PDB Short entry for 4YKL HEADER HYDROLASE/DNA 04-MAR-15 4YKL TITLE HNT3 IN COMPLEX WITH DNA AND GUANOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: APRATAXIN-LIKE PROTEIN; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 33-232; COMPND 5 SYNONYM: HIT FAMILY PROTEIN 3; COMPND 6 EC: 3.-.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'); COMPND 10 CHAIN: A; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC SOURCE 3 24843); SOURCE 4 ORGANISM_COMMON: FISSION YEAST; SOURCE 5 ORGANISM_TAXID: 284812; SOURCE 6 STRAIN: 972 / ATCC 24843; SOURCE 7 GENE: HNT3, SPCC18.09C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET28B-HIS10-SMT3; SOURCE 13 MOL_ID: 2; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS GMP, NUCLEOTIDYL TRANSFERASE, HYDROLASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.JACEWICZ,M.CHAULEAU,S.SHUMAN REVDAT 7 27-SEP-23 4YKL 1 REMARK REVDAT 6 25-DEC-19 4YKL 1 REMARK REVDAT 5 13-SEP-17 4YKL 1 REMARK REVDAT 4 27-JUL-16 4YKL 1 REMARK REVDAT 3 22-JUL-15 4YKL 1 JRNL REVDAT 2 10-JUN-15 4YKL 1 JRNL REVDAT 1 03-JUN-15 4YKL 0 JRNL AUTH M.CHAULEAU,A.JACEWICZ,S.SHUMAN JRNL TITL DNA3'PP5'G DE-CAPPING ACTIVITY OF APRATAXIN: EFFECT OF CAP JRNL TITL 2 NUCLEOSIDE ANALOGS AND STRUCTURAL BASIS FOR GUANOSINE JRNL TITL 3 RECOGNITION. JRNL REF NUCLEIC ACIDS RES. V. 43 6075 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26007660 JRNL DOI 10.1093/NAR/GKV501 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14364 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.030 REMARK 3 FREE R VALUE TEST SET COUNT : 866 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 59.5623 - 4.0884 1.00 2297 175 0.1653 0.2175 REMARK 3 2 4.0884 - 3.2451 1.00 2282 125 0.1671 0.2453 REMARK 3 3 3.2451 - 2.8349 1.00 2224 139 0.1934 0.2623 REMARK 3 4 2.8349 - 2.5757 1.00 2253 136 0.2065 0.2595 REMARK 3 5 2.5757 - 2.3911 1.00 2239 134 0.2131 0.2624 REMARK 3 6 2.3911 - 2.2501 1.00 2203 157 0.2127 0.2776 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.80 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 : 0.008 1907 REMARK 3 ANGLE : 1.188 2620 REMARK 3 CHIRALITY : 0.044 289 REMARK 3 PLANARITY : 0.006 291 REMARK 3 DIHEDRAL : 17.471 717 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 33 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.5852 83.6782 32.5301 REMARK 3 T TENSOR REMARK 3 T11: 0.5098 T22: 0.5001 REMARK 3 T33: 0.4986 T12: 0.0022 REMARK 3 T13: 0.0531 T23: -0.0354 REMARK 3 L TENSOR REMARK 3 L11: 0.1932 L22: 0.0455 REMARK 3 L33: 0.0452 L12: 0.0896 REMARK 3 L13: -0.0477 L23: -0.0385 REMARK 3 S TENSOR REMARK 3 S11: -0.1485 S12: -0.3948 S13: 0.1029 REMARK 3 S21: 0.4580 S22: 0.4075 S23: 0.5016 REMARK 3 S31: -0.5458 S32: -0.2828 S33: 0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 44 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.4256 73.5162 28.5211 REMARK 3 T TENSOR REMARK 3 T11: 0.3056 T22: 0.4451 REMARK 3 T33: 0.2721 T12: -0.0447 REMARK 3 T13: -0.0039 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 