HEADER LIGASE 06-AUG-12 2LWR TITLE SOLUTION STRUCTURE OF RING2 DOMAIN FROM PARKIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SD01679P; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 417-482; COMPND 5 SYNONYM: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: PARK, CG10523; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-2; SOURCE 9 OTHER_DETAILS: GST-FUSION PROTEIN WITH TEV CLEAVABLE TAG. KEYWDS PARKIN, RING, E3 LIGASE, ZN-BINDING, METAL BINDING PROTEIN, KEYWDS 2 STRUCTURAL PROTEIN, LIGASE EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR P.MERCIER,D.E.SPRATT,N.MANCZYK,G.S.SHAW REVDAT 4 14-JUN-23 2LWR 1 REMARK SEQADV LINK REVDAT 3 15-OCT-14 2LWR 1 COMPND REVDAT 2 03-JUL-13 2LWR 1 JRNL REVDAT 1 12-JUN-13 2LWR 0 JRNL AUTH D.E.SPRATT,R.JULIO MARTINEZ-TORRES,Y.J.NOH,P.MERCIER, JRNL AUTH 2 N.MANCZYK,K.R.BARBER,J.D.AGUIRRE,L.BURCHELL,A.PURKISS, JRNL AUTH 3 H.WALDEN,G.S.SHAW JRNL TITL A MOLECULAR EXPLANATION FOR THE RECESSIVE NATURE OF JRNL TITL 2 PARKIN-LINKED PARKINSON'S DISEASE. JRNL REF NAT COMMUN V. 4 1983 2013 JRNL REFN ESSN 2041-1723 JRNL PMID 23770917 JRNL DOI 10.1038/NCOMMS2983 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ VARIAN VNMRJ 2.2D, X-PLOR NIH 2.31 REMARK 3 AUTHORS : VARIAN (VNMRJ), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WITH EXPLICIT SOLVENT AND FULL REMARK 3 ELECTROSTATICS REMARK 4 REMARK 4 2LWR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000102928. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.25 REMARK 210 IONIC STRENGTH : 0.120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM TRIS, 120 MM SODIUM REMARK 210 CHLORIDE, 5 MM DTT, 500 UM [U-98% REMARK 210 15N] PROTEIN_1, 90% H2O/10% D2O; REMARK 210 20 MM TRIS, 120 MM SODIUM REMARK 210 CHLORIDE, 5 MM DTT, 500 UM [U-98% REMARK 210 13C; U-98% 15N] PROTEIN_1, 90% REMARK 210 H2O/10% D2O; 20 MM TRIS, 120 MM REMARK 210 SODIUM CHLORIDE, 5 MM DTT, 500 REMARK 210 UM [U-98% 13C; U-98% 15N] REMARK 210 PROTEIN_1, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D 1H-15N NOESY; 3D REMARK 210 HCCH-TOCSY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HNHA; 3D C(CO)NH; 2D REMARK 210 (HB)CB(CGCD)HD; 2D (HB)CB(CGCDCE) REMARK 210 HE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2011.084.20.33, NMRDRAW REMARK 210 VER 5.7 REV 2011.084.20.33, REMARK 210 NMRVIEW 8.2.33 WITH JAVA 1.6.0_ REMARK 210 31, CYANA 2.1, TALOS TALOSPLUS, REMARK 210 PROCHECK 3.5.4 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 VAL A 431 147.05 -176.39 REMARK 500 1 CYS A 459 -82.80 -105.70 REMARK 500 1 TRP A 465 -74.96 19.30 REMARK 500 1 THR A 469 -148.60 -168.82 REMARK 500 1 HIS A 479 -154.79 -88.06 REMARK 500 1 TRP A 480 -53.01 73.38 REMARK 500 2 SER A 425 -79.36 -79.29 REMARK 500 2 PRO A 442 90.81 -69.62 REMARK 500 2 CYS A 459 -67.38 -120.00 REMARK 500 2 TRP A 480 -88.61 -104.94 REMARK 500 3 THR A 428 16.67 -155.06 REMARK 500 3 LYS A 430 -79.10 -70.52 REMARK 500 3 LYS A 438 -74.58 -110.20 REMARK 500 3 PRO A 442 99.52 -63.39 REMARK 500 3 MET A 450 33.78 -99.50 REMARK 500 3 CYS A 459 -76.60 -85.56 REMARK 500 3 ALA A 478 33.42 -148.77 REMARK 500 3 HIS A 479 -9.10 -149.81 REMARK 500 3 PHE A 481 -44.54 175.72 REMARK 500 4 ASN