HEADER HYDROLASE 24-AUG-05 2D1I TITLE STRUCTURE OF HUMAN ATG4B COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE PROTEASE APG4B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: AUTOPHAGY 4 HOMOLOG B, HAPG4B, AUTOPHAGIN-1, AUTOPHAGY- COMPND 5 RELATED CYSTEINE ENDOPEPTIDASE 1, AUT-LIKE 1 CYSTEINE ENDOPEPTIDASE, COMPND 6 ATG4B; COMPND 7 EC: 3.4.22.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P KEYWDS CYSTEINE PROTEASE, AUTOPHAGY, ATG, APG, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.KUMANOMIDOU,T.MIZUSHIMA,M.KOMATSU,A.SUZUKI,I.TANIDA,Y.S.SOU,T.UENO, AUTHOR 2 E.KOMINAMI,K.TANAKA,T.YAMANE REVDAT 3 13-MAR-24 2D1I 1 SEQADV REVDAT 2 24-FEB-09 2D1I 1 VERSN REVDAT 1 10-JAN-06 2D1I 0 JRNL AUTH T.KUMANOMIDOU,T.MIZUSHIMA,M.KOMATSU,A.SUZUKI,I.TANIDA, JRNL AUTH 2 Y.S.SOU,T.UENO,E.KOMINAMI,K.TANAKA,T.YAMANE JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN ATG4B, A PROCESSING AND JRNL TITL 2 DE-CONJUGATING ENZYME FOR AUTOPHAGOSOME-FORMING MODIFIERS JRNL REF J.MOL.BIOL. V. 355 612 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16325851 JRNL DOI 10.1016/J.JMB.2005.11.018 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 45690 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2435 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3411 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5386 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 338 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : 0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.226 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.141 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.916 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5538 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7528 ; 1.422 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 674 ; 7.085 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 252 ;36.552 ;23.651 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 900 ;15.789 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;15.819 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 812 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4246 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2726 ; 0.222 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3779 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 388 ; 0.144 ; 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): 119 ; 0.211 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.186 ; 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): 3467 ; 0.955 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5488 ; 1.648 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2379 ; 1.816 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2040 ; 2.838 ; 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 2D1I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000024871. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 7 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48166 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 44.