HEADER TRANSFERASE 21-JUN-16 5KK8 TITLE CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM SCHISTOSOMA TITLE 2 MANSONI IN COMPLEX WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.4.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHISTOSOMA MANSONI; SOURCE 3 ORGANISM_COMMON: BLOOD FLUKE; SOURCE 4 ORGANISM_TAXID: 6183; SOURCE 5 GENE: SMP_092750; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NUCLEOSIDE DIPHOSPHATE KINASE, ENZYME, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.R.S.TORINI,L.ROMANELLO,L.E.BIRD,J.E.NETTLESHIP,R.J.OWENS,P.ALLER, AUTHOR 2 R.DEMARCO,J.BRANDAO-NETO,H.M.PEREIRA REVDAT 5 27-SEP-23 5KK8 1 REMARK REVDAT 4 01-JAN-20 5KK8 1 REMARK REVDAT 3 29-MAY-19 5KK8 1 JRNL REVDAT 2 17-APR-19 5KK8 1 REMARK REVDAT 1 21-JUN-17 5KK8 0 JRNL AUTH J.R.TORINI,A.DE FREITAS FERNANDES,V.H.BALASCO SERRAO, JRNL AUTH 2 L.ROMANELLO,L.E.BIRD,J.E.NETTLESHIP,R.J.OWENS, JRNL AUTH 3 J.BRANDAO-NETO,A.E.ZERAIK,R.DEMARCO,H.D'MUNIZ PEREIRA JRNL TITL CHARACTERIZATION OF A SCHISTOSOMA MANSONI NDPK EXPRESSED IN JRNL TITL 2 SEXUAL AND DIGESTIVE ORGANS. JRNL REF MOL.BIOCHEM.PARASITOL. 11187 2019 JRNL REFN ISSN 0166-6851 JRNL PMID 31103556 JRNL DOI 10.1016/J.MOLBIOPARA.2019.111187 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20023 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) : 0.168 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1020 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 59.5768 - 4.0360 1.00 2958 163 0.1684 0.1706 REMARK 3 2 4.0360 - 3.2036 1.00 2771 127 0.1525 0.1994 REMARK 3 3 3.2036 - 2.7986 1.00 2701 145 0.1729 0.2123 REMARK 3 4 2.7986 - 2.5427 1.00 2644 158 0.1791 0.2268 REMARK 3 5 2.5427 - 2.3605 1.00 2669 145 0.1812 0.2210 REMARK 3 6 2.3605 - 2.2213 1.00 2610 152 0.1754 0.2057 REMARK 3 7 2.2213 - 2.1101 1.00 2650 130 0.1779 0.2353 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.28 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 2466 REMARK 3 ANGLE : 0.962 3342 REMARK 3 CHIRALITY : 0.051 355 REMARK 3 PLANARITY : 0.005 426 REMARK 3 DIHEDRAL : 17.848 1482 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 73.2130 107.8768 47.5305 REMARK 3 T TENSOR REMARK 3 T11: 0.1732 T22: 0.1571 REMARK 3 T33: 0.2274 T12: 0.0051 REMARK 3 T13: -0.0061 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 1.2559 L22: 0.4255 REMARK 3 L33: 1.4009 L12: -0.1179 REMARK 3 L13: -0.0317 L23: -0.1406 REMARK 3 S TENSOR REMARK 3 S11: 0.0734 S12: 0.0368 S13: -0.1113 REMARK 3 S21: -0.0444 S22: -0.0264 S23: -0.0178 REMARK 3 S31: 0.0336 S32: -0.1155 S33: -0.0180 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.8401 99.6538 42.6272 REMARK 3 T TENSOR REMARK 3 T11: 0.2356 T22: 0.1525 REMARK 3 T33: 0.2640 T12: -0.0056 REMARK 3 T13: -0.0244 T23: -0.0255 REMARK 3 L TENSOR REMARK 3 L11: 1.5376 L22: 0.7266 REMARK 3 L33: 1.9269 L12: -0.2177 REMARK 3 L13: 0.1434 