PDB Short entry for 6J4V HEADER HYDROLASE 10-JAN-19 6J4V 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; COMPND 12 MUTATION: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: TUBULIN ALPHA-1B CHAIN; COMPND 15 CHAIN: C; COMPND 16 SYNONYM: ALPHA-TUBULIN UBIQUITOUS,TUBULIN K-ALPHA-1,TUBULIN ALPHA- COMPND 17 UBIQUITOUS CHAIN; COMPND 18 ENGINEERED: YES; COMPND 19 MUTATION: 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; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: TUBA1B; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 27 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 28 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 29 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 30 EXPRESSION_SYSTEM_PLASMID: PGEX6P KEYWDS CARBOXYPEPTIDASE, TUBULIN, MICROTUBULE., HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.WANG,H.BAO,H.HUANG REVDAT 4 22-NOV-23 6J4V 1 REMARK REVDAT 3 15-JAN-20 6J4V 1 COMPND SOURCE DBREF SEQADV REVDAT 2 13-NOV-19 6J4V 1 JRNL REVDAT 1 01-MAY-19 6J4V 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 28518 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1436 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 38.0512 - 4.5222 1.00 2865 147 0.1625 0.1793 REMARK 3 2 4.5222 - 3.5902 1.00 2761 140 0.1306 0.1593 REMARK 3 3 3.5902 - 3.1367 1.00 2733 152 0.1623 0.1888 REMARK 3 4 3.1367 - 2.8500 1.00 2717 154 0.1847 0.2150 REMARK 3 5 2.8500 - 2.6458 1.00 2718 142 0.1786 0.2372 REMARK 3 6 2.6458 - 2.4898 1.00 2733 141 0.1899 0.2105 REMARK 3 7 2.4898 - 2.3651 1.00 2713 143 0.1908 0.2208 REMARK 3 8 2.3651 - 2.2622 1.00 2689 150 0.1914 0.2405 REMARK 3 9 2.2622 - 2.1751 0.99 2686 115 0.2188 0.2888 REMARK 3 10 2.1751 - 2.1001 0.92 2467 152 0.2532 0.2997 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.80 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 : 0.007 2434 REMARK 3 ANGLE : 0.787 3271 REMARK 3 CHIRALITY : 0.050 341 REMARK 3 PLANARITY : 0.005 412 REMARK 3 DIHEDRAL : 11.119 1466 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.6519 28.3943 89.6191 REMARK 3 T TENSOR REMARK 3 T11: 0.3397 T22: 0.6522 REMARK 3 T33: 0.2994 T12: -0.0299 REMARK 3 T13: 0.0836 T23: -0.0146 REMARK 3 L TENSOR REMARK 3 L11: 5.8922 L22: 4.3557 REMARK 3 L33: 4.8483 L12: -2.6774 REMARK 3 L13: 0.3493 L23: -1.3255 REMARK 3 S TENSOR REMARK 3 S11: -0.1175 S12: -0.7234 S13: -0.0936 REMARK 3 S21: 0.3220 S22: 0.1332 S23: 0.3445 REMARK 3 S31: 0.1683 S32: -0.8010 S33: -0.0709 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.2248 29.0871 90.8074 REMARK 3 T TENSOR REMARK 3 T11: 0.2590 T22: 0.6849 REMARK 3 T33: 0.3183 T12: -0.0001 REMARK 3 T13: -0.0396 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 4.6037 L22: 8.4908 REMARK 3 L33: 3.9123 L12: 5.1375 REMARK 3 L13: -1.1569 L23: 0.8547 REMARK 3 S TENSOR REMARK 3 S11: 0.1591 S12: -0.9961 S13: -0.0844 REMARK 3 S21: 0.6058 S22: -0.3496 S23: -0.6411 REMARK 3 S31: -0.0220 S32: 0.3516 S33: 0.1771 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 121 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.8858 31.5399 60.8811 REMARK 3 T TENSOR REMARK 3 T11: 0.2364 T22: 0.3249 REMARK 3 T33: 0.2429 T12: -0.0561 REMARK 3 T13: 0.0125 T23: 0.0342 REMARK 3 L TENSOR REMARK 3 L11: 2.9742 L22: 0.2353 REMARK 3 L33: 8.7578 L12: -0.5691 REMARK 3 L13: 2.4415 L23: 0.3247 REMARK 3 S TENSOR REMARK 3 S11: 0.0908 S12: 0.2551 S13: -0.0654 REMARK 3 S21: -0.0828 S22: -0.0729 S23: -0.0111 REMARK 3 S31: -0.4155 S32: 0.3484 S33: 0.0295 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 122 