PDB Short entry for 3S1K HEADER SIGNALING PROTEIN 15-MAY-11 3S1K TITLE THE DEVELOPMENT OF PEPTIDE-BASED TOOLS FOR THE ANALYSIS OF TITLE 2 ANGIOGENESIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: Z-DOMAIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 7 CHAIN: V, W; COMPND 8 SYNONYM: VEGF-A, VASCULAR PERMEABILITY FACTOR, VPF; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: FMOC SOLID-PHASE PEPTIDE SYNTHESIS; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_COMMON: HUMAN; SOURCE 7 ORGANISM_TAXID: 9606; SOURCE 8 GENE: VEGF; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS VEGF, CYSTINE KNOT, Z-DOMAIN, PHAGE-DISPLAY, CYSTINE-KNOT, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.MURRAY,C.WIESMANN REVDAT 1 17-AUG-11 3S1K 0 JRNL AUTH A.FEDOROVA,K.ZOBEL,H.S.GILL,A.OGASAWARA,J.E.FLORES, JRNL AUTH 2 J.N.TINIANOW,A.N.VANDERBILT,P.WU,Y.G.MENG,S.P.WILLIAMS, JRNL AUTH 3 C.WIESMANN,J.MURRAY,J.MARIK,K.DESHAYES JRNL TITL THE DEVELOPMENT OF PEPTIDE-BASED TOOLS FOR THE ANALYSIS OF JRNL TITL 2 ANGIOGENESIS. JRNL REF CHEM.BIOL. V. 18 839 2011 JRNL REFN ISSN 1074-5521 JRNL PMID 21802005 JRNL DOI 10.1016/J.CHEMBIOL.2011.05.011 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_751) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 12982 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 632 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 41.9232 - 4.3593 1.00 2583 144 0.1868 0.2144 REMARK 3 2 4.3593 - 3.4607 0.98 2432 124 0.2086 0.2632 REMARK 3 3 3.4607 - 3.0234 1.00 2462 126 0.2525 0.3282 REMARK 3 4 3.0234 - 2.7470 1.00 2461 110 0.2878 0.3687 REMARK 3 5 2.7470 - 2.5501 0.99 2412 128 0.3181 0.3399 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 21.97 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.700 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.01680 REMARK 3 B22 (A**2) : 7.68650 REMARK 3 B33 (A**2) : 1.33030 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : -0.00000 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 : 0.004 2404 REMARK 3 ANGLE : 0.785 3241 REMARK 3 CHIRALITY : 0.053 346 REMARK 3 PLANARITY : 0.004 431 REMARK 3 DIHEDRAL : 17.443 911 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 16 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain 'A' and (resseq 6:23) REMARK 3 ORIGIN FOR THE GROUP (A): -11.2979 -38.5589 -7.4930 REMARK 3 T TENSOR REMARK 3 T11: 1.2482 T22: 0.1921 REMARK 3 T33: 0.5348 T12: 0.1135 REMARK 3 T13: 0.1958 T23: -0.1011 REMARK 3 L TENSOR REMARK 3 L11: 3.2156 L22: 4.1031 REMARK 3 L33: 3.4904 L12: 2.4133 REMARK 3 L13: -0.6997 L23: 0.4050 REMARK 3 S TENSOR REMARK 3 S11: 0.4567 S12: -0.1322 S13: -0.7571 REMARK 3 S21: -0.0559 S22: -0.5755 S23: -0.1769 REMARK 3 S31: 0.8544 S32: 0.4634 