HEADER OXIDOREDUCTASE 14-SEP-16 5TC4 TITLE CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL METHYLENETETRAHYDROFOLATE TITLE 2 DEHYDROGENASE-CYCLOHYDROLASE (MTHFD2) IN COMPLEX WITH LY345899 AND TITLE 3 COFACTORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL METHYLENETETRAHYDROFOLATE COMPND 3 DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 36-350; COMPND 6 EC: 1.5.1.15,3.5.4.9; COMPND 7 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: MTHFD2, NMDMC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS INHIBITOR, FOLATE, COFACTOR, DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.GUSTAFSSON,A.-S.JEMTH,N.GUSTAFSSON SHEPPARD,K.FARNEGARDH,O.LOSEVA, AUTHOR 2 E.WIITA,N.BONAGAS,L.DAHLLUND,S.LLONA-MINGUEZ,M.HAGGBLAD, AUTHOR 3 M.HENRIKSSON,Y.ANDERSSON,E.HOMAN,T.HELLEDAY,P.STENMARK REVDAT 5 17-JAN-24 5TC4 1 COMPND HETNAM REVDAT 4 13-SEP-17 5TC4 1 REMARK REVDAT 3 16-AUG-17 5TC4 1 REMARK REVDAT 2 01-MAR-17 5TC4 1 JRNL REVDAT 1 14-DEC-16 5TC4 0 JRNL AUTH R.GUSTAFSSON,A.S.JEMTH,N.M.GUSTAFSSON,K.FARNEGARDH,O.LOSEVA, JRNL AUTH 2 E.WIITA,N.BONAGAS,L.DAHLLUND,S.LLONA-MINGUEZ,M.HAGGBLAD, JRNL AUTH 3 M.HENRIKSSON,Y.ANDERSSON,E.HOMAN,T.HELLEDAY,P.STENMARK JRNL TITL CRYSTAL STRUCTURE OF THE EMERGING CANCER TARGET MTHFD2 IN JRNL TITL 2 COMPLEX WITH A SUBSTRATE-BASED INHIBITOR. JRNL REF CANCER RES. V. 77 937 2017 JRNL REFN ESSN 1538-7445 JRNL PMID 27899380 JRNL DOI 10.1158/0008-5472.CAN-16-1476 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 20245 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1073 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1463 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.3480 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2216 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 83 REMARK 3 SOLVENT ATOMS : 214 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.08000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.158 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.139 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.818 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2379 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2346 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3244 ; 2.276 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5401 ; 1.170 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 296 ; 6.042 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;42.827 ;24.778 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 410 ;15.236 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.267 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2646 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 497 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1184 ; 0.901 ; 1.295 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1184 ; 0.897 ; 1.295 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1480 ; 1.430 ; 1.927 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1481 ; 1.431 ; 1.930 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1195 ; 1.642 ; 1.663 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1192 ; 1.640 ; 1.663 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1759 ; 2.602 ; 2.412 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2789 ; 6.253 ;12.452 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2715 ; 6.066 ;11.835 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 36 A 59 REMARK 3 ORIGIN FOR THE GROUP (A): 84.4053 9.5968 -2.9965 REMARK 3 T TENSOR REMARK 3 T11: 0.0726 T22: 0.2043 REMARK 3 T33: 0.2370 T12: -0.0230 REMARK 3 T13: -0.0114 T23: -0.0814 REMARK 3 L TENSOR REMARK 3 L11: 1.9396 L22: 