L23: -0.4542 REMARK 3 S TENSOR REMARK 3 S11: 0.0064 S12: 0.1149 S13: -0.1411 REMARK 3 S21: -0.0946 S22: -0.0550 S23: -0.0156 REMARK 3 S31: 0.2582 S32: 0.1023 S33: 0.0241 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 77 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 65.1425 110.5827 37.5554 REMARK 3 T TENSOR REMARK 3 T11: 0.2758 T22: 0.2641 REMARK 3 T33: 0.2536 T12: 0.0001 REMARK 3 T13: -0.0581 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 5.1606 L22: 2.9052 REMARK 3 L33: 3.3431 L12: 2.1965 REMARK 3 L13: 0.2964 L23: -0.1817 REMARK 3 S TENSOR REMARK 3 S11: -0.1760 S12: 0.7231 S13: 0.2991 REMARK 3 S21: -0.6530 S22: 0.0220 S23: 0.1893 REMARK 3 S31: 0.0353 S32: -0.1933 S33: -0.0315 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 89 THROUGH 130 ) REMARK 3 ORIGIN FOR THE GROUP (A): 76.3394 108.1356 38.8497 REMARK 3 T TENSOR REMARK 3 T11: 0.1870 T22: 0.1893 REMARK 3 T33: 0.2438 T12: 0.0135 REMARK 3 T13: -0.0009 T23: -0.0419 REMARK 3 L TENSOR REMARK 3 L11: 0.9307 L22: 0.8130 REMARK 3 L33: 1.6466 L12: 0.2260 REMARK 3 L13: 0.1298 L23: -0.0481 REMARK 3 S TENSOR REMARK 3 S11: 0.0152 S12: 0.1487 S13: -0.0172 REMARK 3 S21: -0.1875 S22: 0.0163 S23: 0.0118 REMARK 3 S31: -0.0484 S32: -0.0724 S33: -0.0102 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 131 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.7262 103.0807 48.7295 REMARK 3 T TENSOR REMARK 3 T11: 0.2673 T22: 0.2434 REMARK 3 T33: 0.3323 T12: -0.0480 REMARK 3 T13: -0.0536 T23: -0.0238 REMARK 3 L TENSOR REMARK 3 L11: 2.2778 L22: 2.1666 REMARK 3 L33: 0.9688 L12: -1.6232 REMARK 3 L13: -0.4194 L23: 0.4258 REMARK 3 S TENSOR REMARK 3 S11: 0.0754 S12: -0.0565 S13: -0.4477 REMARK 3 S21: -0.2329 S22: -0.0155 S23: 0.5412 REMARK 3 S31: 0.0308 S32: -0.0581 S33: -0.0594 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 80.1159 109.6922 6.6456 REMARK 3 T TENSOR REMARK 3 T11: 0.4431 T22: 0.3932 REMARK 3 T33: 0.2208 T12: 0.0244 REMARK 3 T13: -0.0527 T23: -0.0252 REMARK 3 L TENSOR REMARK 3 L11: 0.9056 L22: 0.9493 REMARK 3 L33: 1.4947 L12: 0.0262 REMARK 3 L13: -0.1490 L23: 0.0892 REMARK 3 S TENSOR REMARK 3 S11: 0.0753 S12: 0.1833 S13: -0.0445 REMARK 3 S21: 0.1302 S22: 0.0163 S23: -0.1386 REMARK 3 S31: 0.1453 S32: 0.1335 S33: -0.0202 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 39 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 76.1384 93.2817 17.9372 REMARK 3 T TENSOR REMARK 3 T11: 0.6505 T22: 0.3637 REMARK 3 T33: 0.3238 T12: 0.0439 REMARK 3 T13: -0.0794 T23: -0.0412 REMARK 3 L TENSOR REMARK 3 L11: 0.9726 L22: 0.7456 REMARK 3 L33: 3.2037 L12: -0.1963 REMARK 3 L13: -1.2141 L23: -0.0288 REMARK 3 S TENSOR REMARK 3 S11: -0.1201 S12: -0.0281 S13: -0.3863 REMARK 3 S21: 0.1645 S22: -0.0261 S23: -0.0202 REMARK 3 S31: 0.7671 S32: 0.0736 S33: 0.0476 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 58 