S33: -0.3387 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain 'A' and (resseq 24:37) REMARK 3 ORIGIN FOR THE GROUP (A): -14.9533 -37.6830 1.7290 REMARK 3 T TENSOR REMARK 3 T11: 1.0754 T22: 0.3441 REMARK 3 T33: 0.6970 T12: 0.0541 REMARK 3 T13: 0.1531 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 7.0742 L22: 4.3749 REMARK 3 L33: 4.1374 L12: 0.7901 REMARK 3 L13: -0.7836 L23: 1.3097 REMARK 3 S TENSOR REMARK 3 S11: 0.1869 S12: -0.7936 S13: -0.7620 REMARK 3 S21: 0.5362 S22: -0.4935 S23: -0.0644 REMARK 3 S31: 1.6293 S32: 0.2646 S33: -0.1005 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: chain 'A' and (resseq 38:57) REMARK 3 ORIGIN FOR THE GROUP (A): -13.2330 -46.9787 -3.6233 REMARK 3 T TENSOR REMARK 3 T11: 1.5751 T22: 0.3888 REMARK 3 T33: 0.7974 T12: 0.1430 REMARK 3 T13: 0.1698 T23: 0.0323 REMARK 3 L TENSOR REMARK 3 L11: 6.5687 L22: 4.7654 REMARK 3 L33: 4.2825 L12: 1.0032 REMARK 3 L13: 0.7473 L23: 0.6125 REMARK 3 S TENSOR REMARK 3 S11: -0.1905 S12: 0.5485 S13: -1.5005 REMARK 3 S21: 0.0858 S22: 0.1220 S23: -0.2118 REMARK 3 S31: 1.0681 S32: 0.4817 S33: -0.2138 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: chain 'B' and (resseq 6:23) REMARK 3 ORIGIN FOR THE GROUP (A): -12.7717 9.0830 18.9883 REMARK 3 T TENSOR REMARK 3 T11: 0.4408 T22: 0.1661 REMARK 3 T33: 0.2201 T12: -0.0677 REMARK 3 T13: -0.0020 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 4.1250 L22: 5.7524 REMARK 3 L33: 2.3226 L12: -2.4752 REMARK 3 L13: -1.1873 L23: 0.1909 REMARK 3 S TENSOR REMARK 3 S11: -0.1446 S12: -0.0209 S13: 0.3236 REMARK 3 S21: -0.2581 S22: -0.0039 S23: -0.4041 REMARK 3 S31: -0.0200 S32: 0.2052 S33: -0.0562 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: chain 'B' and (resseq 24:37) REMARK 3 ORIGIN FOR THE GROUP (A): -12.2876 8.5498 9.0301 REMARK 3 T TENSOR REMARK 3 T11: 0.6530 T22: 0.2751 REMARK 3 T33: 0.2186 T12: -0.0847 REMARK 3 T13: 0.0169 T23: 0.0257 REMARK 3 L TENSOR REMARK 3 L11: 6.1530 L22: 5.1287 REMARK 3 L33: 3.8200 L12: -1.5620 REMARK 3 L13: 0.0897 L23: 1.7523 REMARK 3 S TENSOR REMARK 3 S11: 0.3976 S12: -0.5839 S13: 0.3372 REMARK 3 S21: -0.6732 S22: 0.1782 S23: -0.3263 REMARK 3 S31: -0.0706 S32: -0.3762 S33: -0.0856 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: chain 'B' and (resseq 38:57) REMARK 3 ORIGIN FOR THE GROUP (A): -10.8715 17.5202 15.3876 REMARK 3 T TENSOR REMARK 3 T11: 0.6562 T22: 0.1813 REMARK 3 T33: 0.3945 T12: -0.0596 REMARK 3 T13: 0.1349 T23: 0.0581 REMARK 3 L TENSOR REMARK 3 L11: 5.4575 L22: 4.1714 REMARK 3 L33: 3.3804 L12: -1.8218 REMARK 3 L13: -0.1568 L23: 0.6031 REMARK 3 S TENSOR REMARK 3 S11: 0.2166 S12: 0.0761 S13: 0.6313 REMARK 3 S21: -0.2360 S22: -0.0202 S23: -0.3572 REMARK 3 S31: -0.6353 S32: 0.1664 S33: -0.2692 