PDB Short entry for 4I1H HEADER LIGASE 20-NOV-12 4I1H TITLE STRUCTURE OF PARKIN E3 LIGASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: R0RBR (UNP RESIDUES 141-465); COMPND 5 SYNONYM: PARKINSON JUVENILE DISEASE PROTEIN 2, PARKINSON DISEASE COMPND 6 PROTEIN 2; COMPND 7 EC: 6.3.2.-; 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 GENE: PARK2, PRKN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RBR E3 UBIQUITIN LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.C.LOUGHEED,E.BRECHT,N.H.YAO REVDAT 4 20-SEP-23 4I1H 1 REMARK LINK REVDAT 3 31-JAN-18 4I1H 1 REMARK REVDAT 2 03-JUL-13 4I1H 1 JRNL REVDAT 1 19-JUN-13 4I1H 0 JRNL AUTH B.E.RILEY,J.C.LOUGHEED,K.CALLAWAY,M.VELASQUEZ,E.BRECHT, JRNL AUTH 2 L.NGUYEN,T.SHALER,D.WALKER,Y.YANG,K.REGNSTROM,L.DIEP, JRNL AUTH 3 Z.ZHANG,S.CHIOU,M.BOVA,D.R.ARTIS,N.YAO,J.BAKER,T.YEDNOCK, JRNL AUTH 4 J.A.JOHNSTON JRNL TITL STRUCTURE AND FUNCTION OF PARKIN E3 UBIQUITIN LIGASE REVEALS JRNL TITL 2 ASPECTS OF RING AND HECT LIGASES. JRNL REF NAT COMMUN V. 4 1982 2013 JRNL REFN ESSN 2041-1723 JRNL PMID 23770887 JRNL DOI 10.1038/NCOMMS2982 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 16.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 82.0 REMARK 3 NUMBER OF REFLECTIONS : 21783 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1089 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) : 523 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 29.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2399 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 263 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.68000 REMARK 3 B22 (A**2) : 0.24000 REMARK 3 B33 (A**2) : 0.44000 REMARK 3 B12 (A**2) : 0.00000 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): 0.203 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.398 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2467 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3343 ; 1.842 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 305 ; 6.750 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;36.570 ;23.559 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 405 ;14.071 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;16.963 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 350 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1920 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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: REMARK 3 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4I1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000076184. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21783 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 16.971 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.1000 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 36.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.39800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 4I1F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 6.5, 0.2 M SODIUM REMARK 280 CHLORIDE, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 383K, TEMPERATURE 283.