1.2393 REMARK 3 L33: 20.9785 L12: 1.0531 REMARK 3 L13: -5.9999 L23: -3.5590 REMARK 3 S TENSOR REMARK 3 S11: -0.0955 S12: 0.3022 S13: 0.0086 REMARK 3 S21: -0.0205 S22: -0.1128 S23: 0.2910 REMARK 3 S31: 0.1668 S32: -0.8843 S33: 0.2083 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 60 A 142 REMARK 3 ORIGIN FOR THE GROUP (A): 99.1696 17.9708 14.3693 REMARK 3 T TENSOR REMARK 3 T11: 0.1952 T22: 0.1584 REMARK 3 T33: 0.0436 T12: 0.0362 REMARK 3 T13: 0.0265 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.5046 L22: 1.1266 REMARK 3 L33: 0.2349 L12: 0.4644 REMARK 3 L13: 0.2387 L23: 0.2556 REMARK 3 S TENSOR REMARK 3 S11: -0.0815 S12: -0.0363 S13: 0.1079 REMARK 3 S21: 0.1764 S22: 0.0059 S23: 0.1258 REMARK 3 S31: -0.0367 S32: 0.0032 S33: 0.0757 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 143 A 185 REMARK 3 ORIGIN FOR THE GROUP (A): 102.3112 4.1313 5.7143 REMARK 3 T TENSOR REMARK 3 T11: 0.1881 T22: 0.1583 REMARK 3 T33: 0.0419 T12: -0.0019 REMARK 3 T13: 0.0208 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.0305 L22: 0.3582 REMARK 3 L33: 1.2147 L12: 0.0736 REMARK 3 L13: 0.0037 L23: 0.4351 REMARK 3 S TENSOR REMARK 3 S11: -0.0027 S12: -0.0094 S13: 0.0311 REMARK 3 S21: 0.0935 S22: -0.0449 S23: 0.0977 REMARK 3 S31: 0.0599 S32: -0.0037 S33: 0.0476 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 186 A 275 REMARK 3 ORIGIN FOR THE GROUP (A): 105.0876 4.8474 -12.7991 REMARK 3 T TENSOR REMARK 3 T11: 0.1703 T22: 0.1630 REMARK 3 T33: 0.0204 T12: 0.0047 REMARK 3 T13: -0.0111 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 0.6548 L22: 0.6972 REMARK 3 L33: 0.4834 L12: 0.0098 REMARK 3 L13: -0.1159 L23: -0.1043 REMARK 3 S TENSOR REMARK 3 S11: 0.0184 S12: 0.0796 S13: 0.0056 REMARK 3 S21: 0.0062 S22: -0.0029 S23: 0.0631 REMARK 3 S31: -0.0014 S32: -0.0026 S33: -0.0154 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 276 A 289 REMARK 3 ORIGIN FOR THE GROUP (A): 101.3750 28.4525 -10.3762 REMARK 3 T TENSOR REMARK 3 T11: 0.3838 T22: 0.1374 REMARK 3 T33: 0.5440 T12: 0.1689 REMARK 3 T13: 0.1662 T23: -0.0548 REMARK 3 L TENSOR REMARK 3 L11: 3.6544 L22: 33.9544 REMARK 3 L33: 4.7511 L12: -9.2438 REMARK 3 L13: 2.6314 L23: -1.1798 REMARK 3 S TENSOR REMARK 3 S11: -0.6429 S12: -0.4810 S13: 0.4208 REMARK 3 S21: 0.6170 S22: 0.3327 S23: -1.1395 REMARK 3 S31: -0.9317 S32: -0.8034 S33: 0.3103 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 290 A 320 REMARK 3 ORIGIN FOR THE GROUP (A): 95.0852 14.6726 -13.7554 REMARK 3 T TENSOR REMARK 3 T11: 0.1198 T22: 0.1032 REMARK 3 T33: 0.2906 T12: 0.0415 REMARK 3 T13: -0.0617 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 1.1838 L22: 0.4256 REMARK 3 L33: 3.8727 L12: -0.2800 REMARK 3 L13: -1.0008 L23: 0.2205 REMARK 3 S TENSOR REMARK 3 S11: 0.0774 S12: 0.0929 S13: 0.2825 REMARK 3 S21: -0.1298 S22: -0.0751 S23: 0.2008 REMARK 3 S31: 0.0423 S32: -0.0237 S33: -0.0023 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 321 A 332 REMARK 3 ORIGIN FOR THE GROUP (A): 92.3162 3.7785 12.0475 REMARK 3 T TENSOR REMARK 3 T11: 0.1655 T22: 0.1476 REMARK 3 T33: 0.1654 T12: -0.0085 REMARK 3 T13: 0.0396 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 1.2974 L22: 5.2598 REMARK 3 L33: 9.4520 L12: 1.3564 REMARK 3 L13: -1.7021 L23: -2.0232 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: -0.1073 S13: -0.2726 REMARK 3 S21: -0.0232 S22: -0.0022 S23: 0.1225 REMARK 3 S31: 0.6935 S32: 0.1980 S33: 0.0213 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5TC4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9677 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21322 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 37.