0.7508 L22: 0.8964 REMARK 3 L33: 0.8682 L12: -0.3538 REMARK 3 L13: -0.2513 L23: -0.3089 REMARK 3 S TENSOR REMARK 3 S11: 0.0977 S12: -0.2568 S13: 0.1437 REMARK 3 S21: 0.1328 S22: -0.0320 S23: 0.0291 REMARK 3 S31: -0.1444 S32: -0.1007 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 77 THROUGH 93 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.5006 90.0854 23.8774 REMARK 3 T TENSOR REMARK 3 T11: 0.4091 T22: 0.3274 REMARK 3 T33: 0.4206 T12: -0.1788 REMARK 3 T13: -0.0265 T23: -0.0716 REMARK 3 L TENSOR REMARK 3 L11: 1.5102 L22: 2.2503 REMARK 3 L33: 0.1069 L12: -0.0354 REMARK 3 L13: 0.2598 L23: 0.0358 REMARK 3 S TENSOR REMARK 3 S11: 0.0264 S12: -0.1432 S13: 1.0452 REMARK 3 S21: -0.2540 S22: -0.0427 S23: -0.2198 REMARK 3 S31: -0.7039 S32: 0.3128 S33: 0.1631 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 94 THROUGH 119 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.0364 71.8881 20.5309 REMARK 3 T TENSOR REMARK 3 T11: 0.2722 T22: 0.4628 REMARK 3 T33: 0.3569 T12: 0.0267 REMARK 3 T13: 0.0175 T23: 0.0316 REMARK 3 L TENSOR REMARK 3 L11: 0.4332 L22: 0.8525 REMARK 3 L33: 1.1491 L12: -0.3556 REMARK 3 L13: 0.1157 L23: 0.4185 REMARK 3 S TENSOR REMARK 3 S11: -0.0223 S12: 0.0325 S13: -0.0378 REMARK 3 S21: -0.0770 S22: 0.0676 S23: -0.2125 REMARK 3 S31: 0.2703 S32: 0.2766 S33: 0.0135 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 120 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.8006 61.2750 12.5791 REMARK 3 T TENSOR REMARK 3 T11: 0.4374 T22: 0.3913 REMARK 3 T33: 0.4400 T12: 0.0340 REMARK 3 T13: 0.0533 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 0.8460 L22: 1.0797 REMARK 3 L33: 1.1341 L12: -0.8911 REMARK 3 L13: 0.2571 L23: -0.2392 REMARK 3 S TENSOR REMARK 3 S11: -0.1199 S12: 0.5095 S13: -0.3042 REMARK 3 S21: -0.1676 S22: -0.1196 S23: -0.0640 REMARK 3 S31: 0.6860 S32: 0.4076 S33: 0.0035 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 133 THROUGH 183 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.6180 79.8705 15.0257 REMARK 3 T TENSOR REMARK 3 T11: 0.2543 T22: 0.3257 REMARK 3 T33: 0.2939 T12: -0.0424 REMARK 3 T13: 0.0058 T23: -0.0242 REMARK 3 L TENSOR REMARK 3 L11: 0.3879 L22: 1.0559 REMARK 3 L33: 0.3866 L12: 0.4144 REMARK 3 L13: 0.3041 L23: -0.1170 REMARK 3 S TENSOR REMARK 3 S11: -0.1175 S12: -0.1060 S13: 0.0118 REMARK 3 S21: -0.1616 S22: 0.0665 S23: 0.0801 REMARK 3 S31: -0.0302 S32: -0.0180 S33: 0.0042 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 184 THROUGH 195 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.6149 90.4102 9.1605 REMARK 3 T TENSOR REMARK 3 T11: 0.5332 T22: 0.3700 REMARK 3 T33: 0.6617 T12: 0.1064 REMARK 3 T13: -0.1033 T23: 0.0593 REMARK 3 L TENSOR REMARK 3 L11: 0.0047 L22: 0.0426 REMARK 3 L33: 0.3248 L12: -0.0219 REMARK 3 L13: -0.0263 L23: 0.1152 REMARK 3 S TENSOR REMARK 3 S11: -0.1847 S12: 0.0208 S13: 0.3358 REMARK 3 S21: 0.1315 S22: -0.3041 S23: 0.2034 REMARK 3 S31: -0.3077 S32: -0.8935 S33: 0.0024 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 