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.65M TRI-SODIUM CITRATE DIHYDRATE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 80.66050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 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 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 THR A 5 REMARK 465 LEU A 6 REMARK 465 THR A 7 REMARK 465 TYR A 8 REMARK 465 ASP A 9 REMARK 465 GLY A 191 REMARK 465 ALA A 192 REMARK 465 THR A 193 REMARK 465 ALA A 194 REMARK 465 PHE A 195 REMARK 465 PRO A 196 REMARK 465 ALA A 197 REMARK 465 ASP A 198 REMARK 465 SER A 199 REMARK 465 ASP A 200 REMARK 465 ARG A 201 REMARK 465 HIS A 202 REMARK 465 CYS A 203 REMARK 465 ASN A 204 REMARK 465 GLY A 205 REMARK 465 PHE A 206 REMARK 465 PRO A 207 REMARK 465 ALA A 208 REMARK 465 GLY A 209 REMARK 465 ALA A 210 REMARK 465 GLU A 211 REMARK 465 VAL A 212 REMARK 465 THR A 213 REMARK 465 ASN A 214 REMARK 465 ARG A 215 REMARK 465 VAL A 374 REMARK 465 GLU A 375 REMARK 465 ARG A 376 REMARK 465 LEU A 377 REMARK 465 GLU A 378 REMARK 465 ARG A 379 REMARK 465 PHE A 380 REMARK 465 PHE A 381 REMARK 465 ASP A 382 REMARK 465 SER A 383 REMARK 465 GLU A 384 REMARK 465 ASP A 385 REMARK 465 GLU A 386 REMARK 465 ASP A 387 REMARK 465 PHE A 388 REMARK 465 GLU A 389 REMARK 465 ILE A 390 REMARK 465 LEU A 391 REMARK 465 SER A 392 REMARK 465 LEU A 393 REMARK 465 GLY B -4 REMARK 465 PRO B -3 REMARK 465 LEU B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 ALA B 3 REMARK 465 ALA B 4 REMARK 465 THR B 5 REMARK 465 LEU B 6 REMARK 465 THR B 7 REMARK 465 TYR B 8 REMARK 465 ASP B 9 REMARK 465 GLY B 191 REMARK 465 ALA B 192 REMARK 465 THR B 193 REMARK 465 ALA B 194 REMARK 465 PHE B 195 REMARK 465 PRO B 196 REMARK 465 ALA B 197 REMARK 465 ASP B 198 REMARK 465 SER B 199 REMARK 465 ASP B 200 REMARK 465 ARG B 201 REMARK 465 HIS B 202 REMARK 465 CYS B 203 REMARK 465 ASN B 204 REMARK 465 GLY B 205 REMARK 465 PHE B 206 REMARK 465 PRO B 207 REMARK 465 ALA B 208 REMARK 465 GLY B 209 REMARK 465 ALA B 210 REMARK 465 GLU B 211 REMARK 465 VAL B 212 REMARK 465 THR B 213 REMARK 465 ASN B 214 REMARK 465 ARG B 215 REMARK 465 VAL B 374 REMARK 465 GLU B 375 REMARK 465 ARG B 376 REMARK 465 LEU B 377 REMARK 465 GLU B 378 REMARK 465 ARG B 379 REMARK 465 PHE B 380 REMARK 465 PHE B 381 REMARK 465 ASP B 382 REMARK 465 SER B 383 REMARK 465 GLU B 384 REMARK 465 ASP B 385 REMARK 465 GLU B 386 REMARK 465 ASP B 387 REMARK 465 PHE B 388 REMARK 465 GLU B 389 REMARK 465 ILE B 390 REMARK 465 LEU B 391 REMARK 465 SER B 392 REMARK 465 LEU B 393 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 CZ ARG A 31 O HOH A 514 2.13 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 ARG A 94 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 49 NE - CZ - NH2 ANGL. DEV. = -3.0 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 PHE A 19 51.83 32.92 REMARK 500 PRO A 20 -121.73 -70.73 REMARK 500 LYS A 259 84.48 94.26 REMARK 500 SER A 262 47.24 -146.56 REMARK 500 PRO A 288 165.30 -48.79 REMARK 500 LEU A 342 171.42 67.97 REMARK 500 ALA A 345 142.36 -38.07 REMARK 500 LEU A 346 72.21 