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.10500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.10500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 43.55500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.96500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.55500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.96500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.10500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.55500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.96500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 33.10500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.55500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 66.96500 REMARK 290 SMTRY3 8 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 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 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 710 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 354 REMARK 465 GLY A 355 REMARK 465 ASN A 356 REMARK 465 GLY A 357 REMARK 465 LEU A 358 REMARK 465 ALA A 379 REMARK 465 VAL A 380 REMARK 465 PHE A 381 REMARK 465 GLU A 382 REMARK 465 ALA A 383 REMARK 465 SER A 384 REMARK 465 GLY A 385 REMARK 465 THR A 386 REMARK 465 THR A 387 REMARK 465 THR A 388 REMARK 465 GLN A 389 REMARK 465 ALA A 390 REMARK 465 TYR A 391 REMARK 465 ARG A 392 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 NZ LYS A 151 O HOH A 759 2.10 REMARK 500 O HOH A 716 O HOH A 828 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 215 CG HIS A 215 CD2 0.061 REMARK 500 HIS A 257 CG HIS A 257 CD2 0.061 REMARK 500 HIS A 302 CG HIS A 302 CD2 0.056 REMARK 500 HIS A 303 CG HIS A 303 CD2 0.062 REMARK 500 TRP A 403 CE2 TRP A 403 CD2 0.072 REMARK 500 HIS A 422 CG HIS A 422 CD2 0.069 REMARK 500 HIS A 433 CG HIS A 433 CD2 0.072 REMARK 500 TRP A 453 CE2 TRP A 453 CD2 0.081 REMARK 500 HIS A 461 CG HIS A 461 CD2 0.058 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 THR A 242 14.53 52.10 REMARK 500 LEU A 283 -44.09 -135.08 REMARK 500 SER A 286 -169.54 -160.40 REMARK 500 CYS A 337 -83.66 -97.85 REMARK 500 LYS A 369 -1.24 72.04 REMARK 500 CYS A 441 -71.20 -100.10 REMARK 500 HIS A 461 55.74 -160.74 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 150 SG REMARK 620 2 CYS A 154 SG 112.4 REMARK 620 3 CYS A 212 SG 111.0 113.0 REMARK 620 4 HIS A 215 NE2 111.8 104.0 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 166 SG REMARK 620 2 CYS A 169 SG 105.6 REMARK 620 3 CYS A 196 SG 112.9 111.7 REMARK 620 4 CYS A 201 SG 107.6 110.6 108.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 238 SG REMARK 620 2 CYS A 241 SG 104.5 REMARK 620 3 CYS A 260 SG 114.2 117.6 REMARK 620 4 CYS A 263 SG 108.6 108.4 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 253 SG REMARK 620 2 HIS A 257 ND1 108.3 REMARK 620 3 CYS A 289 SG 114.9 104.1 REMARK 620 4 CYS A 293 SG 111.3 100.0 116.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 332 SG REMARK 620 2 CYS A 337 SG 116.3 REMARK 620 3 CYS A 352 SG 111.6 105.7 REMARK 620 4 CYS A 360 SG 102.6 112.9 107.