196 THROUGH 230 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.6646 69.4793 4.9807 REMARK 3 T TENSOR REMARK 3 T11: 0.4047 T22: 0.3801 REMARK 3 T33: 0.3012 T12: -0.0244 REMARK 3 T13: -0.0312 T23: -0.0235 REMARK 3 L TENSOR REMARK 3 L11: 2.2191 L22: 0.9970 REMARK 3 L33: 0.4928 L12: 0.0250 REMARK 3 L13: 0.2155 L23: -0.2549 REMARK 3 S TENSOR REMARK 3 S11: 0.1008 S12: 0.5466 S13: -0.0557 REMARK 3 S21: -0.5701 S22: -0.1217 S23: 0.1765 REMARK 3 S31: 0.0565 S32: 0.0362 S33: -0.1601 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -48.0335 81.5460 18.5756 REMARK 3 T TENSOR REMARK 3 T11: 0.4491 T22: 0.2672 REMARK 3 T33: 0.7233 T12: 0.0109 REMARK 3 T13: -0.0396 T23: 0.0978 REMARK 3 L TENSOR REMARK 3 L11: 1.1028 L22: 0.1510 REMARK 3 L33: 0.5748 L12: 0.1115 REMARK 3 L13: -0.3602 L23: -0.4800 REMARK 3 S TENSOR REMARK 3 S11: 0.2800 S12: -0.5688 S13: 0.5570 REMARK 3 S21: -0.2875 S22: 0.2582 S23: 0.4736 REMARK 3 S31: -0.6286 S32: 0.1215 S33: 0.1565 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 4YKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207612. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.77 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14369 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 59.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : 0.07300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : 0.72200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 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: 4XBA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG-3350, 0.15 M MG-ACETATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-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 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 36.56400 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 B 188 REMARK 465 THR B 189 REMARK 465 LEU B 190 REMARK 465 SER B 231 REMARK 465 MET B 232 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 ARG B 187 CZ NH1 NH2 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 N1 DA A 3 N6 DA A 8 6556 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 DA A 3 O3' DA A 3 C3' -0.038 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 DT A 7 O4' - C1' - N1 ANGL. DEV. = 8.6 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 ASP B 55 -159.57 -139.85 REMARK 500 LEU B 120 -69.81 -109.27 REMARK 500 SER B 157 136.86 -171.44 REMARK 500 THR B 186 138.48 -179.76 REMARK 500 SER B 192 0.79 -150.10 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 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 200 SG REMARK 620 2 CYS B 203 SG 118.0 REMARK 620 3 HIS B 217 NE2 106.7 110.4 REMARK 620 4 GLU B 221 OE1 115.5 103.2 101.