HEADER HYDROLASE 10-JAN-19 6J4S TITLE STRUCTURAL BASIS OF TUBULIN DETYROSINATION BY VASOHIBINS-SVBP ENZYME TITLE 2 COMPLEX AND FUNCTIONAL IMPLICATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUBULINYL-TYR CARBOXYPEPTIDASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VASOHIBIN-2,VASOHIBIN-LIKE PROTEIN; COMPND 5 EC: 3.4.17.17; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SMALL VASOHIBIN-BINDING PROTEIN; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: COILED COIL DOMAIN-CONTAINING PROTEIN 23; COMPND 11 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: VASH2, VASHL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: RSFDUET; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: SVBP, CCDC23; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: RSFDUET KEYWDS CARBOXYPEPTIDASE, TUBULIN, MICROTUBULE., HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.WANG,H.BAO,H.HUANG REVDAT 3 22-NOV-23 6J4S 1 REMARK REVDAT 2 13-NOV-19 6J4S 1 JRNL REVDAT 1 01-MAY-19 6J4S 0 JRNL AUTH N.WANG,C.BOSC,S.RYUL CHOI,B.BOULAN,L.PERIS,N.OLIERIC,H.BAO, JRNL AUTH 2 F.KRICHEN,L.CHEN,A.ANDRIEUX,V.OLIERIC,M.J.MOUTIN, JRNL AUTH 3 M.O.STEINMETZ,H.HUANG JRNL TITL STRUCTURAL BASIS OF TUBULIN DETYROSINATION BY THE JRNL TITL 2 VASOHIBIN-SVBP ENZYME COMPLEX. JRNL REF NAT.STRUCT.MOL.BIOL. V. 26 571 2019 JRNL REFN ESSN 1545-9985 JRNL PMID 31235911 JRNL DOI 10.1038/S41594-019-0241-Y REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 12747 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.540 REMARK 3 FREE R VALUE TEST SET COUNT : 706 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 44.3099 - 4.7865 0.98 2562 147 0.1810 0.2203 REMARK 3 2 4.7865 - 3.7998 1.00 2555 125 0.1424 0.1925 REMARK 3 3 3.7998 - 3.3197 1.00 2488 150 0.1634 0.2135 REMARK 3 4 3.3197 - 3.0162 1.00 2447 165 0.1940 0.2608 REMARK 3 5 3.0162 - 2.8001 0.80 1989 119 0.2174 0.2990 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.75 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 : 0.009 2385 REMARK 3 ANGLE : 1.015 3208 REMARK 3 CHIRALITY : 0.052 339 REMARK 3 PLANARITY : 0.010 404 REMARK 3 DIHEDRAL : 12.518 1448 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.6139 -27.6531 1.8736 REMARK 3 T TENSOR REMARK 3 T11: 0.2034 T22: 0.2854 REMARK 3 T33: 0.2443 T12: 0.0225 REMARK 3 T13: 0.0696 T23: 0.0577 REMARK 3 L TENSOR REMARK 3 L11: 3.4082 L22: 3.6460 REMARK 3 L33: 1.5844 L12: 1.0861 REMARK 3 L13: -0.5635 L23: -1.1344 REMARK 3 S TENSOR REMARK 3 S11: 0.1464 S12: 0.2794 S13: 0.7824 REMARK 3 S21: -0.0764 S22: 0.2134 S23: 0.2666 REMARK 3 S31: -0.3610 S32: -0.1819 S33: -0.2028 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 298 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.7305 -42.8076 18.0454 REMARK 3 T TENSOR REMARK 3 T11: 0.3385 T22: 0.2550 REMARK 3 T33: 0.1213 T12: 0.0710 REMARK 3 T13: 0.0619 T23: 0.0863 REMARK 3 L TENSOR REMARK 3 L11: 2.7762 L22: 2.2757 REMARK 3 L33: 3.4542 L12: 0.2702 REMARK 3 L13: -0.0055 L23: 0.1400 REMARK 3 S TENSOR REMARK 3 S11: 