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 506 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 365 SG REMARK 620 2 CYS A 368 SG 104.8 REMARK 620 3 HIS A 373 NE2 111.5 109.1 REMARK 620 4 CYS A 377 SG 106.2 110.9 113.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 507 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 418 SG REMARK 620 2 CYS A 421 SG 112.5 REMARK 620 3 CYS A 436 SG 107.3 102.1 REMARK 620 4 CYS A 441 SG 105.7 113.8 115.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 508 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 446 SG REMARK 620 2 CYS A 449 SG 116.0 REMARK 620 3 CYS A 457 SG 112.3 112.7 REMARK 620 4 HIS A 461 NE2 99.6 106.8 108.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 508 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4I1F RELATED DB: PDB REMARK 900 STRUCTURE OF PARKIN R0RBR-P223S DBREF 4I1H A 141 465 UNP O60260 PRKN2_HUMAN 141 465 SEQRES 1 A 325 SER ILE TYR ASN SER PHE TYR VAL TYR CYS LYS GLY PRO SEQRES 2 A 325 CYS GLN ARG VAL GLN PRO GLY LYS LEU ARG VAL GLN CYS SEQRES 3 A 325 SER THR CYS ARG GLN ALA THR LEU THR LEU THR GLN GLY SEQRES 4 A 325 PRO SER CYS TRP ASP ASP VAL LEU ILE PRO ASN ARG MET SEQRES 5 A 325 SER GLY GLU CYS GLN SER PRO HIS CYS PRO GLY THR SER SEQRES 6 A 325 ALA GLU PHE PHE PHE LYS CYS GLY ALA HIS PRO THR SER SEQRES 7 A 325 ASP LYS GLU THR SER VAL ALA LEU HIS LEU ILE ALA THR SEQRES 8 A 325 ASN SER ARG ASN ILE THR CYS ILE THR CYS THR ASP VAL SEQRES 9 A 325 ARG SER PRO VAL LEU VAL PHE GLN CYS ASN SER ARG HIS SEQRES 10 A 325 VAL ILE CYS LEU ASP CYS PHE HIS LEU TYR CYS VAL THR SEQRES 11 A 325 ARG LEU ASN ASP ARG GLN PHE VAL HIS ASP PRO GLN LEU SEQRES 12 A 325 GLY TYR SER LEU PRO CYS VAL ALA GLY CYS PRO ASN SER SEQRES 13 A 325 LEU ILE LYS GLU LEU HIS HIS PHE ARG ILE LEU GLY GLU SEQRES 14 A 325 GLU GLN TYR ASN ARG TYR GLN GLN TYR GLY ALA GLU GLU SEQRES 15 A 325 CYS VAL LEU GLN MET GLY GLY VAL LEU CYS PRO ARG PRO SEQRES 16 A 325 GLY CYS GLY ALA GLY LEU LEU PRO GLU PRO ASP GLN ARG SEQRES 17 A 325 LYS VAL THR CYS GLU GLY GLY ASN GLY LEU GLY CYS GLY SEQRES 18 A 325 PHE ALA PHE CYS ARG GLU CYS LYS GLU ALA TYR HIS GLU SEQRES 19 A 325 GLY GLU CYS SER ALA VAL PHE GLU ALA SER GLY THR THR SEQRES 20 A 325 THR GLN ALA TYR ARG VAL ASP GLU ARG ALA ALA GLU GLN SEQRES 21 A 325 ALA ARG TRP GLU ALA ALA SER LYS GLU THR ILE LYS LYS SEQRES 22 A 325 THR THR LYS PRO CYS PRO ARG CYS HIS VAL PRO VAL GLU SEQRES 23 A 325 LYS ASN GLY GLY CYS MET HIS MET LYS CYS PRO GLN PRO SEQRES 24 A 325 GLN CYS ARG LEU GLU TRP CYS TRP ASN CYS GLY CYS GLU SEQRES 25 A 325 TRP ASN ARG VAL CYS MET GLY ASP HIS TRP PHE ASP VAL HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HET ZN A 505 1 HET ZN A 506 1 HET ZN A 507 1 HET ZN A 508 1 HETNAM ZN ZINC ION FORMUL 2 ZN 8(ZN 2+) FORMUL 10 HOH *263(H2 O) HELIX 1 1 CYS A 182 ILE A 188 1 7 HELIX 2 2 LEU A 261 ASP A 274 1 14 HELIX 3 3 GLU A 300 ILE A 306 5 7 HELIX 4 4 LEU A 307 MET A 327 1 21 HELIX 5 5 ARG A 396 ALA A 401 1 6 HELIX 6 6 ASN A 454 TRP A 462 1 9 SHEET 1 A 4 ALA A 206 CYS A 212 0 SHEET 2 A 4 ARG A 156 