HEADER LIGASE 30-JAN-13 2M48 TITLE SOLUTION STRUCTURE OF IBR-RING2 TANDEM DOMAIN FROM PARKIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 3 CHAIN: A; COMPND 4 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: CG10523, PARK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX-6P2; SOURCE 9 OTHER_DETAILS: MODIFIED TO HAVE TEV SITE KEYWDS PARKIN, RING, IBR, E3 LIGASE, ZN-BINDING, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.J.NOH,P.MERCIER,D.E.SPRATT,G.S.SHAW REVDAT 4 13-MAR-24 2M48 1 SOURCE REMARK LINK REVDAT 3 15-OCT-14 2M48 1 COMPND REVDAT 2 10-JUL-13 2M48 1 JRNL REVDAT 1 15-MAY-13 2M48 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 2.33 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 2M48 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000103188. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 0.150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 25 MM TRIS, 150 MM SODIUM REMARK 210 CHLORIDE, 5 MM DTT, 500 UM [U-98% REMARK 210 15N] SD01679P, 90% H2O/10% D2O; REMARK 210 25 MM TRIS, 150 MM SODIUM REMARK 210 CHLORIDE, 5 MM DTT, 500 UM [U-98% REMARK 210 13C; U-98% 15N] SD01679P, 90% REMARK 210 H2O/10% D2O; 25 MM TRIS, 150 MM REMARK 210 SODIUM CHLORIDE-, 5 MM DTT, 500 REMARK 210 UM [U-98% 13C; U-98% 15N] REMARK 210 SD01679P, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 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 HCACO; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HNCO; REMARK 210 3D HNHA; 3D C(CO)NH; 2D (HB) REMARK 210 CB(CGCD)HD; 2D (HB)CB(CGCDCE)HE; REMARK 210 3D HNHB; 2D 1H-13C HSQC AROMATIC; REMARK 210 3D H(CCO)NH; 3D 13C TOCSY REMARK 210 AROMATIC 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 : 20 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 CYS A 358 -147.93 -115.35 REMARK 500 1 TYR A 389 138.51 76.62 REMARK 500 1 CYS A 394 145.61 -174.99 REMARK 500 1 THR A 404 -88.59 -148.88 REMARK 500 1 SER A 406 97.27 -166.56 REMARK 500 1 ASN A 414 -70.77 -117.16 REMARK 500 1 ASN A 426 117.67 72.02 REMARK 500 1 LYS A 438 -66.64 -101.30 REMARK 500 1 CYS A 459 -90.61 -151.34 REMARK 500 1 TRP A 480 45.45 -82.41 REMARK 500 2 CYS A 358 -96.71 -89.03 REMARK 500 2 GLN A 387 32.75 -87.25 REMARK 500 2 TYR A 389 121.98 69.19 REMARK 500 2 ALA A 401 80.16 59.53 REMARK 500 2 ASN A 414 -83.53 -74.61 REMARK 500 2 LYS A 438 -73.56 -103.24 REMARK 500 2 CYS A 459 -90.89 -110.22 REMARK 500 2 TRP A 471 108.12 -56.41 REMARK 500 3 CYS A 358 -82.79 -86.55 REMARK 500 3 CYS A 373 47.47 -77.81 REMARK 500 3 CYS A 377 -131.28 -100.40 REMARK 500 3 CYS A 385 -159.66 -143.02 REMARK 500 3 GLN A 387 25.39 -76.18 REMARK 500 3 TYR A 389 100.49 64.40 REMARK 500 3 ARG A 415 109.24 -166.05 REMARK 500 3 ARG A 420 118.19 -160.18 REMARK 500 3 LYS A 438 -61.25 -109.87 REMARK 500 3 PRO A 442 98.26 -68.64 REMARK 500 3 CYS A 454 103.16 -59.54 REMARK 500 3 CYS A 459 -90.33 -152.09 REMARK 500 4 VAL A 345 26.04 46.58 REMARK 500 4 CYS A 358 -93.56 -104.47 REMARK 500 4 MET A 360 -72.49 -61.74 REMARK 500 4 CYS A 377 -127.20 -89.03 REMARK 500 4 TYR A 389 101.05 63.20 REMARK 500 4 THR A 399 -177.06 -177.63 REMARK 500 4 THR A 404 133.15 -171.83 REMARK 500 4 LYS A 438 -67.49 -96.29 REMARK 500 4 ALA A 457 87.31 -66.65 REMARK 500 4 CYS A 459 -91.90 -145.78 REMARK 500 5 GLU A 343 