN GLU GLU SEQRES 18 A 235 ASP VAL LEU ASN PHE ALA MET LEU GLY LEU GLY PRO ASN SEQRES 19 A 235 TRP SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLZ SEQRES 1 C 235 MET SER GLY GLU ASN ARG ALA VAL VAL PRO ILE GLU SER SEQRES 2 C 235 ASN PRO GLU VAL PHE THR ASN PHE ALA HIS LYS LEU GLY SEQRES 3 C 235 LEU LYS ASN GLU TRP ALA TYR PHE ASP ILE TYR SER LEU SEQRES 4 C 235 THR GLU PRO GLU LEU LEU ALA PHE LEU PRO ARG PRO VAL SEQRES 5 C 235 LYS ALA ILE VAL LEU LEU PHE PRO ILE ASN GLU ASP ARG SEQRES 6 C 235 LYS SER SER THR SER GLN GLN ILE THR SER SER TYR ASP SEQRES 7 C 235 VAL ILE TRP PHE LYS GLN SER VAL LYS ASN ALA CYS GLY SEQRES 8 C 235 LEU TYR ALA ILE LEU HIS SER LEU SER ASN ASN GLN SER SEQRES 9 C 235 LEU LEU GLU PRO GLY SER ASP LEU ASP ASN PHE LEU LYS SEQRES 10 C 235 SER GLN SER ASP THR SER SER SER LYS ASN ARG PHE ASP SEQRES 11 C 235 ASP VAL THR THR ASP GLN PHE VAL LEU ASN VAL ILE LYS SEQRES 12 C 235 GLU ASN VAL GLN THR PHE SER THR GLY GLN SER GLU ALA SEQRES 13 C 235 PRO GLU ALA THR ALA ASP THR ASN LEU HIS TYR ILE THR SEQRES 14 C 235 TYR VAL GLU GLU ASN GLY GLY ILE PHE GLU LEU ASP GLY SEQRES 15 C 235 ARG ASN LEU SER GLY PRO LEU TYR LEU GLY LYS SER ASP SEQRES 16 C 235 PRO THR ALA THR ASP LEU ILE GLU GLN GLU LEU VAL ARG SEQRES 17 C 235 VAL ARG VAL ALA SER TYR MET GLU ASN ALA ASN GLU GLU SEQRES 18 C 235 ASP VAL LEU ASN PHE ALA MET LEU GLY LEU GLY PRO ASN SEQRES 19 C 235 TRP SEQRES 1 D 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 D 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 D 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 D 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 D 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 D 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLZ MODRES 1CMX GLZ B 376 GLY AMINO-ACETALDEHYDE MODRES 1CMX GLZ D 776 GLY AMINO-ACETALDEHYDE HET GLZ B 376 4 HET GLZ D 776 4 HETNAM GLZ AMINO-ACETALDEHYDE FORMUL 2 GLZ 2(C2 H5 N O) FORMUL 5 HOH *75(H2 O) HELIX 1 1 PRO A 15 LEU A 25 1 11 HELIX 2 2 LEU A 44 ALA A 46 5 3 HELIX 3 3 CYS A 90 SER A 100 1 11 HELIX 4 4 GLN A 103 LEU A 105 5 3 HELIX 5 5 ASP A 111 THR A 122 1 12 HELIX 6 6 VAL A 132 LYS A 143 1 12 HELIX 7 7 VAL A 146 SER A 150 1 5 HELIX 8 8 LEU A 201 GLU A 203 5 3 HELIX 9 9 GLU A 205 GLU A 221 1 17 HELIX 10 10 ILE B 323 GLU B 334 1 12 HELIX 11 11 PRO B 338 GLN B 340 5 3 HELIX 12 12 PRO C 415 LEU C 425 1 11 HELIX 13 13 GLU C 443 LEU C 445 5 3 HELIX 14 14 CYS C 490 SER C 500 1 11 HELIX 15 15 GLN C 503 LEU C 505 5 3 HELIX 16 16 ASP C 511 ASP C 521 1 11 HELIX 17 17 VAL C 532 GLU C 544 1 13 HELIX 18 18 VAL C 546 SER C 550 5 5 HELIX 19 19 LEU C 601 GLU C 603 5 3 HELIX 20 20 GLU C 605 GLU C 620 1 16 SHEET 1 A 6 TRP A 31 ILE A 36 0 SHEET 2 A 6 ALA A 227 PRO A 233 -1 N GLY A 232 O ALA A 32 SHEET 3 A 6 ALA A 54 PRO A 60 -1 N LEU A 58 O ALA A 227 SHEET 4 A 6 LEU A 165 GLU A 172 -1 N TYR A 170 O ILE A 55 SHEET 5 A 6 GLY A 176 LEU A 180 -1 N LEU A 180 O THR A 169 SHEET 