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: chain 'V' and (resseq 13:38) REMARK 3 ORIGIN FOR THE GROUP (A): -17.4804 -8.6034 6.0645 REMARK 3 T TENSOR REMARK 3 T11: 0.4277 T22: 0.1581 REMARK 3 T33: 0.2270 T12: -0.0196 REMARK 3 T13: -0.0148 T23: 0.0350 REMARK 3 L TENSOR REMARK 3 L11: 2.0896 L22: 2.1339 REMARK 3 L33: 6.4502 L12: 0.2734 REMARK 3 L13: 0.4420 L23: 2.6777 REMARK 3 S TENSOR REMARK 3 S11: -0.1716 S12: -0.1678 S13: -0.1862 REMARK 3 S21: -0.0772 S22: 0.2061 S23: -0.0813 REMARK 3 S31: -0.0993 S32: -0.1112 S33: 0.0834 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: chain 'V' and (resseq 39:45) REMARK 3 ORIGIN FOR THE GROUP (A): -28.3557 -25.0762 -15.3196 REMARK 3 T TENSOR REMARK 3 T11: 1.1111 T22: -0.1504 REMARK 3 T33: 0.9819 T12: -0.0301 REMARK 3 T13: -0.4276 T23: -0.0968 REMARK 3 L TENSOR REMARK 3 L11: 4.1442 L22: 2.4116 REMARK 3 L33: 2.1982 L12: 3.0169 REMARK 3 L13: 1.8133 L23: 0.7664 REMARK 3 S TENSOR REMARK 3 S11: -0.1148 S12: 1.1124 S13: -1.5279 REMARK 3 S21: -1.7435 S22: -0.0218 S23: 1.2965 REMARK 3 S31: 1.1644 S32: -0.1362 S33: -0.3388 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: chain 'V' and (resseq 46:65) REMARK 3 ORIGIN FOR THE GROUP (A): -21.4680 -12.5731 -1.7789 REMARK 3 T TENSOR REMARK 3 T11: 0.5110 T22: 0.1981 REMARK 3 T33: 0.1776 T12: -0.1166 REMARK 3 T13: 0.1086 T23: 0.1344 REMARK 3 L TENSOR REMARK 3 L11: 1.5315 L22: 5.8521 REMARK 3 L33: 4.2658 L12: -0.2652 REMARK 3 L13: 1.2361 L23: 0.4462 REMARK 3 S TENSOR REMARK 3 S11: 0.0346 S12: -0.1545 S13: -0.1364 REMARK 3 S21: -0.2206 S22: 0.0361 S23: 0.0986 REMARK 3 S31: 0.0734 S32: -1.1288 S33: 0.1124 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: chain 'V' and (resseq 66:83) REMARK 3 ORIGIN FOR THE GROUP (A): -17.6850 -14.3148 -9.3731 REMARK 3 T TENSOR REMARK 3 T11: 0.5569 T22: 0.2006 REMARK 3 T33: 0.0380 T12: 0.0132 REMARK 3 T13: 0.0116 T23: 0.1429 REMARK 3 L TENSOR REMARK 3 L11: 1.7197 L22: 3.9529 REMARK 3 L33: 3.0473 L12: -0.9177 REMARK 3 L13: 0.2452 L23: -0.8636 REMARK 3 S TENSOR REMARK 3 S11: -0.0267 S12: 0.6972 S13: -0.4002 REMARK 3 S21: -0.7144 S22: -0.0808 S23: 0.1612 REMARK 3 S31: 0.0613 S32: -0.1709 S33: 0.1066 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: chain 'V' and (resseq 84:107) REMARK 3 ORIGIN FOR THE GROUP (A): -19.8212 -17.4925 -10.3621 REMARK 3 T TENSOR REMARK 3 T11: 0.4978 T22: 0.3608 REMARK 3 T33: 0.2415 T12: -0.0438 REMARK 3 T13: 0.0395 T23: 0.0557 REMARK 3 L TENSOR REMARK 3 L11: 3.2980 L22: 4.9518 REMARK 3 L33: 4.7353 L12: -1.2938 REMARK 3 L13: 0.7278 L23: -0.4108 REMARK 3 S TENSOR REMARK 3 S11: 0.2210 S12: 0.3041 S13: -0.5740 REMARK 3 S21: -0.4167 S22: -0.1009 S23: 0.1919 REMARK 3 S31: 0.7215 S32: -0.0705 S33: -0.0098 