HEADER HYDROLASE/SIGNALING PROTEIN 05-SEP-16 5GVI TITLE ZEBRAFISH USP30 IN COMPLEX WITH LYS6-LINKED DIUBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 30; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 61-501; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UBIQUITIN; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: UBIQUITIN; COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: USP30; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOLD-SUMO; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 GENE: RPS27A, UBA80, UBCEP1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET26B; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 23 ORGANISM_COMMON: MOUSE; SOURCE 24 ORGANISM_TAXID: 10090; SOURCE 25 GENE: RPS27A, UBA80, UBCEP1; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 28 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 29 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 30 EXPRESSION_SYSTEM_PLASMID: PET26B KEYWDS COMPLEX, MITOPHAGY, HYDROLASE-SIGNALING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.SATO,S.FUKAI REVDAT 5 08-NOV-23 5GVI 1 REMARK REVDAT 4 22-NOV-17 5GVI 1 JRNL REVDAT 3 18-OCT-17 5GVI 1 JRNL REVDAT 2 27-SEP-17 5GVI 1 JRNL REMARK REVDAT 1 13-SEP-17 5GVI 0 JRNL AUTH Y.SATO,K.OKATSU,Y.SAEKI,K.YAMANO,N.MATSUDA,A.KAIHO, JRNL AUTH 2 A.YAMAGATA,S.GOTO-ITO,M.ISHIKAWA,Y.HASHIMOTO,K.TANAKA, JRNL AUTH 3 S.FUKAI JRNL TITL STRUCTURAL BASIS FOR SPECIFIC CLEAVAGE OF LYS6-LINKED JRNL TITL 2 POLYUBIQUITIN CHAINS BY USP30 JRNL REF NAT. STRUCT. MOL. BIOL. V. 24 911 2017 JRNL REFN ESSN 1545-9985 JRNL PMID 28945247 JRNL DOI 10.1038/NSMB.3469 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 47938 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 2378 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.0951 - 4.8054 0.99 2774 129 0.1732 0.1847 REMARK 3 2 4.8054 - 3.8148 1.00 2733 127 0.1472 0.1566 REMARK 3 3 3.8148 - 3.3328 1.00 2676 148 0.1679 0.1971 REMARK 3 4 3.3328 - 3.0282 1.00 2713 142 0.1775 0.2275 REMARK 3 5 3.0282 - 2.8112 1.00 2682 136 0.1911 0.2373 REMARK 3 6 2.8112 - 2.6454 1.00 2699 137 0.1839 0.2145 REMARK 3 7 2.6454 - 2.5130 1.00 2681 125 0.1838 0.2260 REMARK 3 8 2.5130 - 2.4036 1.00 2697 147 0.1814 0.2270 REMARK 3 9 2.4036 - 2.3111 1.00 2645 153 0.1814 0.2151 REMARK 3 10 2.3111 - 2.2313 1.00 2700 127 0.1741 0.2406 REMARK 3 11 2.2313 - 2.1616 1.00 2682 129 0.1858 0.2099 REMARK 3 12 2.1616 - 2.0998 1.00 2644 157 0.1980 0.2469 REMARK 3 13 2.0998 - 2.0445 0.99 2650 138 0.2009 0.2669 REMARK 3 14 2.0445 - 1.9946 1.00 2616 164 0.2107 0.2570 REMARK 3 15 1.9946 - 1.9493 0.99 2699 123 0.2389 0.2580 REMARK 3 16 1.9493 - 1.9078 0.99 2638 130 0.2596 0.2959 REMARK 3 17 1.9078 - 1.8696 1.00 2631 166 0.2751 0.3033 