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 75.4046 99.0336 10.8548 REMARK 3 T TENSOR REMARK 3 T11: 0.4908 T22: 0.3761 REMARK 3 T33: 0.2813 T12: 0.0298 REMARK 3 T13: -0.0261 T23: -0.0255 REMARK 3 L TENSOR REMARK 3 L11: 0.3596 L22: 1.1682 REMARK 3 L33: 2.1028 L12: 0.1879 REMARK 3 L13: 0.0729 L23: -0.2833 REMARK 3 S TENSOR REMARK 3 S11: 0.1586 S12: 0.4154 S13: -0.1110 REMARK 3 S21: 0.2594 S22: 0.0101 S23: 0.0522 REMARK 3 S31: 0.0733 S32: -0.1611 S33: -0.0383 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 77 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 83.6696 115.2434 16.8949 REMARK 3 T TENSOR REMARK 3 T11: 0.4253 T22: 0.4064 REMARK 3 T33: 0.1898 T12: -0.0096 REMARK 3 T13: -0.0454 T23: 0.0155 REMARK 3 L TENSOR REMARK 3 L11: 6.6603 L22: 2.0242 REMARK 3 L33: 5.0511 L12: -1.5428 REMARK 3 L13: 0.6553 L23: 0.6480 REMARK 3 S TENSOR REMARK 3 S11: 0.1972 S12: -0.2695 S13: -0.1294 REMARK 3 S21: 0.5092 S22: -0.1646 S23: -0.3961 REMARK 3 S31: 0.3414 S32: 0.3178 S33: -0.0310 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 89 THROUGH 130 ) REMARK 3 ORIGIN FOR THE GROUP (A): 75.1017 107.7372 15.9394 REMARK 3 T TENSOR REMARK 3 T11: 0.4531 T22: 0.3640 REMARK 3 T33: 0.2568 T12: -0.0105 REMARK 3 T13: -0.0411 T23: 0.0268 REMARK 3 L TENSOR REMARK 3 L11: 0.9811 L22: 0.6304 REMARK 3 L33: 1.8360 L12: -0.2144 REMARK 3 L13: -0.0227 L23: -0.3569 REMARK 3 S TENSOR REMARK 3 S11: 0.1363 S12: 0.0151 S13: -0.0450 REMARK 3 S21: 0.2269 S22: -0.0041 S23: -0.0513 REMARK 3 S31: 0.0585 S32: -0.0945 S33: -0.0113 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 131 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 94.3587 113.5805 6.1898 REMARK 3 T TENSOR REMARK 3 T11: 0.4866 T22: 0.6245 REMARK 3 T33: 0.2988 T12: 0.0263 REMARK 3 T13: -0.0433 T23: -0.0582 REMARK 3 L TENSOR REMARK 3 L11: 0.8023 L22: 2.7471 REMARK 3 L33: 1.2437 L12: 0.8213 REMARK 3 L13: -0.2239 L23: -0.5967 REMARK 3 S TENSOR REMARK 3 S11: 0.1350 S12: -0.1287 S13: 0.1298 REMARK 3 S21: 0.3473 S22: -0.0300 S23: -0.1013 REMARK 3 S31: 0.0700 S32: 0.1591 S33: -0.0325 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 5KK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222380. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9200 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20075 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 61.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.90 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.60 REMARK 200 R MERGE FOR SHELL (I) : 0.71000 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: 5IOM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG-8000, 100MM TRIS PH 7.0, REMARK 280 200MM MGCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 0.00000 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 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 