HEADER HYDROLASE/HYDROLASE INHIBITOR 20-NOV-13 4YIH TITLE CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'(3')-DEOXYRIBONUCLEOTIDASE IN TITLE 2 COMPLEX WITH THE INHIBITOR PB-PVU COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'(3')-DEOXYRIBONUCLEOTIDASE, CYTOSOLIC TYPE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-195; COMPND 5 SYNONYM: CYTOSOLIC 5',3'-PYRIMIDINE NUCLEOTIDASE,DEOXY-5'- COMPND 6 NUCLEOTIDASE 1,DNT-1; COMPND 7 EC: 3.1.3.-; COMPND 8 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: NT5C, DNT1, UMPH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 5'-NUCLEOTIDASE, DEPHOSPHORYLATION, PHOSPHORYLATION, HAD-LIKE, KEYWDS 2 MITOCHONDRIA, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.PACHL,P.REZACOVA,J.BRYNDA REVDAT 4 10-JAN-24 4YIH 1 LINK REVDAT 3 06-FEB-19 4YIH 1 JRNL REVDAT 2 06-SEP-17 4YIH 1 REMARK LINK SITE ATOM REVDAT 1 09-SEP-15 4YIH 0 JRNL AUTH P.PACHL,O.SIMAK,P.REZACOVA,M.FABRY,M.BUDESINSKY,I.ROSENBERG, JRNL AUTH 2 J.BRYNDA JRNL TITL STRUCTURE-BASED DESIGN OF A BISPHOSPHONATE JRNL TITL 2 5'(3')-DEOXYRIBONUCLEOTIDASE INHIBITOR JRNL REF MEDCHEMCOMM V. 6 1635 2015 JRNL REFN ISSN 2040-2503 JRNL DOI 10.1039/C5MD00235D REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 33458 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1672 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2337 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 123 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3066 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82000 REMARK 3 B22 (A**2) : 0.69000 REMARK 3 B33 (A**2) : -0.29000 REMARK 3 B12 (A**2) : -0.58000 REMARK 3 B13 (A**2) : -0.20000 REMARK 3 B23 (A**2) : 0.87000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.148 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.638 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3232 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3033 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4407 ; 2.083 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6939 ; 1.256 ; 3.005 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 378 ; 6.248 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;27.563 ;22.229 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 520 ;13.029 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;19.675 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 482 ; 0.171 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3576 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 781 ; 0.005 ; 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): 1515 ; 1.987 ; 2.063 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1514 ; 1.985 ; 2.061 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1889 ; 2.693 ; 3.076 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 4 195 B 4 195 11304 0.070 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 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 4 A 121 REMARK 3 ORIGIN FOR THE GROUP (A): -1.7944 6.1705 -1.1549 REMARK 3 T TENSOR REMARK 3 T11: 0.1070 T22: 0.0468 REMARK 3 T33: 0.1647 