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3848 REMARK 3 ANGLE : 1.022 5191 REMARK 3 CHIRALITY : 0.044 586 REMARK 3 PLANARITY : 0.004 668 REMARK 3 DIHEDRAL : 14.209 1447 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 36.5575 29.4764 -0.6696 REMARK 3 T TENSOR REMARK 3 T11: 0.2464 T22: 0.2179 REMARK 3 T33: 0.2043 T12: 0.0314 REMARK 3 T13: -0.0728 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 3.0657 L22: 2.5741 REMARK 3 L33: 1.5193 L12: 0.9701 REMARK 3 L13: -0.4050 L23: -0.1344 REMARK 3 S TENSOR REMARK 3 S11: 0.0183 S12: -0.0781 S13: 0.2229 REMARK 3 S21: 0.0521 S22: 0.0774 S23: -0.0085 REMARK 3 S31: -0.0326 S32: 0.0534 S33: -0.0580 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5GVI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001526. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47938 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 42.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.380 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3I3T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 90 MM TRIS-HCL, 180 MM AMMONIUM REMARK 280 ACETATE, 23% PEG3350, 10 MM TCEP, PH 9.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 39.92067 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 19.96033 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 29.94050 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 9.98017 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.90083 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLN A 98 REMARK 465 ASN A 99 REMARK 465 SER A 100 REMARK 465 ALA A 101 REMARK 465 ASP A 102 REMARK 465 ARG A 103 REMARK 465 GLU A 104 REMARK 465 ARG A 105 REMARK 465 THR A 106 REMARK 465 GLN A 176 REMARK 465 PRO A 177 REMARK 465 ARG A 178 REMARK 465 VAL A 179 REMARK 465 ALA A 180 REMARK 465 HIS A 181 REMARK 465 LEU A 182 REMARK 465 PHE A 183 REMARK 465 ASP A 184 REMARK 465 MET A 185 REMARK 465 GLN A 186 REMARK 465 THR A 187 REMARK 465 LEU A 188 REMARK 465 GLU A 189 REMARK 465 LYS A 190 REMARK 465 SER A 191 REMARK 465 VAL A 192 REMARK 465 GLU A 193 REMARK 465 SER A 194 REMARK 465 LYS A 195 REMARK 465 GLU A 196 REMARK 465 LYS A 197 REMARK 465 ASN A 198 REMARK 465 ILE A 199 REMARK 465 SER A 200 REMARK 465 CYS A 201 REMARK 465 ARG A 202 REMARK 465 SER A 203 REMARK 465 GLY A 204 REMARK 465 GLY A 205 REMARK 465 PRO A 206 REMARK 465 LEU A 207 REMARK 465 HIS A 208 REMARK 465 PRO A 209 REMARK 465 ILE A 210 REMARK 465 PRO A 211 REMARK 465 SER A 212 REMARK 465 LEU A 213 REMARK 465 TRP A 214 REMARK 465 ILE A 254 REMARK 465 GLN A 255 REMARK 465 TRP A 256 REMARK 465 GLY A 257 REMARK 465 ASN A 293 REMARK 465 HIS A 352 REMARK 465 CYS A 353 REMARK 465 SER A 354 REMARK 465 ALA A 355 REMARK 465 ALA A 356 REMARK 465 GLN A 357 REMARK 465 SER A 358 REMARK 465 GLN A 