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.0764 29.8624 73.2473 REMARK 3 T TENSOR REMARK 3 T11: 0.2341 T22: 0.2582 REMARK 3 T33: 0.2686 T12: -0.0328 REMARK 3 T13: 0.0295 T23: -0.0118 REMARK 3 L TENSOR REMARK 3 L11: 6.0061 L22: 1.4805 REMARK 3 L33: 7.2671 L12: -0.9792 REMARK 3 L13: 4.0581 L23: -0.3233 REMARK 3 S TENSOR REMARK 3 S11: 0.0567 S12: -0.4379 S13: 0.0732 REMARK 3 S21: 0.1254 S22: -0.0258 S23: 0.2708 REMARK 3 S31: -0.1029 S32: -0.4006 S33: -0.0353 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.6768 17.0783 65.6026 REMARK 3 T TENSOR REMARK 3 T11: 0.2466 T22: 0.2061 REMARK 3 T33: 0.2478 T12: -0.0386 REMARK 3 T13: -0.0356 T23: -0.0332 REMARK 3 L TENSOR REMARK 3 L11: 2.9946 L22: 6.6223 REMARK 3 L33: 7.3806 L12: 0.4476 REMARK 3 L13: 0.4468 L23: -2.9546 REMARK 3 S TENSOR REMARK 3 S11: 0.1797 S12: -0.1963 S13: -0.2237 REMARK 3 S21: 0.5233 S22: 0.1446 S23: 0.1932 REMARK 3 S31: 0.2704 S32: -0.2906 S33: -0.2462 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 201 THROUGH 239 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.6187 12.9400 61.5963 REMARK 3 T TENSOR REMARK 3 T11: 0.2186 T22: 0.1759 REMARK 3 T33: 0.2533 T12: 0.0179 REMARK 3 T13: 0.0180 T23: -0.0300 REMARK 3 L TENSOR REMARK 3 L11: 3.3376 L22: 6.8508 REMARK 3 L33: 4.0813 L12: 1.3623 REMARK 3 L13: 1.1927 L23: -1.1654 REMARK 3 S TENSOR REMARK 3 S11: 0.0034 S12: 0.1297 S13: -0.3485 REMARK 3 S21: -0.2201 S22: 0.0455 S23: -0.2176 REMARK 3 S31: 0.4832 S32: 0.1283 S33: -0.0381 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 240 THROUGH 258 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.3946 18.7951 63.6176 REMARK 3 T TENSOR REMARK 3 T11: 0.2157 T22: 0.3155 REMARK 3 T33: 0.2967 T12: -0.0658 REMARK 3 T13: -0.0203 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 4.1755 L22: 8.0709 REMARK 3 L33: 4.0512 L12: -1.3547 REMARK 3 L13: 1.4381 L23: -2.3072 REMARK 3 S TENSOR REMARK 3 S11: -0.0083 S12: 0.0320 S13: -0.0494 REMARK 3 S21: -0.0249 S22: 0.3792 S23: 0.7162 REMARK 3 S31: 0.0902 S32: -0.5608 S33: -0.4794 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 259 THROUGH 275 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9303 14.2948 64.5790 REMARK 3 T TENSOR REMARK 3 T11: 0.3233 T22: 0.3379 REMARK 3 T33: 0.4122 T12: -0.0899 REMARK 3 T13: -0.0358 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 3.6074 L22: 2.1678 REMARK 3 L33: 2.6175 L12: -2.7453 REMARK 3 L13: -0.7803 L23: 0.9149 REMARK 3 S TENSOR REMARK 3 S11: -0.2079 S12: -0.0156 S13: -0.1079 REMARK 3 S21: 0.3580 S22: 0.1458 S23: 0.7213 REMARK 3 S31: 0.3591 S32: -0.3469 S33: 0.0805 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 276 THROUGH 294 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.4682 10.3552 53.0038 REMARK 3 T TENSOR REMARK 3 T11: 0.4492 T22: 0.3683 REMARK 3 T33: 0.3796 T12: -0.0873 REMARK 3 T13: -0.1452 T23: -0.0482 REMARK 3 L TENSOR REMARK 3 L11: 5.4669 L22: 6.8137 REMARK 3 L33: 7.2799 L12: -2.5843 REMARK 3 L13: -0.0771 L23: -2.8744 REMARK 3 S TENSOR REMARK 3 S11: 0.0352 S12: 0.5553 S13: -0.1059 REMARK 3 S21: -1.2745 S22: 0.0762 S23: 0.6177 REMARK 3 S31: 0.2974 S32: -0.7964 S33: -0.2385 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 24 THROUGH 59 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.8120 26.9573 83.5135 REMARK 3 T TENSOR REMARK 3 T11: 0.2161 T22: 0.4497 REMARK 3 T33: 0.1760 T12: -0.0815 REMARK 3 T13: 0.0270 T23: 0.0176 REMARK 3 L TENSOR REMARK 3 L11: 7.6974 L22: 7.7227 REMARK 3 L33: 5.2770 L12: -4.1185 REMARK 3 L13: 1.0535 L23: 0.8301 REMARK 3 S TENSOR REMARK 3 S11: 0.0009 S12: -0.2714 S13: -0.0955 REMARK 3 S21: 0.1960 S22: 0.0379 S23: -0.3361 REMARK 3 S31: -0.0958 S32: 0.4999 S33: -0.0364 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 6J4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010473. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 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 : 28792 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.56100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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 (%): 60.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: FOR CRYSTALLIZATION OF V2C-SVBP C58S REMARK 280 IN COMPLEX WITH THE MATAIL PEPTIDE THE COMPONENTS WERE MIXED IN REMARK 280 A 1:3 MOLAR RATIO AND INCUBATED AT ROOM TEMPERATURE FOR 24 H REMARK 280 BEFORE SETTING UP CRYSTALLIZATION TRIALS. THE RESULTING V2C-SVBP REMARK 280 S58C-MATAIL COMPLEX WAS CRYSTALLIZED IN 1.4 M SODIUM/POTASSIUM REMARK 280 PHOSPHATE, PH 8.2., EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: F 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.20650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 97.13450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.20650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 97.13450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.20650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 97.13450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.20650 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 97.13450 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 41.14050 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 97.13450 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 41.14050 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 97.13450 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 41.14050 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 97.13450 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 41.14050 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 97.13450 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 41.14050 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 61.20650 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 41.14050 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 61.20650 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 41.14050 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 61.20650 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 41.14050 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 61.20650 REMARK 290 SMTRY3 16 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: 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 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 625 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 46 REMARK 465 VAL A 47 REMARK 465 LEU A 48 REMARK 465 LEU A 295 REMARK 465 LYS A 296 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 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 465 ASP C 431 REMARK 465 TYR C 432 REMARK 465 GLU C 433 REMARK 465 GLU C 434 REMARK 465 VAL C 435 REMARK 465 GLY C 436 REMARK 465 VAL C 437 REMARK 465 ASP C 438 REMARK 465 SER C 439 REMARK 465 VAL C 440 REMARK 465 GLU C 441 REMARK 465 GLY C 442 REMARK 465 GLU C 443 REMARK 465 GLY C 444 REMARK 465 GLU C 445 REMARK 465 GLU C 446 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 GLU B 56 CG CD OE1 OE2 REMARK 470 LYS B 59 CG CD CE NZ REMARK 470 TYR C 451 C O 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 OE1 GLU A 214 OH TYR A 239 2.09 REMARK 500 O HOH A 510 O HOH A 618 2.17 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 