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.31600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 4.34800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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: 1B0A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PHOSPHATE/CITRATE PH 4.1, 38 % REMARK 280 V/V PEG300, IN PRESENCE OF 1:50 RATIO EACH OF TRYPSIN, ALPHA- REMARK 280 CHYMOTRYPSIN, PEPSIN, PAPAIN, PROTEINASE K AND SUBTILISIN TO REMARK 280 MTHFD2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,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 -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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 37.16150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.16150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.31000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.16150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.16150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.31000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 37.16150 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 37.16150 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 49.31000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 37.16150 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 37.16150 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 49.31000 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: 6150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 222.96900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 599 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 MET A 35 REMARK 465 ASP A 281 REMARK 465 PRO A 282 REMARK 465 VAL A 283 REMARK 465 THR A 284 REMARK 465 ALA A 285 REMARK 465 ARG A 333 REMARK 465 LEU A 334 REMARK 465 GLU A 335 REMARK 465 GLU A 336 REMARK 465 ARG A 337 REMARK 465 GLU A 338 REMARK 465 VAL A 339 REMARK 465 LEU A 340 REMARK 465 LYS A 341 REMARK 465 SER A 342 REMARK 465 LYS A 343 REMARK 465 GLU A 344 REMARK 465 LEU A 345 REMARK 465 GLY A 346 REMARK 465 VAL A 347 REMARK 465 ALA A 348 REMARK 465 THR A 349 REMARK 465 ASN A 350 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 170 CE1 TYR A 170 CZ 0.095 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 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 123 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 124 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 LYS A 185 CD - CE - NZ ANGL. DEV. = 14.3 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 VAL A 205 -73.02 -128.84 REMARK 500 HIS A 232 -164.87 -162.13 REMARK 500 ALA A 253 55.04 -140.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 711 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 712 DISTANCE = 7.14 ANGSTROMS REMARK 525 HOH A 713 DISTANCE = 7.31 ANGSTROMS REMARK 525 HOH A 714 DISTANCE = 12.68 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue L34 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 403 DBREF 5TC4 A 36 350 UNP P13995 MTDC_HUMAN 36 350 SEQADV 5TC4 MET A 35 UNP P13995 INITIATING METHIONINE SEQRES 1 A 316 MET GLU ALA VAL VAL ILE SER GLY ARG LYS LEU ALA GLN SEQRES 2 A 316 GLN ILE LYS GLN GLU VAL ARG GLN GLU VAL GLU GLU TRP SEQRES 3 A 316 VAL ALA SER GLY ASN LYS ARG PRO HIS LEU SER VAL ILE SEQRES 4 A 316 LEU VAL GLY GLU ASN PRO ALA SER HIS SER TYR VAL LEU SEQRES 5 A 316 ASN LYS THR ARG ALA ALA ALA VAL VAL GLY ILE ASN SER SEQRES 6 A 316 GLU THR ILE MET LYS PRO ALA SER ILE SER GLU GLU GLU SEQRES 7 A 316 LEU LEU ASN LEU ILE ASN LYS LEU ASN ASN ASP ASP ASN SEQRES 8 A 316 VAL ASP GLY LEU LEU VAL GLN LEU PRO LEU PRO GLU HIS SEQRES 9 A 316 ILE