359 REMARK 465 GLN A 360 REMARK 465 LYS A 361 REMARK 465 THR A 362 REMARK 465 SER A 363 REMARK 465 ARG A 364 REMARK 465 THR A 365 REMARK 465 ASN A 366 REMARK 465 LYS A 367 REMARK 465 ALA A 368 REMARK 465 LYS A 369 REMARK 465 ALA A 370 REMARK 465 SER A 371 REMARK 465 ALA A 372 REMARK 465 ASP A 373 REMARK 465 PRO A 374 REMARK 465 LYS A 375 REMARK 465 ASP A 376 REMARK 465 LYS A 377 REMARK 465 ASN A 389 REMARK 465 ASN A 390 REMARK 465 ASN A 391 REMARK 465 LYS A 392 REMARK 465 PRO A 393 REMARK 465 GLN A 394 REMARK 465 SER A 395 REMARK 465 ASN A 396 REMARK 465 GLY A 397 REMARK 465 THR A 398 REMARK 465 PHE A 399 REMARK 465 PRO A 400 REMARK 465 SER A 401 REMARK 465 VAL A 402 REMARK 465 PHE A 403 REMARK 465 LEU A 404 REMARK 465 HIS A 405 REMARK 465 SER A 406 REMARK 465 PRO A 407 REMARK 465 GLY A 408 REMARK 465 LEU A 409 REMARK 465 SER A 410 REMARK 465 SER A 411 REMARK 465 GLN A 412 REMARK 465 LEU A 413 REMARK 465 ASN A 414 REMARK 465 LEU A 415 REMARK 465 THR A 416 REMARK 465 TYR A 417 REMARK 465 ASP A 418 REMARK 465 TYR A 419 REMARK 465 SER A 420 REMARK 465 THR A 421 REMARK 465 GLY A 496 REMARK 465 LEU A 497 REMARK 465 ARG A 498 REMARK 465 VAL A 499 REMARK 465 GLU A 500 REMARK 465 GLU A 501 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 175 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 215 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 258 CG CD NE CZ NH1 NH2 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 OD2 ASP A 132 O HOH A 701 2.18 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 MET A 62 -148.22 -129.65 REMARK 500 THR A 96 37.00 -81.84 REMARK 500 GLU A 174 49.79 -82.06 REMARK 500 TYR A 424 72.45 -119.42 REMARK 500 ASP A 437 -156.30 -108.61 REMARK 500 ASP A 468 -107.48 49.91 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 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 230 SG REMARK 620 2 CYS A 233 SG 107.4 REMARK 620 3 CYS A 280 SG 111.2 111.1 REMARK 620 4 CYS A 283 SG 107.7 107.1 112.1 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 601 DBREF1 5GVI A 61 501 UNP A0A0R4ILB8_DANRE DBREF2 5GVI A A0A0R4ILB8 61 501 DBREF 5GVI B 1 76 UNP P62983 RS27A_MOUSE 1 76 DBREF 5GVI C 1 72 UNP P62983 RS27A_MOUSE 1 72 SEQADV 5GVI SER A 58 UNP A0A0R4ILB EXPRESSION TAG SEQADV 5GVI HIS A 59 UNP A0A0R4ILB EXPRESSION TAG SEQADV 5GVI MET A 60 UNP A0A0R4ILB EXPRESSION TAG SEQADV 5GVI ALA A 73 UNP A0A0R4ILB CYS 73 ENGINEERED MUTATION SEQADV 5GVI VAL A 127 UNP A0A0R4ILB ASP 127 ENGINEERED MUTATION SEQADV 5GVI ARG B 6 UNP P62983 LYS 6 ENGINEERED MUTATION SEQRES 1 A 444 SER HIS MET GLY MET VAL PRO GLY LEU LEU ASN LEU GLY SEQRES 2 A 444 ASN THR ALA PHE MET ASN SER LEU LEU GLN GLY LEU ALA SEQRES 3 A 444 ALA CYS PRO SER PHE ILE ARG TRP LEU GLU ASP PHE THR SEQRES 4 A 444 SER GLN ASN