T12: 0.0248 REMARK 3 T13: 0.0027 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 1.5124 L22: 0.4168 REMARK 3 L33: 0.0805 L12: -0.2257 REMARK 3 L13: -0.1018 L23: 0.0865 REMARK 3 S TENSOR REMARK 3 S11: -0.0129 S12: 0.0212 S13: 0.1141 REMARK 3 S21: 0.0799 S22: -0.0154 S23: 0.0159 REMARK 3 S31: 0.0161 S32: 0.0304 S33: 0.0283 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 122 A 162 REMARK 3 ORIGIN FOR THE GROUP (A): 1.3702 -8.6220 -5.2535 REMARK 3 T TENSOR REMARK 3 T11: 0.1044 T22: 0.0421 REMARK 3 T33: 0.1743 T12: 0.0315 REMARK 3 T13: 0.0055 T23: -0.0261 REMARK 3 L TENSOR REMARK 3 L11: 1.5482 L22: 0.8067 REMARK 3 L33: 0.7407 L12: 0.3271 REMARK 3 L13: 0.1634 L23: -0.4153 REMARK 3 S TENSOR REMARK 3 S11: 0.0327 S12: 0.1459 S13: -0.1811 REMARK 3 S21: 0.0521 S22: 0.0378 S23: 0.0422 REMARK 3 S31: 0.0309 S32: 0.0412 S33: -0.0705 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 163 A 195 REMARK 3 ORIGIN FOR THE GROUP (A): 1.3429 -9.1263 9.4198 REMARK 3 T TENSOR REMARK 3 T11: 0.1672 T22: 0.0931 REMARK 3 T33: 0.1732 T12: 0.0367 REMARK 3 T13: -0.0037 T23: 0.0723 REMARK 3 L TENSOR REMARK 3 L11: 3.0002 L22: 0.6091 REMARK 3 L33: 0.5277 L12: -0.3284 REMARK 3 L13: -0.8730 L23: 0.4496 REMARK 3 S TENSOR REMARK 3 S11: -0.0061 S12: -0.4378 S13: -0.2927 REMARK 3 S21: 0.1132 S22: -0.0185 S23: 0.0170 REMARK 3 S31: -0.0032 S32: 0.0529 S33: 0.0246 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 : B 4 B 44 REMARK 3 ORIGIN FOR THE GROUP (A): 11.2831 -0.5661 -34.0712 REMARK 3 T TENSOR REMARK 3 T11: 0.0143 T22: 0.4170 REMARK 3 T33: 0.0234 T12: -0.0127 REMARK 3 T13: -0.0073 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 2.5571 L22: 2.4087 REMARK 3 L33: 1.8827 L12: 1.6060 REMARK 3 L13: -1.9521 L23: -1.6029 REMARK 3 S TENSOR REMARK 3 S11: -0.0735 S12: 0.7943 S13: -0.0951 REMARK 3 S21: -0.0445 S22: 0.0314 S23: -0.1451 REMARK 3 S31: 0.1147 S32: -0.4256 S33: 0.0422 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 : B 45 B 94 REMARK 3 ORIGIN FOR THE GROUP (A): 8.9826 -0.2329 -30.6337 REMARK 3 T TENSOR REMARK 3 T11: 0.0118 T22: 0.4149 REMARK 3 T33: 0.0500 T12: 0.0130 REMARK 3 T13: 0.0142 T23: 0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.8283 L22: 0.5111 REMARK 3 L33: 1.1278 L12: 0.1392 REMARK 3 L13: -0.6509 L23: -0.7178 REMARK 3 S TENSOR REMARK 3 S11: 0.0363 S12: 0.7406 S13: 0.0691 REMARK 3 S21: -0.0378 S22: -0.1170 S23: -0.0637 REMARK 3 S31: 0.0456 S32: -0.0437 S33: 0.0807 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 : B 95 B 195 REMARK 3 ORIGIN FOR THE GROUP (A): 4.0192 -9.3416 -24.7311 REMARK 3 T TENSOR REMARK 3 T11: 0.0449 T22: 0.5049 REMARK 3 T33: 0.0869 T12: 0.0229 REMARK 3 T13: -0.0024 T23: -0.1055 REMARK 3 L TENSOR REMARK 3 L11: 0.3924 L22: 0.4472 REMARK 3 L33: 0.9182 L12: -0.0957 REMARK 3 L13: -0.2279 L23: -0.1115 REMARK 3 S TENSOR REMARK 3 S11: -0.0420 S12: 0.3825 S13: -0.0674 REMARK 3 S21: 0.0655 S22: 0.0512 S23: -0.0122 REMARK 3 S31: 0.1511 S32: -0.0318 S33: -0.0092 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 202 A 202 REMARK 3 ORIGIN FOR THE GROUP (A): -8.4144 2.5711 -5.2095 REMARK 3 T TENSOR REMARK 3 T11: 0.1174 T22: 0.0816 REMARK 3 T33: 0.1398 T12: -0.0075 REMARK 3 T13: 0.0240 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.5841 L22: 0.2132 REMARK 3 L33: 10.2905 L12: -0.3264 REMARK 3 L13: -1.4719 L23: 0.3767 REMARK 3 S TENSOR REMARK 3 S11: 0.0287 S12: 0.0361 S13: 0.0451 REMARK 3 S21: -0.0153 S22: -0.0160 S23: -0.0353 REMARK 3 S31: -0.1234 S32: -0.0562 S33: -0.0127 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 202 B 202 REMARK 3 ORIGIN FOR THE GROUP (A): 14.9966 -1.3346 -24.9350 REMARK 3 T TENSOR REMARK 3 T11: 0.1064 T22: 0.1531 REMARK 3 T33: 0.1338 T12: -0.0222 REMARK 3 T13: 0.0308 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.4114 L22: 0.1278 REMARK 3 L33: 23.2057 L12: 0.4164 REMARK 3 L13: 5.7167 L23: 1.7022 REMARK 3 S TENSOR REMARK 3 S11: -0.1002 S12: 0.0671 S13: 0.0114 REMARK 3 S21: -0.0420 S22: 0.0439 S23: 0.0064 REMARK 3 S31: -0.4549 S32: 0.3397 S33: 0.0562 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 4YIH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207528. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33500 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 57.443 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 2.110 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.090 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4L57 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MM POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 6% PEG8000, 20% GYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K, PH 4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 3080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ARG A 3 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ARG B 3 REMARK 465 VAL B 172 REMARK 465 LEU B 173 REMARK 465 PRO B 174 REMARK 465 PRO B 175 REMARK 465 THR B 176 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 75 OE1 OE2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 ARG A 150 CD NE CZ NH1 NH2 REMARK 470 GLU A 154 CG CD OE1 OE2 REMARK 470 ARG B 28 CD NE CZ NH1 NH2 REMARK 470 GLU B 39 CG CD OE1 OE2 REMARK 470 GLU B 75 CD OE1 OE2 REMARK 470 LYS B 104 CG CD CE NZ REMARK 470 ASP B 147 CG OD1 OD2 REMARK 470 GLU B 154 CG CD OE1 OE2 REMARK 470 GLU B 159 CG CD OE1 OE2 REMARK 470 ARG B 169 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 177 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 178 NE CZ NH1 NH2 REMARK 470 GLU B 189 CG CD OE1 OE2 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 OXT ARG A 195 O HOH A 301 2.12 REMARK 500 O THR B 164 O HOH B 301 2.16 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 A 10 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG B 85 NE - CZ - NH2 ANGL. DEV. = 4.0 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 MET A 11 -65.50 -96.47 REMARK 500 VAL A 14 -50.46 -125.90 REMARK 500 MET B 11 -67.64 -98.36 REMARK 500 VAL B 14 -50.86 -125.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD2 REMARK 620 2 ASP A 12 O 77.4 REMARK 620 3 ASP A 145 OD1 96.2 83.3 REMARK 620 4 PO4 A 202 O4 86.9 102.0 174.3 REMARK 620 5 GOL A 204 O1 155.8 103.5 60.3 116.0 REMARK 620 6 HOH A 358 O 92.2 165.9 88.5 86.7 82.