109.67000 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 109.67000 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 109.67000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 109.67000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 109.67000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 109.67000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 142.90000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 109.67000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 302 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 416 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 421 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 422 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 361 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 362 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 0 REMARK 465 GLY B 0 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 GLU A 42 CG CD OE1 OE2 REMARK 470 GLN B 43 CG CD OE1 NE2 REMARK 470 GLN B 134 CG CD OE1 NE2 REMARK 470 LYS B 140 CG CD CE NZ 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 O HOH B 319 O HOH B 359 2.02 REMARK 500 NH2 ARG B 27 O HOH B 301 2.12 REMARK 500 O HOH A 326 O HOH A 398 2.13 REMARK 500 OE1 GLU A 82 O HOH A 301 2.14 REMARK 500 O HOH A 365 O HOH A 399 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 306 O HOH A 402 3795 1.89 REMARK 500 O HOH A 410 O HOH A 410 10995 2.12 REMARK 500 O HOH A 357 O HOH A 395 2975 2.15 REMARK 500 O HOH A 403 O HOH A 420 3795 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 VAL A 113 -36.18 77.54 REMARK 500 TYR B 49 31.76 -98.74 REMARK 500 VAL B 113 -40.36 75.38 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 ADP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IOM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM SCHISTOSOMA REMARK 900 MANSONI IS SPACE GROUP P6322 REMARK 900 RELATED ID: 5IOL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM SCHISTOSOMA REMARK 900 MANSONI DBREF 5KK8 A 2 149 UNP G4VJY9 G4VJY9_SCHMA 2 149 DBREF 5KK8 B 2 149 UNP G4VJY9 G4VJY9_SCHMA 2 149 SEQADV 5KK8 GLY A 0 UNP G4VJY9 EXPRESSION TAG SEQADV 5KK8 PRO A 1 UNP G4VJY9 EXPRESSION TAG SEQADV 5KK8 GLY B 0 UNP G4VJY9 EXPRESSION TAG SEQADV 5KK8 PRO B 1 UNP G4VJY9 EXPRESSION TAG SEQRES 1 A 150 GLY PRO GLU ARG THR PHE ILE MET VAL LYS PRO ASP GLY SEQRES 2 A 150 VAL GLN ARG GLY LEU VAL GLY GLU VAL ILE GLN ARG PHE SEQRES 3 A 150 GLU ARG ARG GLY TYR LYS LEU VAL ALA ILE LYS MET MET SEQRES 4 A 150 HIS ALA SER GLU GLN LEU LEU GLN THR HIS TYR GLU ALA SEQRES 5 A 150 LEU LYS SER LEU SER PHE PHE PRO LYS LEU VAL ALA TYR SEQRES 6 A 150 MET SER SER GLY PRO VAL VAL PRO MET VAL PHE GLU GLY SEQRES 7 A 150 ARG LYS VAL VAL GLU ASN GLY ARG THR MET LEU GLY ALA SEQRES 8 A 150 THR LYS PRO GLU ALA SER CYS PRO GLY SER ILE ARG GLY SEQRES 9 A 150 ASP TYR CYS GLN