SER ALA ASP ARG GLU ARG THR GLU ARG GLU SEQRES 5 A 444 THR GLN LEU SER ARG SER LEU MET GLN LEU LEU LYS ALA SEQRES 6 A 444 LEU SER SER HIS VAL PRO GLY GLU ASP ASP VAL LEU ASP SEQRES 7 A 444 ALA GLY GLY LEU LEU GLU ALA LEU ARG LEU TYR ARG TRP SEQRES 8 A 444 HIS ILE SER SER PHE GLU GLU GLN ASP ALA HIS GLU LEU SEQRES 9 A 444 PHE HIS VAL LEU THR SER SER LEU GLU GLU GLU GLN GLU SEQRES 10 A 444 ARG GLN PRO ARG VAL ALA HIS LEU PHE ASP MET GLN THR SEQRES 11 A 444 LEU GLU LYS SER VAL GLU SER LYS GLU LYS ASN ILE SER SEQRES 12 A 444 CYS ARG SER GLY GLY PRO LEU HIS PRO ILE PRO SER LEU SEQRES 13 A 444 TRP ARG THR ARG HIS PRO PHE HIS GLY ARG LEU THR SER SEQRES 14 A 444 TYR MET ALA CYS LYS ARG CYS GLU GLN GLN SER PRO VAL SEQRES 15 A 444 HIS TYR ASP SER PHE ASP SER LEU SER LEU SER ILE PRO SEQRES 16 A 444 SER ILE GLN TRP GLY ARG PRO VAL THR LEU ASP GLN CYS SEQRES 17 A 444 LEU GLN HIS PHE ILE SER SER GLU THR ILE LYS GLU VAL SEQRES 18 A 444 GLU CYS GLU ASN CYS THR LYS GLN GLN ALA GLY GLU LEU SEQRES 19 A 444 VAL ASN GLY GLU VAL LEU GLU SER GLN ARG THR THR PHE SEQRES 20 A 444 VAL LYS GLN LEU LYS LEU GLY LYS LEU PRO GLN CYS LEU SEQRES 21 A 444 CYS ILE HIS LEU GLN ARG LEU THR TRP SER LYS GLU GLY SEQRES 22 A 444 SER PRO ILE LYS ARG GLN GLU HIS VAL GLN PHE THR GLU SEQRES 23 A 444 TYR LEU SER LEU ASP ARG TYR LYS HIS CYS SER ALA ALA SEQRES 24 A 444 GLN SER GLN GLN LYS THR SER ARG THR ASN LYS ALA LYS SEQRES 25 A 444 ALA SER ALA ASP PRO LYS ASP LYS ALA ILE ALA ASN GLY SEQRES 26 A 444 VAL ASP SER GLU HIS CYS ASN ASN ASN LYS PRO GLN SER SEQRES 27 A 444 ASN GLY THR PHE PRO SER VAL PHE LEU HIS SER PRO GLY SEQRES 28 A 444 LEU SER SER GLN LEU ASN LEU THR TYR ASP TYR SER THR SEQRES 29 A 444 SER GLU TYR LEU PHE ARG LEU THR ALA VAL LEU VAL HIS SEQRES 30 A 444 HIS GLY ASP MET HIS SER GLY HIS PHE ILE THR TYR ARG SEQRES 31 A 444 ARG CYS PRO ALA ALA PRO ARG GLY THR SER PRO PHE SER SEQRES 32 A 444 SER GLN TRP LEU TRP VAL SER ASP ASP SER VAL ARG LYS SEQRES 33 A 444 ALA SER LEU GLN GLU VAL LEU SER SER SER ALA TYR LEU SEQRES 34 A 444 LEU PHE TYR GLU ARG MET GLN ARG PRO GLY LEU ARG VAL SEQRES 35 A 444 GLU GLU SEQRES 1 B 76 MET GLN ILE PHE VAL ARG 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 GLY SEQRES 1 C 72 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 72 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 72 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 72 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 72 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 72 THR LEU HIS LEU VAL LEU ARG HET ZN A 601 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *123(H2 O) HELIX 1 AA1 THR A 72 ALA A 83 1 12 HELIX 2 AA2 CYS A 85 THR A 96 1 12 HELIX 3 AA3 THR A 110 LEU A 123 1 14 HELIX 4 AA4 ALA A 136 ARG A 147 1 12 HELIX 