0.0046 S12: -0.2457 S13: -0.2872 REMARK 3 S21: 0.7364 S22: 0.2929 S23: 0.2885 REMARK 3 S31: 0.0095 S32: -0.0952 S33: -0.0143 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 24 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9912 -19.7658 1.1054 REMARK 3 T TENSOR REMARK 3 T11: 0.2898 T22: 0.3085 REMARK 3 T33: 0.3668 T12: -0.0981 REMARK 3 T13: 0.1963 T23: 0.0729 REMARK 3 L TENSOR REMARK 3 L11: 6.5984 L22: 8.7711 REMARK 3 L33: 7.5626 L12: 0.8645 REMARK 3 L13: 0.9313 L23: 0.1617 REMARK 3 S TENSOR REMARK 3 S11: 0.2122 S12: 0.0172 S13: 0.4602 REMARK 3 S21: 0.2697 S22: 0.1722 S23: -0.3422 REMARK 3 S31: -0.6047 S32: 0.3222 S33: -0.1707 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 6J4S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010468. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14701 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.14700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 1.20300 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6J4O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: FULL-LENGTH V2-SVBP COMPLEX AT A REMARK 280 CONCENTRATION OF 15 MG/ML WAS CRYSTALLIZED IN 1.8 M SODIUM/ REMARK 280 POTASSIUM PHOSPHATE, PH 6.8, EVAPORATION, TEMPERATURE 293K 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 63.57550 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 63.57550 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 37.09900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.76150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.09900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.76150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.57550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.09900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 55.76150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.57550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.09900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 55.76150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 THR A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 ALA A 5 REMARK 465 ALA A 6 REMARK 465 ASP A 7 REMARK 465 THR A 8 REMARK 465 HIS A 9 REMARK 465 ARG A 10 REMARK 465 CYS A 11 REMARK 465 PRO A 12 REMARK 465 HIS A 13 REMARK 465 PRO A 14 REMARK 465 LYS A 15 REMARK 465 GLY A 16 REMARK 465 ALA A 17 REMARK 465 LYS A 18 REMARK 465 GLY A 19 REMARK 465 THR A 20 REMARK 465 ARG A 21 REMARK 465 SER A 22 REMARK 465 ARG A 23 REMARK 465 SER A 24 REMARK 465 SER A 25 REMARK 465 HIS A 26 REMARK 465 ALA A 27 REMARK 465 ARG A 28 REMARK 465 PRO A 29 REMARK 465 VAL A 30 REMARK 465 SER A 31 REMARK 465 LEU A 32 REMARK 465 ALA A 33 REMARK 465 THR A 34 REMARK 465 SER A 35 REMARK 465 GLY A 36 REMARK 465 GLY A 37 REMARK 465 SER A 38 REMARK 465 GLU A 39 REMARK 465 GLU A 40 REMARK 465 GLU A 41 REMARK 465 ASP A 42 REMARK 465 LYS A 43 REMARK 465 ASP A 44 REMARK 465 GLY A 45 REMARK 465 GLY A 46 REMARK 465 VAL A 47 REMARK 465 LEU A 48 REMARK 465 SER A 299 REMARK 465 ALA A 300 REMARK 465 HIS A 301 