53.30 REMARK 500 PRO A 356 87.60 -61.51 REMARK 500 LEU A 359 110.96 99.08 REMARK 500 ALA A 360 -136.75 -159.16 REMARK 500 SER A 368 41.13 93.15 REMARK 500 SER A 372 68.09 -111.34 REMARK 500 GLU B 17 -85.83 -133.87 REMARK 500 ASP B 18 -82.53 -151.54 REMARK 500 PRO B 20 -129.51 -77.42 REMARK 500 ILE B 139 106.28 -51.21 REMARK 500 ASN B 172 29.05 49.11 REMARK 500 LYS B 259 87.68 85.11 REMARK 500 PRO B 288 121.06 -15.29 REMARK 500 CYS B 292 -17.31 -149.20 REMARK 500 LEU B 341 -139.38 -139.48 REMARK 500 LEU B 342 -153.16 46.79 REMARK 500 ALA B 345 116.27 62.84 REMARK 500 GLN B 355 -59.47 -152.95 REMARK 500 PRO B 356 82.56 -15.93 REMARK 500 HIS B 358 -58.63 -168.34 REMARK 500 ALA B 360 -93.97 -98.61 REMARK 500 CYS B 361 -72.05 -139.39 REMARK 500 ASP B 363 21.37 -154.58 REMARK 500 SER B 368 48.90 83.58 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 20 GLU A 21 -34.10 REMARK 500 PRO B 20 GLU B 21 -145.96 REMARK 500 REMARK 500 REMARK: NULL DBREF 2D1I A 1 393 UNP Q9Y4P1 ATG4B_HUMAN 1 393 DBREF 2D1I B 1 393 UNP Q9Y4P1 ATG4B_HUMAN 1 393 SEQADV 2D1I GLY A -4 UNP Q9Y4P1 CLONING ARTIFACT SEQADV 2D1I PRO A -3 UNP Q9Y4P1 CLONING ARTIFACT SEQADV 2D1I LEU A -2 UNP Q9Y4P1 CLONING ARTIFACT SEQADV 2D1I GLY A -1 UNP Q9Y4P1 CLONING ARTIFACT SEQADV 2D1I SER A 0 UNP Q9Y4P1 CLONING ARTIFACT SEQADV 2D1I GLY B -4 UNP Q9Y4P1 CLONING ARTIFACT SEQADV 2D1I PRO B -3 UNP Q9Y4P1 CLONING ARTIFACT SEQADV 2D1I LEU B -2 UNP Q9Y4P1 CLONING ARTIFACT SEQADV 2D1I GLY B -1 UNP Q9Y4P1 CLONING ARTIFACT SEQADV 2D1I SER B 0 UNP Q9Y4P1 CLONING ARTIFACT SEQRES 1 A 398 GLY PRO LEU GLY SER MET ASP ALA ALA THR LEU THR TYR SEQRES 2 A 398 ASP THR LEU ARG PHE ALA GLU PHE GLU ASP PHE PRO GLU SEQRES 3 A 398 THR SER GLU PRO VAL TRP ILE LEU GLY ARG LYS TYR SER SEQRES 4 A 398 ILE PHE THR GLU LYS ASP GLU ILE LEU SER ASP VAL ALA SEQRES 5 A 398 SER ARG LEU TRP PHE THR TYR ARG LYS ASN PHE PRO ALA SEQRES 6 A 398 ILE GLY GLY THR GLY PRO THR SER ASP THR GLY TRP GLY SEQRES 7 A 398 CYS MET LEU ARG CYS GLY GLN MET ILE PHE ALA GLN ALA SEQRES 8 A 398 LEU VAL CYS ARG HIS LEU GLY ARG ASP TRP ARG TRP THR SEQRES 9 A 398 GLN ARG LYS ARG GLN PRO ASP SER TYR PHE SER VAL LEU SEQRES 10 A 398 ASN ALA PHE ILE ASP ARG LYS ASP SER TYR TYR SER ILE SEQRES 11 A 398 HIS GLN ILE ALA GLN MET GLY VAL GLY GLU GLY LYS SER SEQRES 12 A 398 ILE GLY GLN TRP TYR GLY PRO ASN THR VAL ALA GLN VAL SEQRES 13 A 398 LEU LYS LYS LEU ALA VAL PHE ASP THR TRP SER SER LEU SEQRES 14 A 398 ALA VAL HIS ILE ALA MET ASP ASN THR VAL VAL MET GLU SEQRES 15 A 398 GLU ILE ARG ARG LEU CYS ARG THR SER VAL PRO CYS ALA SEQRES 16 A 398 GLY ALA THR ALA PHE PRO ALA ASP SER ASP ARG HIS CYS SEQRES 17 A 398 ASN GLY PHE PRO ALA GLY ALA GLU VAL THR ASN ARG PRO SEQRES 18 A 398 SER PRO TRP ARG PRO LEU VAL LEU LEU ILE PRO LEU ARG SEQRES 19 A 398 LEU GLY LEU THR ASP ILE ASN GLU ALA TYR VAL GLU THR SEQRES 20 A 398 LEU LYS HIS CYS PHE MET MET PRO GLN SER LEU GLY VAL SEQRES 21 A 398 ILE GLY GLY LYS PRO ASN SER ALA HIS TYR PHE ILE GLY SEQRES 22 A 398 TYR VAL GLY GLU GLU LEU ILE TYR LEU ASP PRO HIS THR SEQRES 23 A 