CYS A 166 -1 N ARG A 163 O PHE A 209 SHEET 3 A 4 TYR A 147 CYS A 150 -1 N CYS A 150 O ARG A 156 SHEET 4 A 4 VAL A 224 ALA A 225 -1 O VAL A 224 N TYR A 149 SHEET 1 B 2 LEU A 174 LEU A 176 0 SHEET 2 B 2 GLY A 194 CYS A 196 -1 O GLU A 195 N THR A 175 SHEET 1 C 3 ILE A 229 ALA A 230 0 SHEET 2 C 3 VAL A 248 VAL A 250 -1 O VAL A 248 N ALA A 230 SHEET 3 C 3 VAL A 258 CYS A 260 -1 O ILE A 259 N LEU A 249 SHEET 1 D 2 VAL A 278 ASP A 280 0 SHEET 2 D 2 GLY A 284 SER A 286 -1 O GLY A 284 N ASP A 280 SHEET 1 E 2 VAL A 330 LEU A 331 0 SHEET 2 E 2 GLY A 340 LEU A 341 -1 O LEU A 341 N VAL A 330 SHEET 1 F 2 LYS A 349 THR A 351 0 SHEET 2 F 2 ALA A 363 CYS A 365 -1 O PHE A 364 N VAL A 350 SHEET 1 G 2 THR A 415 PRO A 417 0 SHEET 2 G 2 PRO A 424 GLU A 426 -1 O VAL A 425 N LYS A 416 SHEET 1 H 2 HIS A 433 LYS A 435 0 SHEET 2 H 2 GLU A 444 CYS A 446 -1 O TRP A 445 N MET A 434 LINK SG CYS A 150 ZN ZN A 501 1555 1555 2.22 LINK SG CYS A 154 ZN ZN A 501 1555 1555 2.29 LINK SG CYS A 166 ZN ZN A 502 1555 1555 2.45 LINK SG CYS A 169 ZN ZN A 502 1555 1555 2.38 LINK SG CYS A 196 ZN ZN A 502 1555 1555 2.04 LINK SG CYS A 201 ZN ZN A 502 1555 1555 2.46 LINK SG CYS A 212 ZN ZN A 501 1555 1555 2.31 LINK NE2 HIS A 215 ZN ZN A 501 1555 1555 2.17 LINK SG CYS A 238 ZN ZN A 503 1555 1555 2.41 LINK SG CYS A 241 ZN ZN A 503 1555 1555 2.33 LINK SG CYS A 253 ZN ZN A 504 1555 1555 2.32 LINK ND1 HIS A 257 ZN ZN A 504 1555 1555 2.04 LINK SG CYS A 260 ZN ZN A 503 1555 1555 2.39 LINK SG CYS A 263 ZN ZN A 503 1555 1555 2.40 LINK SG CYS A 289 ZN ZN A 504 1555 1555 2.29 LINK SG CYS A 293 ZN ZN A 504 1555 1555 2.34 LINK SG CYS A 332 ZN ZN A 505 1555 1555 2.22 LINK SG CYS A 337 ZN ZN A 505 1555 1555 2.42 LINK SG CYS A 352 ZN ZN A 505 1555 1555 2.34 LINK SG CYS A 360 ZN ZN A 505 1555 1555 2.39 LINK SG CYS A 365 ZN ZN A 506 1555 1555 2.46 LINK SG CYS A 368 ZN ZN A 506 1555 1555 2.45 LINK NE2 HIS A 373 ZN ZN A 506 1555 1555 2.19 LINK SG CYS A 377 ZN ZN A 506 1555 1555 2.32 LINK SG CYS A 418 ZN ZN A 507 1555 1555 2.36 LINK SG CYS A 421 ZN ZN A 507 1555 1555 2.41 LINK SG CYS A 436 ZN ZN A 507 1555 1555 2.35 LINK SG CYS A 441 ZN ZN A 507 1555 1555 2.28 LINK SG CYS A 446 ZN ZN A 508 1555 1555 2.25 LINK SG CYS A 449 ZN ZN A 508 1555 1555 2.40 LINK SG CYS A 457 ZN ZN A 508 1555 1555 2.29 LINK NE2 HIS A 461 ZN ZN A 508 1555 1555 2.01 CISPEP 1 GLY A 152 PRO A 153 0 1.37 CISPEP 2 SER A 246 PRO A 247 0 -5.45 SITE 1 AC1 4 CYS A 150 CYS A 154 CYS A 212 HIS A 215 SITE 1 AC2 4 CYS A 166 CYS A 169 CYS A 196 CYS A 201 SITE 1 AC3 4 CYS A 238 CYS A 241 CYS A 260 CYS A 263 SITE 1 AC4 4 CYS A 253 HIS A 257 CYS A 289 CYS A 293 SITE 1 AC5 4 CYS A 332 CYS A 337 CYS A 352 CYS A 360 SITE 1 AC6 4 CYS A 365 CYS A 368 HIS A 373 CYS A 377 SITE 1 AC7 4 CYS A 418 CYS A 421 CYS A 436 CYS A 441 SITE 1 AC8 4 CYS A 446 CYS A 449 CYS A 457 HIS A 461 CRYST1 87.110 133.930 66.210 90.00 90.00 90.00 C 2 2 21 8 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 0.011480 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007467 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015103 0.00000