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: chain 'W' and (resseq 14:38) REMARK 3 ORIGIN FOR THE GROUP (A): -18.2667 -19.8636 3.4202 REMARK 3 T TENSOR REMARK 3 T11: 0.6409 T22: 0.1886 REMARK 3 T33: 0.4034 T12: 0.0060 REMARK 3 T13: 0.0610 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 0.3941 L22: 2.9507 REMARK 3 L33: 4.4183 L12: -0.8709 REMARK 3 L13: -1.1959 L23: 2.4739 REMARK 3 S TENSOR REMARK 3 S11: 0.0110 S12: -0.0720 S13: -0.4562 REMARK 3 S21: 0.2314 S22: -0.3119 S23: 0.0802 REMARK 3 S31: 0.6183 S32: 0.0604 S33: 0.2807 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: chain 'W' and (resseq 39:45) REMARK 3 ORIGIN FOR THE GROUP (A): -34.2440 -1.2555 17.8129 REMARK 3 T TENSOR REMARK 3 T11: 0.5402 T22: 0.4143 REMARK 3 T33: 0.5429 T12: 0.0986 REMARK 3 T13: -0.1549 T23: -0.1086 REMARK 3 L TENSOR REMARK 3 L11: 4.1010 L22: 3.6795 REMARK 3 L33: 0.6129 L12: -1.2482 REMARK 3 L13: -0.5650 L23: -1.1444 REMARK 3 S TENSOR REMARK 3 S11: -0.7636 S12: -1.4681 S13: 0.5899 REMARK 3 S21: 0.9605 S22: -0.6178 S23: 1.2269 REMARK 3 S31: 0.0141 S32: -1.1343 S33: 0.4129 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: chain 'W' and (resseq 46:66) REMARK 3 ORIGIN FOR THE GROUP (A): -24.2203 -15.7497 8.2828 REMARK 3 T TENSOR REMARK 3 T11: 0.6915 T22: 0.2206 REMARK 3 T33: 0.2778 T12: -0.1761 REMARK 3 T13: 0.1076 T23: 0.0268 REMARK 3 L TENSOR REMARK 3 L11: 0.6580 L22: 5.7952 REMARK 3 L33: 3.6663 L12: -1.6454 REMARK 3 L13: -1.0336 L23: 3.0465 REMARK 3 S TENSOR REMARK 3 S11: -0.1196 S12: 0.1305 S13: -0.3525 REMARK 3 S21: 0.2793 S22: -0.5546 S23: 0.5748 REMARK 3 S31: 0.9227 S32: -0.6194 S33: 0.3899 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: chain 'W' and (resseq 67:83) REMARK 3 ORIGIN FOR THE GROUP (A): -23.3187 -12.3769 17.6445 REMARK 3 T TENSOR REMARK 3 T11: 0.7546 T22: 0.1919 REMARK 3 T33: 0.2680 T12: -0.0989 REMARK 3 T13: 0.0486 T23: 0.0266 REMARK 3 L TENSOR REMARK 3 L11: 0.4823 L22: 6.1100 REMARK 3 L33: 2.6612 L12: 0.6455 REMARK 3 L13: -0.1132 L23: 3.1517 REMARK 3 S TENSOR REMARK 3 S11: 0.1434 S12: 0.0407 S13: -0.2501 REMARK 3 S21: 1.3629 S22: -0.6280 S23: 0.0057 REMARK 3 S31: 1.1763 S32: -0.3530 S33: 0.4089 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: chain 'W' and (resseq 84:106) REMARK 3 ORIGIN FOR THE GROUP (A): -25.0990 -9.1325 17.5058 REMARK 3 T TENSOR REMARK 3 T11: 0.6157 T22: 0.2167 REMARK 3 T33: -0.1322 T12: -0.2270 REMARK 3 T13: 0.0194 T23: 0.1454 REMARK 3 L TENSOR REMARK 3 L11: 1.3461 L22: 3.5221 REMARK 3 L33: 4.4330 L12: 0.4828 REMARK 3 L13: 0.4394 L23: 4.0530 REMARK 3 S TENSOR REMARK 3 S11: -0.6459 S12: -0.9253 S13: -0.5255 REMARK 3 S21: -0.3784 S22: -0.7112 S23: 0.5517 REMARK 3 S31: 0.7567 S32: -0.3790 S33: -0.0142 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 3S1K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-11. REMARK 100 THE RCSB ID CODE IS RCSB065644. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14337 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 52.706 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : 0.09200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.55700 REMARK 200 R SYM FOR SHELL (I) : 0.55700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M KI, 0.1 M MES, PEG 4000 25.0% V/ REMARK 280 V, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 34.61400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.17200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.17200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.61400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.38000 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: V, W, 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 VAL A 0 REMARK 465 ASP A 1 REMARK 465 ASN A 2 REMARK 465 LYS A 3 REMARK 465 PHE A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 58 REMARK 465 VAL B 0 REMARK 465 ASP B 1 REMARK 465 ASN B 2 REMARK 465 LYS B 3 REMARK 465 PHE B 4 REMARK 465 ASN B 5 REMARK 465 LYS B 58 REMARK 465 GLY V 8 REMARK 465 GLN V 9 REMARK 465 ASN V 10 REMARK 465 HIS V 11 REMARK 465 HIS V 12 REMARK 465 LYS V 108 REMARK 465 ASP V 109 REMARK 465 GLY W 8 REMARK 465 GLN W 9 REMARK 465 ASN W 10 REMARK 465 HIS W 11 REMARK 465 HIS W 12 REMARK 465 GLU W 13 REMARK 465 LYS W 107 REMARK 465 LYS W 108 REMARK 465 ASP W 109 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 SG CYS W 26 SG CYS W 68 1.40 REMARK 500 SG CYS V 26 SG CYS V 68 1.53 REMARK 500 O HOH V 114 O HOH V 120 2.03 REMARK 500 N CYS W 104 O HOH W 115 2.07 REMARK 500 O PRO A 38 OG SER A 41 2.16 REMARK 500 O PRO B 38 OG SER B 41 2.17 REMARK 500 O HOH W 1 O HOH W 3 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP W 63 CB - CA - C ANGL. DEV. = 25.0 DEGREES REMARK 500 ASP W 63 N - CA - C ANGL. DEV. = -20.3 DEGREES 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 HIS V 86 -4.57 67.48 REMARK 500 GLN W 87 63.16 -158.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP W 63 45.3 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3S1B RELATED DB: PDB DBREF 3S1K V 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 3S1K W 8 109 UNP P15692 VEGFA_HUMAN 34 135 DBREF 3S1K A 0 58 PDB 3S1K 3S1K 0 58 DBREF 3S1K B 0 58 PDB 3S1K 3S1K 0 58 SEQRES 1 A 59 VAL ASP ASN LYS PHE ASN LYS GLU MET HIS ASN ALA TYR SEQRES 2 A 59 ALA ILE GLU ILE ALA LEU LEU PRO ASN LEU ASN ASP GLN SEQRES 3 A 59 GLN PHE HIS ALA PHE ILE TRP SER LEU ILE ASP ASP PRO SEQRES 4 A 59 SER GLN SER ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU SEQRES 5 A 59 ASN ASP ALA GLN ALA PRO LYS