5 AA5 ASP A 157 GLU A 174 1 18 HELIX 6 AA6 LEU A 262 SER A 271 1 10 HELIX 7 AA7 CYS A 280 GLN A 286 1 7 HELIX 8 AA8 ASP A 348 LYS A 351 5 4 HELIX 9 AA9 SER A 475 SER A 481 1 7 HELIX 10 AB1 THR B 22 GLY B 35 1 14 HELIX 11 AB2 PRO B 37 GLN B 41 5 5 HELIX 12 AB3 LEU B 56 ASN B 60 5 5 HELIX 13 AB4 THR C 22 GLY C 35 1 14 HELIX 14 AB5 PRO C 37 ASP C 39 5 3 HELIX 15 AB6 LEU C 56 ASN C 60 5 5 SHEET 1 AA1 2 GLY A 65 LEU A 66 0 SHEET 2 AA1 2 VAL A 133 LEU A 134 1 O LEU A 134 N GLY A 65 SHEET 1 AA2 6 GLU A 273 GLU A 279 0 SHEET 2 AA2 6 ARG A 301 LYS A 312 -1 O THR A 302 N VAL A 278 SHEET 3 AA2 6 GLY A 222 CYS A 230 -1 N THR A 225 O LYS A 309 SHEET 4 AA2 6 HIS A 240 PHE A 244 -1 O ASP A 242 N LEU A 224 SHEET 5 AA2 6 ILE A 379 ALA A 380 1 O ILE A 379 N TYR A 241 SHEET 6 AA2 6 VAL A 383 ASP A 384 -1 O VAL A 383 N ALA A 380 SHEET 1 AA3 5 LEU A 247 SER A 250 0 SHEET 2 AA3 5 CYS A 316 GLN A 322 1 O HIS A 320 N LEU A 247 SHEET 3 AA3 5 ALA A 484 ARG A 491 -1 O TYR A 485 N LEU A 321 SHEET 4 AA3 5 LEU A 425 GLY A 436 -1 N THR A 429 O PHE A 488 SHEET 5 AA3 5 TYR A 344 SER A 346 -1 N LEU A 345 O PHE A 426 SHEET 1 AA4 7 LEU A 247 SER A 250 0 SHEET 2 AA4 7 CYS A 316 GLN A 322 1 O HIS A 320 N LEU A 247 SHEET 3 AA4 7 ALA A 484 ARG A 491 -1 O TYR A 485 N LEU A 321 SHEET 4 AA4 7 LEU A 425 GLY A 436 -1 N THR A 429 O PHE A 488 SHEET 5 AA4 7 GLY A 441 ARG A 448 -1 O TYR A 446 N VAL A 431 SHEET 6 AA4 7 TRP A 463 SER A 467 -1 O LEU A 464 N ARG A 447 SHEET 7 AA4 7 SER A 470 ALA A 474 -1 O ARG A 472 N TRP A 465 SHEET 1 AA5 2 VAL A 260 THR A 261 0 SHEET 2 AA5 2 VAL A 339 GLN A 340 1 O GLN A 340 N VAL A 260 SHEET 1 AA6 2 LEU A 324 TRP A 326 0 SHEET 2 AA6 2 PRO A 332 LYS A 334 -1 O ILE A 333 N THR A 325 SHEET 1 AA7 5 THR B 12 GLU B 16 0 SHEET 2 AA7 5 GLN B 2 ARG B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 AA7 5 THR B 66 VAL B 70 1 O LEU B 67 N ARG B 6 SHEET 4 AA7 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA7 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 AA8 5 THR C 12 GLU C 16 0 SHEET 2 AA8 5 GLN C 2 THR C 7 -1 N VAL C 5 O ILE C 13 SHEET 3 AA8 5 THR C 66 LEU C 71 1 O LEU C 67 N PHE C 4 SHEET 4 AA8 5 GLN C 41 PHE C 45 -1 N ARG C 42 O VAL C 70 SHEET 5 AA8 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 LINK C GLY B 76 NZ LYS C 6 1555 1555 1.33 LINK SG CYS A 230 ZN ZN A 601 1555 1555 2.35 LINK SG CYS A 233 ZN ZN A 601 1555 1555 2.30 LINK SG CYS A 280 ZN ZN A 601 1555 1555 2.34 LINK SG CYS A 283 ZN ZN A 601 1555 1555 2.30 SITE 1 AC1 4 CYS A 230 CYS A 233 CYS A 280 CYS A 283 CRYST1 130.270 130.270 59.881 90.00 90.00 120.00 P 65 6 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 0.007676 0.004432 0.000000 0.00000 SCALE2 0.000000 0.008864 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016700 0.00000