REMARK 465 SER A 302 REMARK 465 PRO A 303 REMARK 465 THR A 304 REMARK 465 GLN A 305 REMARK 465 VAL A 306 REMARK 465 ARG A 307 REMARK 465 SER A 308 REMARK 465 ARG A 309 REMARK 465 GLY A 310 REMARK 465 LYS A 311 REMARK 465 SER A 312 REMARK 465 LEU A 313 REMARK 465 SER A 314 REMARK 465 PRO A 315 REMARK 465 ARG A 316 REMARK 465 ARG A 317 REMARK 465 ARG A 318 REMARK 465 GLN A 319 REMARK 465 ALA A 320 REMARK 465 SER A 321 REMARK 465 PRO A 322 REMARK 465 PRO A 323 REMARK 465 ARG A 324 REMARK 465 ARG A 325 REMARK 465 LEU A 326 REMARK 465 GLY A 327 REMARK 465 ARG A 328 REMARK 465 ARG A 329 REMARK 465 GLU A 330 REMARK 465 LYS A 331 REMARK 465 SER A 332 REMARK 465 PRO A 333 REMARK 465 ALA A 334 REMARK 465 LEU A 335 REMARK 465 PRO A 336 REMARK 465 GLU A 337 REMARK 465 LYS A 338 REMARK 465 LYS A 339 REMARK 465 VAL A 340 REMARK 465 ALA A 341 REMARK 465 ASP A 342 REMARK 465 LEU A 343 REMARK 465 SER A 344 REMARK 465 THR A 345 REMARK 465 LEU A 346 REMARK 465 ASN A 347 REMARK 465 GLU A 348 REMARK 465 VAL A 349 REMARK 465 GLY A 350 REMARK 465 TYR A 351 REMARK 465 GLN A 352 REMARK 465 ILE A 353 REMARK 465 ARG A 354 REMARK 465 ILE A 355 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 PRO B 3 REMARK 465 PRO B 4 REMARK 465 ALA B 5 REMARK 465 ARG B 6 REMARK 465 LYS B 7 REMARK 465 GLU B 8 REMARK 465 LYS B 9 REMARK 465 THR B 10 REMARK 465 LYS B 11 REMARK 465 VAL B 12 REMARK 465 LYS B 13 REMARK 465 GLU B 14 REMARK 465 SER B 15 REMARK 465 VAL B 16 REMARK 465 SER B 17 REMARK 465 ARG B 18 REMARK 465 VAL B 19 REMARK 465 GLU B 20 REMARK 465 LYS B 21 REMARK 465 ALA B 22 REMARK 465 LYS B 23 REMARK 465 GLU B 56 REMARK 465 PHE B 57 REMARK 465 CYS B 58 REMARK 465 LYS B 59 REMARK 465 GLN B 60 REMARK 465 MET B 61 REMARK 465 GLN B 62 REMARK 465 PRO B 63 REMARK 465 PRO B 64 REMARK 465 GLY B 65 REMARK 465 GLU B 66 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 PHE A 49 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 24 CG CD OE1 NE2 REMARK 470 LYS B 25 CG CD CE NZ REMARK 470 ASP B 55 CG OD1 OD2 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 GLN A 122 142.43 80.70 REMARK 500 SER A 187 60.41 32.14 REMARK 500 MET A 216 -111.33 -134.87 REMARK 500 LEU A 220 68.94 -67.85 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 PHE A 56 PRO A 57 84.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 404 DBREF 6J4S A 1 355 UNP Q86V25 VASH2_HUMAN 1 355 DBREF 6J4S B 1 66 UNP Q8N300 SVBP_HUMAN 1 66 SEQRES 1 A 355 MET THR GLY SER ALA ALA ASP THR HIS ARG CYS PRO HIS SEQRES 2 A 355 PRO LYS GLY ALA LYS GLY THR ARG SER ARG SER SER HIS SEQRES 3 A 355 ALA ARG PRO VAL SER LEU ALA THR SER GLY GLY SER GLU SEQRES 4 A 355 GLU GLU ASP LYS ASP GLY GLY VAL LEU PHE HIS VAL ASN SEQRES 5 A 355 LYS SER GLY PHE PRO ILE ASP SER HIS THR TRP GLU ARG SEQRES 6 A 355 MET TRP MET HIS VAL ALA LYS VAL HIS PRO LYS GLY GLY SEQRES 7 A 355 GLU MET VAL GLY ALA ILE ARG ASN ALA ALA PHE LEU ALA SEQRES 8 A 355 LYS PRO SER ILE PRO GLN VAL PRO ASN TYR ARG LEU SER SEQRES 9 A 355 MET THR ILE PRO ASP TRP LEU GLN ALA