79.13 -155.05 REMARK 500 5 ALA A 348 -168.52 -113.67 REMARK 500 5 CYS A 358 -97.27 -106.04 REMARK 500 5 CYS A 377 -91.52 -124.70 REMARK 500 5 TYR A 389 120.71 73.45 REMARK 500 5 HIS A 390 -46.81 -148.23 REMARK 500 5 PRO A 413 108.07 -56.32 REMARK 500 5 ALA A 417 100.90 62.76 REMARK 500 5 LYS A 438 -63.99 -107.59 REMARK 500 5 ALA A 457 97.65 -62.33 REMARK 500 REMARK 500 THIS ENTRY HAS 241 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 353 SG REMARK 620 2 CYS A 358 SG 102.1 REMARK 620 3 CYS A 373 SG 115.5 101.2 REMARK 620 4 CYS A 377 SG 115.4 100.0 118.3 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 382 SG REMARK 620 2 CYS A 385 SG 111.9 REMARK 620 3 HIS A 390 NE2 109.3 96.8 REMARK 620 4 CYS A 394 SG 115.4 123.8 94.7 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 436 SG REMARK 620 2 CYS A 439 SG 105.7 REMARK 620 3 CYS A 454 SG 111.2 109.5 REMARK 620 4 CYS A 459 SG 110.9 105.7 113.5 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 464 SG REMARK 620 2 CYS A 467 SG 118.1 REMARK 620 3 CYS A 475 SG 122.7 115.9 REMARK 620 4 HIS A 479 NE2 93.0 90.5 104.3 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JMO RELATED DB: PDB REMARK 900 RELATED ID: 1WD2 RELATED DB: PDB REMARK 900 RELATED ID: 18990 RELATED DB: BMRB DBREF 2M48 A 342 482 UNP Q95TI4 Q95TI4_DROME 342 482 SEQRES 1 A 141 GLU GLU TYR VAL LEU GLN ALA GLY GLY VAL LEU CYS PRO SEQRES 2 A 141 GLN PRO GLY CYS GLY MET GLY LEU LEU VAL GLU PRO ASP SEQRES 3 A 141 CYS ARG LYS VAL THR CYS GLN ASN GLY CYS GLY TYR VAL SEQRES 4 A 141 PHE CYS ARG ASN CYS LEU GLN GLY TYR HIS ILE GLY GLU SEQRES 5 A 141 CYS LEU PRO GLU GLY THR GLY ALA SER ALA THR ASN SER SEQRES 6 A 141 CYS GLU TYR THR VAL ASP PRO ASN ARG ALA ALA GLU ALA SEQRES 7 A 141 ARG TRP ASP GLU ALA SER ASN VAL THR ILE LYS VAL SER SEQRES 8 A 141 THR LYS PRO CYS PRO LYS CYS ARG THR PRO THR GLU ARG SEQRES 9 A 141 ASP GLY GLY CYS MET HIS MET VAL CYS THR ARG ALA GLY SEQRES 10 A 141 CYS GLY PHE GLU TRP CYS TRP VAL CYS GLN THR GLU TRP SEQRES 11 A 141 THR ARG ASP CYS MET GLY ALA HIS TRP PHE GLY HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HETNAM ZN ZINC ION FORMUL 2 ZN 4(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 HIS A 451 VAL A 453 0 SHEET 2 B 2 GLU A 462 CYS A 464 -1 O TRP A 463 N MET A 452 LINK SG CYS A 353 ZN ZN A 501 1555 1555 2.21 LINK SG CYS A 358 ZN ZN A 501 1555 1555 2.52 LINK SG CYS A 373 ZN ZN A 501 1555 1555 2.25 LINK SG CYS A 377 ZN ZN A 501 1555 1555 2.21 LINK SG CYS A 382 ZN ZN A 502 1555 1555 2.18 LINK SG CYS A 385 ZN ZN A 502 1555 1555 2.15 LINK NE2 HIS A 390 ZN ZN A 502 1555 1555 2.16 LINK SG CYS A 394 ZN ZN A 502 1555 1555 2.24 LINK SG CYS A 436 ZN ZN A 503 1555 1555 2.26 LINK SG CYS A 439 ZN ZN A 503 1555 1555 2.25 LINK SG CYS A 454 ZN ZN A 503 1555 1555 2.18 LINK SG CYS A 459 ZN ZN A 503 1555 1555 2.27 LINK SG CYS A 464 ZN ZN A 504 1555 1555 2.19 LINK SG CYS A 467 ZN ZN A 504 1555 1555 2.16 LINK SG CYS A 475 ZN ZN A 504 1555 1555 2.22 LINK NE2 HIS A 479 ZN ZN A 504 1555 1555 2.18 SITE 1 AC1 4 CYS A 353 CYS A 358 CYS A 373 CYS A 377 SITE 1 AC2 4 CYS A 382 CYS A 385 HIS A 390 CYS A 394 SITE 1 AC3 4 CYS A 436 CYS A 439 CYS A 454 CYS A 459 SITE 1 AC4 5 CYS A 464 CYS A 467 THR A 469 CYS A 475 SITE 2 AC4 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