GLN A 122 147.93 86.89 REMARK 500 SER A 153 67.67 60.34 REMARK 500 LYS A 157 -163.00 -112.92 REMARK 500 MET A 216 -99.65 -142.15 REMARK 500 LYS A 265 53.81 -142.79 REMARK 500 SER B 58 35.02 -76.55 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 PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 306 DBREF 6J4V A 46 296 UNP Q86V25 VASH2_HUMAN 46 296 DBREF 6J4V B 1 66 UNP Q8N300 SVBP_HUMAN 1 66 DBREF 6J4V C 431 451 UNP P68363 TBA1B_HUMAN 431 451 SEQADV 6J4V SER B 58 UNP Q8N300 CYS 58 ENGINEERED MUTATION SEQADV 6J4V CYS C 450 UNP P68363 GLU 450 ENGINEERED MUTATION SEQRES 1 A 251 GLY VAL LEU PHE HIS VAL ASN LYS SER GLY PHE PRO ILE SEQRES 2 A 251 ASP SER HIS THR TRP GLU ARG MET TRP MET HIS VAL ALA SEQRES 3 A 251 LYS VAL HIS PRO LYS GLY GLY GLU MET VAL GLY ALA ILE SEQRES 4 A 251 ARG ASN ALA ALA PHE LEU ALA LYS PRO SER ILE PRO GLN SEQRES 5 A 251 VAL PRO ASN TYR ARG LEU SER MET THR ILE PRO ASP TRP SEQRES 6 A 251 LEU GLN ALA ILE GLN ASN TYR MET LYS THR LEU GLN TYR SEQRES 7 A 251 ASN HIS THR GLY THR GLN PHE PHE GLU ILE ARG LYS MET SEQRES 8 A 251 ARG PRO LEU SER GLY LEU MET GLU THR ALA LYS GLU MET SEQRES 9 A 251 THR ARG GLU SER LEU PRO ILE LYS CYS LEU GLU ALA VAL SEQRES 10 A 251 ILE LEU GLY ILE TYR LEU THR ASN GLY GLN PRO SER ILE SEQRES 11 A 251 GLU ARG PHE PRO ILE SER PHE LYS THR TYR PHE SER GLY SEQRES 12 A 251 ASN TYR PHE HIS HIS VAL VAL LEU GLY ILE TYR CYS ASN SEQRES 13 A 251 GLY ARG TYR GLY SER LEU GLY MET SER ARG ARG ALA GLU SEQRES 14 A 251 LEU MET ASP LYS PRO LEU THR PHE ARG THR LEU SER ASP SEQRES 15 A 251 LEU ILE PHE ASP PHE GLU ASP SER TYR LYS LYS TYR LEU SEQRES 16 A 251 HIS THR VAL LYS LYS VAL LYS ILE GLY LEU TYR VAL PRO SEQRES 17 A 251 HIS GLU PRO HIS SER PHE GLN PRO ILE GLU TRP LYS GLN SEQRES 18 A 251 LEU VAL LEU ASN VAL SER LYS MET LEU ARG ALA ASP ILE SEQRES 19 A 251 ARG LYS GLU LEU GLU LYS TYR ALA ARG ASP MET ARG MET SEQRES 20 A 251 LYS ILE LEU LYS 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 SER LYS GLN MET GLN PRO PRO GLY SEQRES 6 B 66 GLU SEQRES 1 C 21 ASP TYR GLU GLU VAL GLY VAL ASP SER VAL GLU GLY GLU SEQRES 2 C 21 GLY GLU GLU GLU GLY GLU CYS TYR HET PO4 A 301 5 HET PO4 A 302 5 HET GOL A 303 6 HET GOL A 304 6 HET GOL A 305 6 HET GOL A 306 6 HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 PO4 2(O4 P 3-) FORMUL 6 GOL 4(C3 H8 O3) FORMUL 10 HOH *239(H2 O) HELIX 1 AA1 ASP A 59 HIS A 74 1 16 HELIX 2 AA2 LYS A 76 ARG A 85 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 THR A 224 TYR A 239 1 16 HELIX 7 AA7 ASN A 270 MET A 274 5 5 HELIX 8 AA8 LEU A 275 LYS A 293 1 19 HELIX 9 AA9 LYS B 25 SER B 58 1 34 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 LEU A 196 O LEU A 207 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 LYS A 244 N LYS A 183 SHEET 6 AA2 6 LEU A 267 LEU A 269 -1 O LEU A 269 N VAL A 246 SSBOND 1 CYS A 158 CYS C 450 1555 1555 2.07 CISPEP 1 PHE A 56 PRO A 57 0 3.43 SITE 1 AC1 3 ARG A 102 SER A 104 HOH A 432 SITE 1 AC2 4 LYS A 183 HIS A 192 LYS A 245 LYS A 247 SITE 1 AC3 5 TRP A 63 ARG A 85 ASN A 86 HOH A 405 SITE 2 AC3 5 GLU B 38 SITE 1 AC4 8 LYS A 119 SER A 210 ARG A 211 ARG A 212 SITE 2 AC4 8 ALA A 213 MET A 216 HOH A 470 HOH A 541 SITE 1 AC5 6 PRO A 93 SER A 94 PRO A 96 THR A 120 SITE 2 AC5 6 HOH A 475 TYR B 40 SITE 1 AC6 3 PRO A 99 ASN A 100 HOH A 426 CRYST1 82.281 122.413 194.269 90.00 90.00 90.00 F 2 2 2 16 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 0.012153 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008169 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005148 0.00000