398 THR GLN PRO ALA VAL GLU PRO THR ASP GLY CYS PHE ILE SEQRES 24 A 398 PRO ASP GLU SER PHE HIS CYS GLN HIS PRO PRO CYS ARG SEQRES 25 A 398 MET SER ILE ALA GLU LEU ASP PRO SER ILE ALA VAL GLY SEQRES 26 A 398 PHE PHE CYS LYS THR GLU ASP ASP PHE ASN ASP TRP CYS SEQRES 27 A 398 GLN GLN VAL LYS LYS LEU SER LEU LEU GLY GLY ALA LEU SEQRES 28 A 398 PRO MET PHE GLU LEU VAL GLU GLN GLN PRO SER HIS LEU SEQRES 29 A 398 ALA CYS PRO ASP VAL LEU ASN LEU SER LEU ASP SER SER SEQRES 30 A 398 ASP VAL GLU ARG LEU GLU ARG PHE PHE ASP SER GLU ASP SEQRES 31 A 398 GLU ASP PHE GLU ILE LEU SER LEU SEQRES 1 B 398 GLY PRO LEU GLY SER MET ASP ALA ALA THR LEU THR TYR SEQRES 2 B 398 ASP THR LEU ARG PHE ALA GLU PHE GLU ASP PHE PRO GLU SEQRES 3 B 398 THR SER GLU PRO VAL TRP ILE LEU GLY ARG LYS TYR SER SEQRES 4 B 398 ILE PHE THR GLU LYS ASP GLU ILE LEU SER ASP VAL ALA SEQRES 5 B 398 SER ARG LEU TRP PHE THR TYR ARG LYS ASN PHE PRO ALA SEQRES 6 B 398 ILE GLY GLY THR GLY PRO THR SER ASP THR GLY TRP GLY SEQRES 7 B 398 CYS MET LEU ARG CYS GLY GLN MET ILE PHE ALA GLN ALA SEQRES 8 B 398 LEU VAL CYS ARG HIS LEU GLY ARG ASP TRP ARG TRP THR SEQRES 9 B 398 GLN ARG LYS ARG GLN PRO ASP SER TYR PHE SER VAL LEU SEQRES 10 B 398 ASN ALA PHE ILE ASP ARG LYS ASP SER TYR TYR SER ILE SEQRES 11 B 398 HIS GLN ILE ALA GLN MET GLY VAL GLY GLU GLY LYS SER SEQRES 12 B 398 ILE GLY GLN TRP TYR GLY PRO ASN THR VAL ALA GLN VAL SEQRES 13 B 398 LEU LYS LYS LEU ALA VAL PHE ASP THR TRP SER SER LEU SEQRES 14 B 398 ALA VAL HIS ILE ALA MET ASP ASN THR VAL VAL MET GLU SEQRES 15 B 398 GLU ILE ARG ARG LEU CYS ARG THR SER VAL PRO CYS ALA SEQRES 16 B 398 GLY ALA THR ALA PHE PRO ALA ASP SER ASP ARG HIS CYS SEQRES 17 B 398 ASN GLY PHE PRO ALA GLY ALA GLU VAL THR ASN ARG PRO SEQRES 18 B 398 SER PRO TRP ARG PRO LEU VAL LEU LEU ILE PRO LEU ARG SEQRES 19 B 398 LEU GLY LEU THR ASP ILE ASN GLU ALA TYR VAL GLU THR SEQRES 20 B 398 LEU LYS HIS CYS PHE MET MET PRO GLN SER LEU GLY VAL SEQRES 21 B 398 ILE GLY GLY LYS PRO ASN SER ALA HIS TYR PHE ILE GLY SEQRES 22 B 398 TYR VAL GLY GLU GLU LEU ILE TYR LEU ASP PRO HIS THR SEQRES 23 B 398 THR GLN PRO ALA VAL GLU PRO THR ASP GLY CYS PHE ILE SEQRES 24 B 398 PRO ASP GLU SER PHE HIS CYS GLN HIS PRO PRO CYS ARG SEQRES 25 B 398 MET SER ILE ALA GLU LEU ASP PRO SER ILE ALA VAL GLY SEQRES 26 B 398 PHE PHE CYS LYS THR GLU ASP ASP PHE ASN ASP TRP CYS SEQRES 27 B 398 GLN GLN VAL LYS LYS LEU SER LEU LEU GLY GLY ALA LEU SEQRES 28 B 398 PRO MET PHE GLU LEU VAL GLU GLN GLN PRO SER HIS LEU SEQRES 29 B 398 ALA CYS PRO ASP VAL LEU ASN LEU SER LEU ASP SER SER SEQRES 30 B 398 ASP VAL GLU ARG LEU GLU ARG PHE PHE ASP SER GLU ASP SEQRES 31 B 398 GLU ASP PHE GLU ILE LEU SER LEU FORMUL 3 HOH *338(H2 O) HELIX 1 1 THR A 10 ALA A 14 5 5 HELIX 2 2 GLU A 38 ARG A 49 1 12 HELIX 3 3 ALA A 60 THR A 64 5 5 HELIX 4 4 GLY A 73 LEU A 92 1 20 HELIX 5 5 PRO A 105 ALA A 114 1 10 HELIX 6 6 SER A 124 GLY A 134 1 11 HELIX 7 7 GLY A 144 VAL A 157 1 14 HELIX 8 8 MET A 176 ARG A 184 1 9 HELIX 9 9 TYR A 239 PHE A 247 1 9 HELIX 10 10 ASP A 296 HIS A 300 5 5 HELIX 11 11 ALA A 