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 10 OD2 REMARK 620 2 ASP B 12 O 78.1 REMARK 620 3 ASP B 145 OD1 100.1 88.4 REMARK 620 4 PO4 B 202 O1 80.5 92.5 179.0 REMARK 620 5 HOH B 344 O 93.6 171.5 91.3 87.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2O2 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2O2 B 203 DBREF 4YIH A 1 195 UNP Q8TCD5 NT5C_HUMAN 1 195 DBREF 4YIH B 1 195 UNP Q8TCD5 NT5C_HUMAN 1 195 SEQRES 1 A 195 MET ALA ARG SER VAL ARG VAL LEU VAL ASP MET ASP GLY SEQRES 2 A 195 VAL LEU ALA ASP PHE GLU ALA GLY LEU LEU ARG GLY PHE SEQRES 3 A 195 ARG ARG ARG PHE PRO GLU GLU PRO HIS VAL PRO LEU GLU SEQRES 4 A 195 GLN ARG ARG GLY PHE LEU ALA ARG GLU GLN TYR ARG ALA SEQRES 5 A 195 LEU ARG PRO ASP LEU ALA ASP LYS VAL ALA SER VAL TYR SEQRES 6 A 195 GLU ALA PRO GLY PHE PHE LEU ASP LEU GLU PRO ILE PRO SEQRES 7 A 195 GLY ALA LEU ASP ALA VAL ARG GLU MET ASN ASP LEU PRO SEQRES 8 A 195 ASP THR GLN VAL PHE ILE CYS THR SER PRO LEU LEU LYS SEQRES 9 A 195 TYR HIS HIS CYS VAL GLY GLU LYS TYR ARG TRP VAL GLU SEQRES 10 A 195 GLN HIS LEU GLY PRO GLN PHE VAL GLU ARG ILE ILE LEU SEQRES 11 A 195 THR ARG ASP LYS THR VAL VAL LEU GLY ASP LEU LEU ILE SEQRES 12 A 195 ASP ASP LYS ASP THR VAL ARG GLY GLN GLU GLU THR PRO SEQRES 13 A 195 SER TRP GLU HIS ILE LEU PHE THR CYS CYS HIS ASN ARG SEQRES 14 A 195 HIS LEU VAL LEU PRO PRO THR ARG ARG ARG LEU LEU SER SEQRES 15 A 195 TRP SER ASP ASN TRP ARG GLU ILE LEU ASP SER LYS ARG SEQRES 1 B 195 MET ALA ARG SER VAL ARG VAL LEU VAL ASP MET ASP GLY SEQRES 2 B 195 VAL LEU ALA ASP PHE GLU ALA GLY LEU LEU ARG GLY PHE SEQRES 3 B 195 ARG ARG ARG PHE PRO GLU GLU PRO HIS VAL PRO LEU GLU SEQRES 4 B 195 GLN ARG ARG GLY PHE LEU ALA ARG GLU GLN TYR ARG ALA SEQRES 5 B 195 LEU ARG PRO ASP LEU ALA ASP LYS VAL ALA SER VAL TYR SEQRES 6 B 195 GLU ALA PRO GLY PHE PHE LEU ASP LEU GLU PRO ILE PRO SEQRES 7 B 195 GLY ALA LEU ASP ALA VAL ARG GLU MET ASN ASP LEU PRO SEQRES 8 B 195 ASP THR GLN VAL PHE ILE CYS THR SER PRO LEU LEU LYS SEQRES 9 B 195 TYR HIS HIS CYS VAL GLY GLU LYS TYR ARG TRP VAL GLU SEQRES 10 B 195 GLN HIS LEU GLY PRO GLN PHE VAL GLU ARG ILE ILE LEU SEQRES 11 B 195 THR ARG ASP LYS THR VAL VAL LEU GLY ASP LEU LEU ILE SEQRES 12 B 195 ASP ASP LYS ASP THR VAL ARG GLY GLN GLU GLU THR PRO SEQRES 13 B 195 SER TRP GLU HIS ILE LEU PHE THR CYS CYS HIS ASN ARG SEQRES 14 B 195 HIS LEU VAL LEU PRO PRO THR ARG ARG ARG LEU LEU SER SEQRES 15 B 195 TRP SER ASP ASN TRP ARG GLU ILE LEU ASP SER LYS ARG HET MG A 201 1 HET PO4 A 202 5 HET 2O2 A 203 33 HET GOL A 204 6 HET MG B 201 1 HET PO4 B 202 5 HET 2O2 B 203 33 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM 2O2 1-{2-DEOXY-3,5-O-[PHENYL(PHOSPHONO)METHYLIDENE]-BETA-D- HETNAM 2 2O2 THREO-PENTOFURANOSYL}-5-[(E)-2- HETNAM 3 2O2 PHOSPHONOETHENYL]PYRIMIDINE-2,4(1H,3H)-DIONE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MG 2(MG 2+) FORMUL 4 PO4 2(O4 P 3-) FORMUL 5 2O2 2(C18 H20 N2 O11 P2) FORMUL 6 GOL C3 H8 O3 FORMUL 10 HOH *190(H2 O) HELIX 1 AA1 ASP A 17 PHE A 30 1 14 