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GMP B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 308 DBREF 4YKL B 33 232 UNP O74859 APTX_SCHPO 33 232 DBREF 4YKL A 1 10 PDB 4YKL 4YKL 1 10 SEQRES 1 B 200 SER PHE ARG ASP ASN LEU LYS VAL TYR ILE GLU SER PRO SEQRES 2 B 200 GLU SER TYR LYS ASN VAL ILE TYR TYR ASP ASP ASP VAL SEQRES 3 B 200 VAL LEU VAL ARG ASP MET PHE PRO LYS SER LYS MET HIS SEQRES 4 B 200 LEU LEU LEU MET THR ARG ASP PRO HIS LEU THR HIS VAL SEQRES 5 B 200 HIS PRO LEU GLU ILE MET MET LYS HIS ARG SER LEU VAL SEQRES 6 B 200 GLU LYS LEU VAL SER TYR VAL GLN GLY ASP LEU SER GLY SEQRES 7 B 200 LEU ILE PHE ASP GLU ALA ARG ASN CYS LEU SER GLN GLN SEQRES 8 B 200 LEU THR ASN GLU ALA LEU CYS ASN TYR ILE LYS VAL GLY SEQRES 9 B 200 PHE HIS ALA GLY PRO SER MET ASN ASN LEU HIS LEU HIS SEQRES 10 B 200 ILE MET THR LEU ASP HIS VAL SER PRO SER LEU LYS ASN SEQRES 11 B 200 SER ALA HIS TYR ILE SER PHE THR SER PRO PHE PHE VAL SEQRES 12 B 200 LYS ILE ASP THR PRO THR SER ASN LEU PRO THR ARG GLY SEQRES 13 B 200 THR LEU THR SER LEU PHE GLN GLU ASP LEU LYS CYS TRP SEQRES 14 B 200 ARG CYS GLY GLU THR PHE GLY ARG HIS PHE THR LYS LEU SEQRES 15 B 200 LYS ALA HIS LEU GLN GLU GLU TYR ASP ASP TRP LEU ASP SEQRES 16 B 200 LYS SER VAL SER MET SEQRES 1 A 10 DG DA DA DT DC DA DT DA DA DC HET ZN B 301 1 HET GMP B 302 20 HET GOL B 303 6 HET GOL B 304 6 HET GOL B 305 6 HET GOL B 306 6 HET CL B 307 1 HET CL B 308 1 HETNAM ZN ZINC ION HETNAM GMP GUANOSINE HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN ZN 2+ FORMUL 4 GMP C10 H13 N5 O5 FORMUL 5 GOL 4(C3 H8 O3) FORMUL 9 CL 2(CL 1-) FORMUL 11 HOH *53(H2 O) HELIX 1 AA1 SER B 33 ASN B 37 5 5 HELIX 2 AA2 LEU B 38 SER B 44 1 7 HELIX 3 AA3 PRO B 45 TYR B 48 5 4 HELIX 4 AA4 HIS B 85 HIS B 93 1 9 HELIX 5 AA5 HIS B 93 GLY B 106 1 14 HELIX 6 AA6 LEU B 108 LEU B 120 1 13 HELIX 7 AA7 THR B 125 ASN B 131 1 7 HELIX 8 AA8 ASN B 162 SER B 171 1 10 HELIX 9 AA9 PRO B 180 LEU B 184 5 5 HELIX 10 AB1 SER B 192 GLU B 196 5 5 HELIX 11 AB2 HIS B 210 VAL B 230 1 21 SHEET 1 AA1 6 VAL B 51 TYR B 54 0 SHEET 2 AA1 6 VAL B 58 ARG B 62 -1 O LEU B 60 N TYR B 53 SHEET 3 AA1 6 HIS B 71 THR B 76 -1 O MET B 75 N VAL B 59 SHEET 4 AA1 6 HIS B 147 THR B 152 -1 O ILE B 150 N LEU B 72 SHEET 5 AA1 6 ILE B 133 HIS B 138 -1 N GLY B 136 O HIS B 149 SHEET 6 AA1 6 PHE B 174 LYS B 176 -1 O VAL B 175 N PHE B 137 SHEET 1 AA2 2 LEU B 198 LYS B 199 0 SHEET 2 AA2 2 THR B 206 GLY B 208 -1 O GLY B 208 N LEU B 198 LINK SG CYS B 200 ZN ZN B 301 1555 1555 2.31 LINK SG CYS B 203 ZN ZN B 301 1555 1555 2.32 LINK NE2 HIS B 217 ZN ZN B 301 1555 1555 2.02 LINK OE1 GLU B 221 ZN ZN B 301 1555 1555 1.96 SITE 1 AC1 4 CYS B 200 CYS B 203 HIS B 217 GLU B 221 SITE 1 AC2 10 DG A 1 TYR B 41 ARG B 62 ASP B 63 SITE 2 AC2 10 MET B 64 PHE B 65 LYS B 67 MET B 143 SITE 3 AC2 10 HIS B 147 HOH B 434 SITE 1 AC3 3 VAL B 104 SER B 109 CYS B 130 SITE 1 AC4 4 DG A 1 GLY B 140 SER B 142 HOH B 424 SITE 1 AC5 4 LYS B 49 HIS B 217 GLU B 220 ASP B 224 SITE 1 AC6 1 SER B 102 SITE 1 AC7 3 GLU B 98 VAL B 101 ASN B 126 SITE 1 AC8 1 LYS B 161 CRYST1 119.083 119.083 36.564 90.00 90.00 120.00 P 3 2 1 6 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 0.008398 0.004848 0.000000 0.00000 SCALE2 0.000000 0.009697 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027349 0.00000