311 LEU A 313 5 3 HELIX 12 12 THR A 325 SER A 340 1 16 HELIX 13 13 THR B 10 ALA B 14 5 5 HELIX 14 14 GLU B 38 ARG B 49 1 12 HELIX 15 15 GLY B 73 LEU B 92 1 20 HELIX 16 16 PRO B 105 ALA B 114 1 10 HELIX 17 17 SER B 124 GLY B 134 1 11 HELIX 18 18 GLY B 144 VAL B 157 1 14 HELIX 19 19 MET B 176 ARG B 184 1 9 HELIX 20 20 ASN B 236 ALA B 238 5 3 HELIX 21 21 TYR B 239 PHE B 247 1 9 HELIX 22 22 ASP B 296 HIS B 300 5 5 HELIX 23 23 ALA B 311 LEU B 313 5 3 HELIX 24 24 THR B 325 LEU B 339 1 15 SHEET 1 A 7 ARG A 31 TYR A 33 0 SHEET 2 A 7 VAL A 26 ILE A 28 -1 N ILE A 28 O ARG A 31 SHEET 3 A 7 HIS A 264 VAL A 270 -1 O TYR A 269 N TRP A 27 SHEET 4 A 7 SER A 252 GLY A 257 -1 N GLY A 257 O HIS A 264 SHEET 5 A 7 SER A 316 CYS A 323 -1 O GLY A 320 N GLY A 254 SHEET 6 A 7 LEU A 222 ARG A 229 -1 N LEU A 222 O CYS A 323 SHEET 7 A 7 ALA A 165 ILE A 168 1 N ALA A 165 O VAL A 223 SHEET 1 B 5 ARG A 31 TYR A 33 0 SHEET 2 B 5 VAL A 26 ILE A 28 -1 N ILE A 28 O ARG A 31 SHEET 3 B 5 HIS A 264 VAL A 270 -1 O TYR A 269 N TRP A 27 SHEET 4 B 5 GLU A 273 LEU A 277 -1 O LEU A 277 N TYR A 265 SHEET 5 B 5 CYS A 306 SER A 309 -1 O MET A 308 N LEU A 274 SHEET 1 C 2 TYR A 54 LYS A 56 0 SHEET 2 C 2 THR A 282 PRO A 284 1 O GLN A 283 N TYR A 54 SHEET 1 D 2 THR A 173 VAL A 175 0 SHEET 2 D 2 GLU A 350 VAL A 352 1 O GLU A 350 N VAL A 174 SHEET 1 E 7 ARG B 31 TYR B 33 0 SHEET 2 E 7 VAL B 26 ILE B 28 -1 N ILE B 28 O ARG B 31 SHEET 3 E 7 HIS B 264 VAL B 270 -1 O TYR B 269 N TRP B 27 SHEET 4 E 7 SER B 252 GLY B 257 -1 N GLY B 257 O HIS B 264 SHEET 5 E 7 SER B 316 CYS B 323 -1 O GLY B 320 N GLY B 254 SHEET 6 E 7 LEU B 222 ARG B 229 -1 N LEU B 224 O PHE B 321 SHEET 7 E 7 ALA B 165 ILE B 168 1 N ALA B 165 O VAL B 223 SHEET 1 F 5 ARG B 31 TYR B 33 0 SHEET 2 F 5 VAL B 26 ILE B 28 -1 N ILE B 28 O ARG B 31 SHEET 3 F 5 HIS B 264 VAL B 270 -1 O TYR B 269 N TRP B 27 SHEET 4 F 5 GLU B 273 LEU B 277 -1 O LEU B 277 N TYR B 265 SHEET 5 F 5 CYS B 306 SER B 309 -1 O MET B 308 N LEU B 274 SHEET 1 G 2 ARG B 55 LYS B 56 0 SHEET 2 G 2 GLN B 283 PRO B 284 1 O GLN B 283 N LYS B 56 SHEET 1 H 2 THR B 173 VAL B 175 0 SHEET 2 H 2 GLU B 350 VAL B 352 1 O GLU B 350 N VAL B 174 CISPEP 1 PRO A 216 SER A 217 0 -0.60 CISPEP 2 GLY A 258 LYS A 259 0 5.16 CISPEP 3 GLY A 344 ALA A 345 0 4.25 CISPEP 4 ALA A 345 LEU A 346 0 -5.53 CISPEP 5 CYS A 361 PRO A 362 0 19.42 CISPEP 6 PRO A 362 ASP A 363 0 8.09 CISPEP 7 LEU A 367 SER A 368 0 16.47 CISPEP 8 SER A 371 SER A 372 0 -2.10 CISPEP 9 ASP B 18 PHE B 19 0 0.70 CISPEP 10 PRO B 216 SER B 217 0 3.36 CISPEP 11 GLY B 258 LYS B 259 0 12.51 CISPEP 12 PRO B 260 ASN B 261 0 -11.76 CISPEP 13 ASN B 261 SER B 262 0 29.12 CISPEP 14 GLY B 344 ALA B 345 0 5.21 CISPEP 15 ALA B 345 LEU B 346 0 15.88 CISPEP 16 CYS B 361 PRO B 362 0 1.13 CISPEP 17 LEU B 367 SER B 368 0 24.85 CISPEP 18 SER B 371 SER B 372 0 -10.13 CRYST1 51.278 161.321 51.271 90.00 119.58 90.00 P 1 21 1 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 0.019502 0.000000 0.011069 0.00000 SCALE2 0.000000 0.006199 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022427 0.00000