ASP GLU ARG ARG ILE CYS ASN ALA VAL SER PRO ASP SEQRES 10 A 316 LYS ASP VAL ASP GLY PHE HIS VAL ILE ASN VAL GLY ARG SEQRES 11 A 316 MET CYS LEU ASP GLN TYR SER MET LEU PRO ALA THR PRO SEQRES 12 A 316 TRP GLY VAL TRP GLU ILE ILE LYS ARG THR GLY ILE PRO SEQRES 13 A 316 THR LEU GLY LYS ASN VAL VAL VAL ALA GLY ARG SER LYS SEQRES 14 A 316 ASN VAL GLY MET PRO ILE ALA MET LEU LEU HIS THR ASP SEQRES 15 A 316 GLY ALA HIS GLU ARG PRO GLY GLY ASP ALA THR VAL THR SEQRES 16 A 316 ILE SER HIS ARG TYR THR PRO LYS GLU GLN LEU LYS LYS SEQRES 17 A 316 HIS THR ILE LEU ALA ASP ILE VAL ILE SER ALA ALA GLY SEQRES 18 A 316 ILE PRO ASN LEU ILE THR ALA ASP MET ILE LYS GLU GLY SEQRES 19 A 316 ALA ALA VAL ILE ASP VAL GLY ILE ASN ARG VAL HIS ASP SEQRES 20 A 316 PRO VAL THR ALA LYS PRO LYS LEU VAL GLY ASP VAL ASP SEQRES 21 A 316 PHE GLU GLY VAL ARG GLN LYS ALA GLY TYR ILE THR PRO SEQRES 22 A 316 VAL PRO GLY GLY VAL GLY PRO MET THR VAL ALA MET LEU SEQRES 23 A 316 MET LYS ASN THR ILE ILE ALA ALA LYS LYS VAL LEU ARG SEQRES 24 A 316 LEU GLU GLU ARG GLU VAL LEU LYS SER LYS GLU LEU GLY SEQRES 25 A 316 VAL ALA THR ASN HET NAD A 401 44 HET L34 A 402 34 HET PO4 A 403 5 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM L34 4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8, HETNAM 2 L34 9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)- HETNAM 3 L34 PHENYLCARBONYL-GLUTAMI C ACID HETNAM PO4 PHOSPHATE ION HETSYN L34 LY345899 FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 L34 C20 H21 N7 O7 FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *214(H2 O) HELIX 1 AA1 SER A 41 SER A 63 1 23 HELIX 2 AA2 ASN A 78 GLY A 96 1 19 HELIX 3 AA3 SER A 109 ASP A 123 1 15 HELIX 4 AA4 ASP A 140 VAL A 148 1 9 HELIX 5 AA5 SER A 149 ASP A 153 5 5 HELIX 6 AA6 HIS A 158 LEU A 167 1 10 HELIX 7 AA7 PRO A 174 GLY A 188 1 15 HELIX 8 AA8 VAL A 205 THR A 215 1 11 HELIX 9 AA9 PRO A 236 ILE A 245 1 10 HELIX 10 AB1 THR A 261 ILE A 265 5 5 HELIX 11 AB2 ASP A 294 ARG A 299 1 6 HELIX 12 AB3 GLY A 311 LYS A 330 1 20 SHEET 1 AA1 6 VAL A 38 VAL A 39 0 SHEET 2 AA1 6 TYR A 304 ILE A 305 1 O ILE A 305 N VAL A 38 SHEET 3 AA1 6 ALA A 270 ASP A 273 1 N VAL A 271 O TYR A 304 SHEET 4 AA1 6 ILE A 249 SER A 252 1 N VAL A 250 O ALA A 270 SHEET 5 AA1 6 ASN A 195 ALA A 199 1 N VAL A 197 O ILE A 251 SHEET 6 AA1 6 THR A 227 SER A 231 1 O THR A 227 N VAL A 196 SHEET 1 AA2 3 ASN A 98 LYS A 104 0 SHEET 2 AA2 3 HIS A 69 VAL A 75 1 N VAL A 72 O GLU A 100 SHEET 3 AA2 3 GLY A 128 VAL A 131 1 O GLY A 128 N SER A 71 SHEET 1 AA3 2 ASN A 277 VAL A 279 0 SHEET 2 AA3 2 LYS A 288 VAL A 290 -1 O LYS A 288 N VAL A 279 CISPEP 1 LEU A 133 PRO A 134 0 14.09 CISPEP 2 VAL A 308 PRO A 309 0 -5.24 SITE 1 AC1 25 THR A 176 GLY A 200 ARG A 201 SER A 202 SITE 2 AC1 25 ASN A 204 VAL A 205 HIS A 232 ARG A 233 SITE 3 AC1 25 ALA A 253 ALA A 254 GLY A 255 ILE A 256 SITE 4 AC1 25 VAL A 274 GLY A 275 ILE A 276 GLY A 313 SITE 5 AC1 25 THR A 316 PO4 A 403 HOH A 537 HOH A 544 SITE 6 AC1 25 HOH A 560 HOH A 567 HOH A 592 HOH A 622 SITE 7 AC1 25 HOH A 629 SITE 1 AC2 21 TYR A 84 ASN A 87 LYS A 88 VAL A 131 SITE 2 AC2 21 GLN A 132 LEU A 133 ASP A 155 PHE A 157 SITE 3 AC2 21 ILE A 276 ARG A 278 LEU A 289 PRO A 309 SITE 4 AC2 21 GLY A 310 PRO A 314 HOH A 501 HOH A 515 SITE 5 AC2 21 HOH A 521 HOH A 522 HOH A 530 HOH A 538 SITE 6 AC2 21 HOH A 561 SITE 1 AC3 5 ARG A 201 ARG A 233 NAD A 401 HOH A 537 SITE 2 AC3 5 HOH A 563 CRYST1 74.323 74.323 98.620 90.00 90.00 90.00 I 4 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 0.013455 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013455 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010140 0.00000