ASP VAL GLY ARG ASN VAL VAL HIS GLY SEQRES 10 A 150 SER ASP SER THR GLU SER ALA ASN ARG GLU ILE ASN LEU SEQRES 11 A 150 TRP PHE SER PRO GLN GLU LEU CYS GLN TYR LYS GLN ALA SEQRES 12 A 150 VAL ASP PRO TRP ILE HIS GLU SEQRES 1 B 150 GLY PRO GLU ARG THR PHE ILE MET VAL LYS PRO ASP GLY SEQRES 2 B 150 VAL GLN ARG GLY LEU VAL GLY GLU VAL ILE GLN ARG PHE SEQRES 3 B 150 GLU ARG ARG GLY TYR LYS LEU VAL ALA ILE LYS MET MET SEQRES 4 B 150 HIS ALA SER GLU GLN LEU LEU GLN THR HIS TYR GLU ALA SEQRES 5 B 150 LEU LYS SER LEU SER PHE PHE PRO LYS LEU VAL ALA TYR SEQRES 6 B 150 MET SER SER GLY PRO VAL VAL PRO MET VAL PHE GLU GLY SEQRES 7 B 150 ARG LYS VAL VAL GLU ASN GLY ARG THR MET LEU GLY ALA SEQRES 8 B 150 THR LYS PRO GLU ALA SER CYS PRO GLY SER ILE ARG GLY SEQRES 9 B 150 ASP TYR CYS GLN ASP VAL GLY ARG ASN VAL VAL HIS GLY SEQRES 10 B 150 SER ASP SER THR GLU SER ALA ASN ARG GLU ILE ASN LEU SEQRES 11 B 150 TRP PHE SER PRO GLN GLU LEU CYS GLN TYR LYS GLN ALA SEQRES 12 B 150 VAL ASP PRO TRP ILE HIS GLU HET ADP A 201 27 HET ADP B 201 27 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 HOH *184(H2 O) HELIX 1 AA1 LYS A 9 ARG A 15 1 7 HELIX 2 AA2 LEU A 17 ARG A 28 1 12 HELIX 3 AA3 SER A 41 TYR A 49 1 9 HELIX 4 AA4 GLU A 50 LYS A 53 5 4 HELIX 5 AA5 PHE A 57 SER A 66 1 10 HELIX 6 AA6 LYS A 79 GLY A 89 1 11 HELIX 7 AA7 LYS A 92 SER A 96 5 5 HELIX 8 AA8 SER A 100 CYS A 106 1 7 HELIX 9 AA9 ASP A 108 ASN A 112 5 5 HELIX 10 AB1 SER A 119 PHE A 131 1 13 HELIX 11 AB2 SER A 132 LEU A 136 5 5 HELIX 12 AB3 VAL A 143 HIS A 148 1 6 HELIX 13 AB4 LYS B 9 ARG B 15 1 7 HELIX 14 AB5 LEU B 17 ARG B 28 1 12 HELIX 15 AB6 SER B 41 TYR B 49 1 9 HELIX 16 AB7 GLU B 50 LYS B 53 5 4 HELIX 17 AB8 PHE B 57 SER B 66 1 10 HELIX 18 AB9 LYS B 79 GLY B 89 1 11 HELIX 19 AC1 LYS B 92 SER B 96 5 5 HELIX 20 AC2 SER B 100 CYS B 106 1 7 HELIX 21 AC3 ASP B 108 ASN B 112 5 5 HELIX 22 AC4 SER B 119 PHE B 131 1 13 HELIX 23 AC5 SER B 132 LEU B 136 5 5 HELIX 24 AC6 VAL B 143 HIS B 148 1 6 SHEET 1 AA1 4 LYS A 31 ILE A 35 0 SHEET 2 AA1 4 VAL A 71 GLU A 76 -1 O VAL A 74 N VAL A 33 SHEET 3 AA1 4 ARG A 3 VAL A 8 -1 N ILE A 6 O MET A 73 SHEET 4 AA1 4 VAL A 114 GLY A 116 -1 O HIS A 115 N MET A 7 SHEET 1 AA2 4 LYS B 31 ILE B 35 0 SHEET 2 AA2 4 VAL B 71 GLU B 76 -1 O GLU B 76 N LYS B 31 SHEET 3 AA2 4 ARG B 3 VAL B 8 -1 N ILE B 6 O MET B 73 SHEET 4 AA2 4 VAL B 114 GLY B 116 -1 O HIS B 115 N MET B 7 SITE 1 AC1 9 LYS A 9 LEU A 52 LEU A 61 THR A 91 SITE 2 AC1 9 ARG A 102 VAL A 109 ASN A 112 HOH A 307 SITE 3 AC1 9 HOH A 312 SITE 1 AC2 8 LYS B 9 PHE B 57 LEU B 61 ARG B 85 SITE 2 AC2 8 THR B 91 VAL B 109 ASN B 112 HOH B 325 CRYST1 71.450 71.450 219.340 90.00 90.00 120.00 P 63 2 2 24 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 0.013996 0.008080 0.000000 0.00000 SCALE2 0.000000 0.016161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004559 0.00000