A 426 -77.59 -85.50 REMARK 500 4 THR A 428 163.64 178.94 REMARK 500 4 PRO A 442 108.64 -57.91 REMARK 500 4 ASP A 446 106.98 -28.37 REMARK 500 4 MET A 450 -7.90 71.75 REMARK 500 4 CYS A 459 -78.04 -129.77 REMARK 500 4 GLN A 468 17.05 -146.18 REMARK 500 4 HIS A 479 -71.88 -104.60 REMARK 500 4 PHE A 481 -20.03 80.25 REMARK 500 5 THR A 428 -20.49 -175.17 REMARK 500 5 LYS A 438 -76.17 -109.43 REMARK 500 5 MET A 450 48.65 -77.31 REMARK 500 5 CYS A 459 -61.55 -141.00 REMARK 500 5 HIS A 479 -66.78 -94.58 REMARK 500 6 ALA A 417 25.94 -151.19 REMARK 500 6 LYS A 438 -61.21 -108.38 REMARK 500 6 PRO A 442 93.46 -66.25 REMARK 500 6 CYS A 459 -75.43 -131.08 REMARK 500 6 GLN A 468 26.41 -141.09 REMARK 500 6 THR A 469 -73.43 -111.94 REMARK 500 6 THR A 472 126.02 69.81 REMARK 500 6 HIS A 479 -75.01 -153.76 REMARK 500 7 GLU A 423 -69.06 -91.92 REMARK 500 7 ALA A 424 131.85 -170.46 REMARK 500 7 SER A 432 -168.63 64.49 REMARK 500 7 LYS A 438 -64.15 -105.50 REMARK 500 7 PRO A 442 88.38 -65.03 REMARK 500 7 CYS A 459 -82.04 -97.98 REMARK 500 7 THR A 469 -136.17 -141.16 REMARK 500 7 TRP A 471 101.94 -55.90 REMARK 500 7 HIS A 479 -74.56 -142.07 REMARK 500 REMARK 500 THIS ENTRY HAS 130 RAMACHANDRAN OUTLIERS. 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 436 SG REMARK 620 2 CYS A 439 SG 103.9 REMARK 620 3 CYS A 454 SG 105.9 120.9 REMARK 620 4 CYS A 459 SG 122.8 101.1 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 464 SG REMARK 620 2 CYS A 467 SG 112.7 REMARK 620 3 CYS A 475 SG 119.0 115.9 REMARK 620 4 HIS A 479 NE2 124.2 91.5 89.0 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JMO RELATED DB: PDB REMARK 900 PARKIN IN-BETWEEN RING DOMAIN REMARK 900 RELATED ID: 15074 RELATED DB: BMRB REMARK 900 PARKIN IN-BETWEEN RING DOMAIN REMARK 900 RELATED ID: 18642 RELATED DB: BMRB DBREF 2LWR A 417 482 UNP Q95TI4 Q95TI4_DROME 417 482 SEQADV 2LWR GLY A -1 UNP Q95TI4 EXPRESSION TAG SEQADV 2LWR SER A 0 UNP Q95TI4 EXPRESSION TAG SEQRES 1 A 68 GLY SER ALA GLU ALA ARG TRP ASP GLU ALA SER ASN VAL SEQRES 2 A 68 THR ILE LYS VAL SER THR LYS PRO CYS PRO LYS CYS ARG SEQRES 3 A 68 THR PRO THR GLU ARG ASP GLY GLY CYS MET HIS MET VAL SEQRES 4 A 68 CYS THR ARG ALA GLY CYS GLY PHE GLU TRP CYS TRP VAL SEQRES 5 A 68 CYS GLN THR GLU TRP THR ARG ASP CYS MET GLY ALA HIS SEQRES 6 A 68 TRP PHE GLY HET ZN A 1 1 HET ZN A 2 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) SHEET 1 A 2 THR A 433 PRO A 435 0 SHEET 2 A 2 PRO A 442 GLU A 444 -1 O THR A 443 N LYS A 434 SHEET 1 B 2 CYS A 449 MET A 450 0 SHEET 2 B 2 TRP A 480 PHE A 481 -1 O TRP A 480 N MET A 450 SHEET 1 C 2 MET A 452 VAL A 453 0 SHEET 2 C 2 GLU A 462 TRP A 463 -1 O TRP A 463 N MET A 452 LINK ZN ZN A 1 SG CYS A 436 1555 1555 2.34 LINK ZN ZN A 1 SG CYS A 439 1555 1555 2.29 LINK ZN ZN A 1 SG CYS A 454 1555 1555 2.26 LINK ZN ZN A 1 SG CYS A 459 1555 1555 2.33 LINK ZN ZN A 2 SG CYS A 464 1555 1555 2.23 LINK ZN ZN A 2 SG CYS A 467 1555 1555 2.24 LINK ZN ZN A 2 SG CYS A 475 1555 1555 2.16 LINK ZN ZN A 2 NE2 HIS A 479 1555 1555 2.47 SITE 1 AC1 4 CYS A 436 CYS A 439 CYS A 454 CYS A 459 SITE 1 AC2 5 CYS A 464 CYS A 467 THR A 472 CYS A 475 SITE 2 AC2 5 HIS A 479 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1