6 A 6 LEU A 189 LYS A 193 -1 N GLY A 192 O ILE A 177 SHEET 1 B 4 THR B 312 GLU B 316 0 SHEET 2 B 4 GLN B 302 LYS B 306 -1 N VAL B 305 O ILE B 313 SHEET 3 B 4 THR B 366 LEU B 371 1 N LEU B 367 O PHE B 304 SHEET 4 B 4 GLN B 341 ILE B 344 -1 N ILE B 344 O HIS B 368 SHEET 1 C 6 TRP C 431 ILE C 436 0 SHEET 2 C 6 ALA C 627 PRO C 633 -1 N GLY C 632 O ALA C 432 SHEET 3 C 6 ALA C 454 PHE C 459 -1 N LEU C 458 O ALA C 627 SHEET 4 C 6 HIS C 566 GLU C 573 -1 N TYR C 570 O ILE C 455 SHEET 5 C 6 GLY C 576 LEU C 580 -1 N LEU C 580 O THR C 569 SHEET 6 C 6 LEU C 589 LYS C 593 -1 N GLY C 592 O ILE C 577 LINK SG CYS A 90 C GLZ B 376 1555 1555 1.80 LINK C GLY B 375 N GLZ B 376 1555 1555 1.32 LINK SG CYS C 490 C GLZ D 776 1555 1555 1.79 LINK C GLY D 775 N GLZ D 776 1555 1555 1.32 CISPEP 1 ARG A 50 PRO A 51 0 -0.64 CISPEP 2 ARG C 450 PRO C 451 0 1.21 SITE 1 CAT 6 CYS A 90 HIS A 166 ASP A 181 CYS C 490 SITE 2 CAT 6 HIS C 566 ASP C 581 CRYST1 199.300 199.300 36.800 90.00 90.00 120.00 H 3 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 0.005017 0.002897 0.000000 0.00000 SCALE2 0.000000 0.005794 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027174 0.00000 MTRIX1 1 -0.996353 -0.018098 0.083380 138.04449 1 MTRIX2 1 0.019361 -0.999709 0.014368 68.79130 1 MTRIX3 1 0.083096 0.015930 0.996414 -5.83210 1 MTRIX1 2 -0.994609 -0.018167 0.102095 137.96919 1 MTRIX2 2 0.019181 -0.999776 0.008960 68.86830 1 MTRIX3 2 0.101909 0.010870 0.994734 -7.48250 1 MTRIX1 3 -0.995485 0.000294 0.094915 137.47340 1 MTRIX2 3 0.001553 -0.999811 0.019376 70.20870 1 MTRIX3 3 0.094902 0.019436 0.995297 -7.09020 1 MTRIX1 4 -0.995746 -0.011196 0.091454 137.91611 1 MTRIX2 4 0.012336 -0.999853 0.011911 69.42240 1 MTRIX3 4 0.091307 0.012988 0.995738 -6.44780 1 MTRIX1 5 -0.995901 -0.070480 0.056695 140.66769 1 MTRIX2 5 0.071614 -0.997266 0.018223 63.28260 1 MTRIX3 5 0.055256 0.022209 0.998225 -3.06350 1 MTRIX1 6 -0.997250 0.003024 0.074050 137.43050 1 MTRIX2 6 -0.004524 -0.999788 -0.020099 70.94470 1 MTRIX3 6 0.073974 -0.020379 0.997052 -3.74590 1 MTRIX1 7 -0.995261 -0.011771 0.096526 137.88541 1 MTRIX2 7 0.010528 -0.999855 -0.013377 69.79420 1 MTRIX3 7 0.096670 -0.012298 0.995241 -6.08560 1 MTRIX1 8 -0.991403 -0.043960 0.123242 138.11839 1 MTRIX2 8 0.042783 -0.999010 -0.012181 67.20250 1 MTRIX3 8 0.123655 -0.006804 0.992302 -8.73930 1 MTRIX1 9 -0.996557 -0.058399 0.058856 139.56320 1 MTRIX2 9 0.058071 -0.998286 -0.007268 66.15950 1 MTRIX3 9 0.059180 -0.003825 0.998240 -3.87380 1 MTRIX1 10 -0.988787 -0.074283 0.129550 137.64050 1 MTRIX2 10 0.083586 -0.994183 0.067916 62.61990 1 MTRIX3 10 0.123751 0.077983 0.989244 -9.97650 1 MTRIX1 11 -0.975822 0.033297 0.216015 133.03300 1 MTRIX2 11 -0.021987 -0.998269 0.054551 71.16090 1 MTRIX3 11 0.217458 0.048483 0.974865 -16.77120 1 MTRIX1 12 -0.996871 -0.046000 0.064286 139.08749 1 MTRIX2 12 0.047578 -0.998597 0.023238 66.20830 1 MTRIX3 12 0.063127 0.026224 0.997661 -4.37030 1