ILE GLN ASN TYR SEQRES 10 A 355 MET LYS THR LEU GLN TYR ASN HIS THR GLY THR GLN PHE SEQRES 11 A 355 PHE GLU ILE ARG LYS MET ARG PRO LEU SER GLY LEU MET SEQRES 12 A 355 GLU THR ALA LYS GLU MET THR ARG GLU SER LEU PRO ILE SEQRES 13 A 355 LYS CYS LEU GLU ALA VAL ILE LEU GLY ILE TYR LEU THR SEQRES 14 A 355 ASN GLY GLN PRO SER ILE GLU ARG PHE PRO ILE SER PHE SEQRES 15 A 355 LYS THR TYR PHE SER GLY ASN TYR PHE HIS HIS VAL VAL SEQRES 16 A 355 LEU GLY ILE TYR CYS ASN GLY ARG TYR GLY SER LEU GLY SEQRES 17 A 355 MET SER ARG ARG ALA GLU LEU MET ASP LYS PRO LEU THR SEQRES 18 A 355 PHE ARG THR LEU SER ASP LEU ILE PHE ASP PHE GLU ASP SEQRES 19 A 355 SER TYR LYS LYS TYR LEU HIS THR VAL LYS LYS VAL LYS SEQRES 20 A 355 ILE GLY LEU TYR VAL PRO HIS GLU PRO HIS SER PHE GLN SEQRES 21 A 355 PRO ILE GLU TRP LYS GLN LEU VAL LEU ASN VAL SER LYS SEQRES 22 A 355 MET LEU ARG ALA ASP ILE ARG LYS GLU LEU GLU LYS TYR SEQRES 23 A 355 ALA ARG ASP MET ARG MET LYS ILE LEU LYS PRO ALA SER SEQRES 24 A 355 ALA HIS SER PRO THR GLN VAL ARG SER ARG GLY LYS SER SEQRES 25 A 355 LEU SER PRO ARG ARG ARG GLN ALA SER PRO PRO ARG ARG SEQRES 26 A 355 LEU GLY ARG ARG GLU LYS SER PRO ALA LEU PRO GLU LYS SEQRES 27 A 355 LYS VAL ALA ASP LEU SER THR LEU ASN GLU VAL GLY TYR SEQRES 28 A 355 GLN ILE ARG ILE SEQRES 1 B 66 MET ASP PRO PRO ALA ARG LYS GLU LYS THR LYS VAL LYS SEQRES 2 B 66 GLU SER VAL SER ARG VAL GLU LYS ALA LYS GLN LYS SER SEQRES 3 B 66 ALA GLN GLN GLU LEU LYS GLN ARG GLN ARG ALA GLU ILE SEQRES 4 B 66 TYR ALA LEU ASN ARG VAL MET THR GLU LEU GLU GLN GLN SEQRES 5 B 66 GLN PHE ASP GLU PHE CYS LYS GLN MET GLN PRO PRO GLY SEQRES 6 B 66 GLU HET GOL A 401 6 HET GOL A 402 6 HET GOL A 403 6 HET PO4 A 404 5 HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 PO4 O4 P 3- FORMUL 7 HOH *68(H2 O) HELIX 1 AA1 ASP A 59 HIS A 74 1 16 HELIX 2 AA2 GLY A 77 ASN A 86 1 10 HELIX 3 AA3 THR A 106 GLN A 122 1 17 HELIX 4 AA4 PRO A 138 SER A 153 1 16 HELIX 5 AA5 LYS A 157 ASN A 170 1 14 HELIX 6 AA6 ARG A 212 MET A 216 5 5 HELIX 7 AA7 THR A 224 LYS A 238 1 15 HELIX 8 AA8 ASN A 270 MET A 274 5 5 HELIX 9 AA9 LEU A 275 MET A 292 1 18 HELIX 10 AB1 LYS B 25 ASP B 55 1 31 SHEET 1 AA1 2 HIS A 50 VAL A 51 0 SHEET 2 AA1 2 THR A 128 GLN A 129 1 O GLN A 129 N HIS A 50 SHEET 1 AA2 6 LYS A 218 PHE A 222 0 SHEET 2 AA2 6 ARG A 203 LEU A 207 -1 N TYR A 204 O PHE A 222 SHEET 3 AA2 6 ASN A 189 CYS A 200 -1 N ILE A 198 O GLY A 205 SHEET 4 AA2 6 GLU A 176 PHE A 186 -1 N PHE A 182 O HIS A 193 SHEET 5 AA2 6 THR A 242 ILE A 248 -1 O THR A 242 N TYR A 185 SHEET 6 AA2 6 LEU A 267 LEU A 269 -1 O LEU A 269 N VAL A 246 SITE 1 AC1 3 GLU A 176 HIS A 254 GLU A 255 SITE 1 AC2 6 TYR A 123 HIS A 125 SER A 210 ARG A 211 SITE 2 AC2 6 ALA A 213 HOH A 537 SITE 1 AC3 2 HIS A 241 HOH A 527 SITE 1 AC4 3 LYS A 183 HIS A 192 LYS A 247 CRYST1 74.198 111.523 127.151 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 0.013477 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008967 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007865 0.00000