SEQRES 1 B 59 VAL ASP ASN LYS PHE ASN LYS GLU MET HIS ASN ALA TYR SEQRES 2 B 59 ALA ILE GLU ILE ALA LEU LEU PRO ASN LEU ASN ASP GLN SEQRES 3 B 59 GLN PHE HIS ALA PHE ILE TRP SER LEU ILE ASP ASP PRO SEQRES 4 B 59 SER GLN SER ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU SEQRES 5 B 59 ASN ASP ALA GLN ALA PRO LYS SEQRES 1 V 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 V 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 V 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 V 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 V 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 V 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 V 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 V 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP SEQRES 1 W 102 GLY GLN ASN HIS HIS GLU VAL VAL LYS PHE MET ASP VAL SEQRES 2 W 102 TYR GLN ARG SER TYR CYS HIS PRO ILE GLU THR LEU VAL SEQRES 3 W 102 ASP ILE PHE GLN GLU TYR PRO ASP GLU ILE GLU TYR ILE SEQRES 4 W 102 PHE LYS PRO SER CYS VAL PRO LEU MET ARG CYS GLY GLY SEQRES 5 W 102 CYS CYS ASN ASP GLU GLY LEU GLU CYS VAL PRO THR GLU SEQRES 6 W 102 GLU SER ASN ILE THR MET GLN ILE MET ARG ILE LYS PRO SEQRES 7 W 102 HIS GLN GLY GLN HIS ILE GLY GLU MET SER PHE LEU GLN SEQRES 8 W 102 HIS ASN LYS CYS GLU CYS ARG PRO LYS LYS ASP FORMUL 5 HOH *37(H2 O) HELIX 1 1 LYS A 6 LEU A 19 1 14 HELIX 2 2 ASN A 23 ASP A 37 1 15 HELIX 3 3 GLN A 40 GLN A 55 1 16 HELIX 4 4 LYS B 6 LEU B 19 1 14 HELIX 5 5 ASN B 23 ASP B 37 1 15 HELIX 6 6 GLN B 40 GLN B 55 1 16 HELIX 7 7 LYS V 16 TYR V 25 1 10 HELIX 8 8 ILE V 35 TYR V 39 1 5 HELIX 9 9 LYS W 16 TYR W 25 1 10 HELIX 10 10 ILE W 35 TYR W 39 1 5 HELIX 11 11 PRO W 40 ILE W 43 5 4 SHEET 1 A 2 HIS V 27 ASP V 34 0 SHEET 2 A 2 CYS V 51 GLY V 58 -1 O ARG V 56 N ILE V 29 SHEET 1 B 3 ILE V 46 LYS V 48 0 SHEET 2 B 3 LEU V 66 ILE V 83 -1 O ILE V 83 N ILE V 46 SHEET 3 B 3 GLN V 89 PRO V 106 -1 O ARG V 105 N GLU V 67 SHEET 1 C 2 HIS W 27 ASP W 34 0 SHEET 2 C 2 CYS W 51 GLY W 58 -1 O ARG W 56 N ILE W 29 SHEET 1 D 3 ILE W 46 LYS W 48 0 SHEET 2 D 3 GLU W 67 ILE W 83 -1 O MET W 81 N LYS W 48 SHEET 3 D 3 GLN W 89 ARG W 105 -1 O GLN W 98 N SER W 74 SSBOND 1 CYS V 51 CYS W 60 1555 1555 2.04 SSBOND 2 CYS V 57 CYS V 102 1555 1555 2.03 SSBOND 3 CYS V 60 CYS W 51 1555 1555 2.05 SSBOND 4 CYS V 61 CYS V 104 1555 1555 2.04 SSBOND 5 CYS W 57 CYS W 102 1555 1555 2.03 SSBOND 6 CYS W 61 CYS W 104 1555 1555 2.03 CISPEP 1 LYS V 48 PRO V 49 0 -4.26 CISPEP 2 LYS W 48 PRO W 49 0 -2.51 CRYST1 69.228 72.760 76.344 90.00 90.00 90.00 P 21 21 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 0.014445 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013744 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013099 0.00000