HELIX 2 AA2 PRO A 37 ARG A 41 5 5 HELIX 3 AA3 LEU A 45 ARG A 54 1 10 HELIX 4 AA4 ASP A 56 GLU A 66 1 11 HELIX 5 AA5 GLY A 79 LEU A 90 1 12 HELIX 6 AA6 CYS A 108 GLY A 121 1 14 HELIX 7 AA7 GLY A 121 GLU A 126 1 6 HELIX 8 AA8 ASP A 133 VAL A 137 5 5 HELIX 9 AA9 ASN A 186 SER A 193 1 8 HELIX 10 AB1 ASP B 17 PHE B 30 1 14 HELIX 11 AB2 PRO B 37 ARG B 41 5 5 HELIX 12 AB3 LEU B 45 ARG B 54 1 10 HELIX 13 AB4 ASP B 56 GLU B 66 1 11 HELIX 14 AB5 GLY B 79 LEU B 90 1 12 HELIX 15 AB6 CYS B 108 GLY B 121 1 14 HELIX 16 AB7 GLY B 121 GLU B 126 1 6 HELIX 17 AB8 ASP B 133 VAL B 137 5 5 HELIX 18 AB9 ASN B 186 SER B 193 1 8 SHEET 1 AA112 ARG A 178 LEU A 180 0 SHEET 2 AA112 GLU A 159 PHE A 163 1 N LEU A 162 O LEU A 180 SHEET 3 AA112 LEU A 141 ASP A 144 1 N LEU A 142 O ILE A 161 SHEET 4 AA112 VAL A 5 VAL A 9 1 N LEU A 8 O LEU A 141 SHEET 5 AA112 THR A 93 THR A 99 1 O PHE A 96 N VAL A 9 SHEET 6 AA112 ILE A 128 THR A 131 1 O ILE A 129 N ILE A 97 SHEET 7 AA112 ILE B 128 LEU B 130 -1 O LEU B 130 N LEU A 130 SHEET 8 AA112 THR B 93 THR B 99 1 N ILE B 97 O ILE B 129 SHEET 9 AA112 VAL B 5 VAL B 9 1 N VAL B 7 O GLN B 94 SHEET 10 AA112 LEU B 141 ASP B 144 1 O LEU B 141 N LEU B 8 SHEET 11 AA112 GLU B 159 PHE B 163 1 O ILE B 161 N LEU B 142 SHEET 12 AA112 ARG B 178 LEU B 180 1 O LEU B 180 N LEU B 162 LINK OD2 ASP A 10 MG MG A 201 1555 1555 2.15 LINK O ASP A 12 MG MG A 201 1555 1555 2.56 LINK OD1 ASP A 145 MG MG A 201 1555 1555 2.38 LINK MG MG A 201 O4 BPO4 A 202 1555 1555 2.07 LINK MG MG A 201 O1 GOL A 204 1555 1555 2.86 LINK MG MG A 201 O HOH A 358 1555 1555 2.02 LINK OD2 ASP B 10 MG MG B 201 1555 1555 2.14 LINK O ASP B 12 MG MG B 201 1555 1555 2.46 LINK OD1 ASP B 145 MG MG B 201 1555 1555 2.27 LINK MG MG B 201 O1 BPO4 B 202 1555 1555 2.50 LINK MG MG B 201 O HOH B 344 1555 1555 1.78 SITE 1 AC1 7 ASP A 10 ASP A 12 ASP A 145 PO4 A 202 SITE 2 AC1 7 2O2 A 203 GOL A 204 HOH A 358 SITE 1 AC2 12 ASP A 10 MET A 11 ASP A 12 THR A 99 SITE 2 AC2 12 SER A 100 LYS A 134 MG A 201 2O2 A 203 SITE 3 AC2 12 HOH A 358 HOH A 313 HOH A 351 HOH A 377 SITE 1 AC3 17 ASP A 12 PHE A 18 PHE A 44 LEU A 45 SITE 2 AC3 17 ALA A 46 ARG A 47 TYR A 65 SER A 100 SITE 3 AC3 17 LEU A 102 LEU A 103 ARG A 132 MG A 201 SITE 4 AC3 17 PO4 A 202 GOL A 204 HOH A 316 HOH A 351 SITE 5 AC3 17 HOH A 377 SITE 1 AC4 11 ASP A 12 GLY A 13 PHE A 18 GLU A 19 SITE 2 AC4 11 PHE A 44 ASP A 145 CYS A 165 HIS A 167 SITE 3 AC4 11 MG A 201 2O2 A 203 HOH A 310 SITE 1 AC5 6 ASP B 10 ASP B 12 ASP B 145 PO4 B 202 SITE 2 AC5 6 2O2 B 203 HOH B 344 SITE 1 AC6 11 ASP B 10 MET B 11 ASP B 12 THR B 99 SITE 2 AC6 11 SER B 100 LYS B 112 LYS B 134 MG B 201 SITE 3 AC6 11 2O2 B 203 HOH B 344 HOH B 317 SITE 1 AC7 15 ASP B 12 PHE B 18 PHE B 44 LEU B 45 SITE 2 AC7 15 ALA B 46 ARG B 47 TYR B 65 LEU B 102 SITE 3 AC7 15 LEU B 103 ARG B 132 MG B 201 PO4 B 202 SITE 4 AC7 15 HOH B 344 HOH B 314 HOH B 304 CRYST1 38.818 46.451 61.738 111.18 88.16 104.70 P 1 2 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 0.025761 0.006758 0.001761 0.00000 SCALE2 0.000000 0.022257 0.008733 0.00000 SCALE3 0.000000 0.000000 0.017409 0.00000