PDB Short entry for 3QEA HEADER HYDROLASE/DNA 20-JAN-11 3QEA TITLE CRYSTAL STRUCTURE OF HUMAN EXONUCLEASE 1 EXO1 (WT) IN COMPLEX WITH DNA TITLE 2 (COMPLEX II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXONUCLEASE 1; COMPND 3 CHAIN: Z; COMPND 4 SYNONYM: HEXO1, EXONUCLEASE I, HEXOI; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3'); COMPND 9 CHAIN: A; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3'); COMPND 13 CHAIN: B; COMPND 14 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: EXO1, EXOI, HEX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES KEYWDS EXONUCLEASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.ORANS,E.A.MCSWEENEY,R.R.IYER,M.A.HAST,H.W.HELLINGA,P.MODRICH, AUTHOR 2 L.S.BEESE REVDAT 3 21-FEB-24 3QEA 1 REMARK LINK REVDAT 2 04-MAY-11 3QEA 1 JRNL REVDAT 1 20-APR-11 3QEA 0 JRNL AUTH J.ORANS,E.A.MCSWEENEY,R.R.IYER,M.A.HAST,H.W.HELLINGA, JRNL AUTH 2 P.MODRICH,L.S.BEESE JRNL TITL STRUCTURES OF HUMAN EXONUCLEASE 1 DNA COMPLEXES SUGGEST A JRNL TITL 2 UNIFIED MECHANISM FOR NUCLEASE FAMILY. JRNL REF CELL(CAMBRIDGE,MASS.) V. 145 212 2011 JRNL REFN ISSN 0092-8674 JRNL PMID 21496642 JRNL DOI 10.1016/J.CELL.2011.03.005 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.540 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16451 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 822 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 35.9074 - 5.6275 1.00 2611 131 0.1968 0.2047 REMARK 3 2 5.6275 - 4.4694 1.00 2596 137 0.2018 0.2151 REMARK 3 3 4.4694 - 3.9052 1.00 2605 138 0.2089 0.2548 REMARK 3 4 3.9052 - 3.5485 1.00 2604 135 0.2359 0.2967 REMARK 3 5 3.5485 - 3.2943 1.00 2619 141 0.2417 0.3170 REMARK 3 6 3.2943 - 3.1000 1.00 2594 140 0.2551 0.3183 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 69.68 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.71290 REMARK 3 B22 (A**2) : 11.71290 REMARK 3 B33 (A**2) : -23.42580 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 3266 REMARK 3 ANGLE : 1.355 4497 REMARK 3 CHIRALITY : 0.092 506 REMARK 3 PLANARITY : 0.004 502 REMARK 3 DIHEDRAL : 17.901 1264 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN Z AND RESID 2:28) REMARK 3 ORIGIN FOR THE GROUP (A): 9.8085 -30.0634 17.6492 REMARK 3 T TENSOR REMARK 3 T11: 0.6484 T22: 0.6024 REMARK 3 T33: 0.4780 T12: 0.0738 REMARK 3 T13: -0.1889 T23: 0.0517 REMARK 3 L TENSOR REMARK 3 L11: 3.8957 L22: 1.7610 REMARK 3 L33: 0.9769 L12: 1.0754 REMARK 3 L13: -1.6867 L23: -0.4075 REMARK 3 S TENSOR REMARK 3 S11: 0.4539 S12: -0.3928 S13: -0.1298 REMARK 3 S21: 0.4216 S22: -0.5908 S23: 0.2905 REMARK 3 S31: -0.8025 S32: 0.1600 S33: 0.0027 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN Z AND RESID 29:86) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0593 -25.0376 -0.8702 REMARK 3 T TENSOR REMARK 3 T11: 0.5797 T22: 0.8590 REMARK 3 T33: 0.6115 T12: -0.0474 REMARK 3 T13: -0.1054 T23: 0.1419 REMARK 3 L TENSOR REMARK 3 L11: 1.4660 L22: 2.5774 REMARK 3 L33: 2.0502 L12: 1.5895 REMARK 3 L13: -0.7752 L23: -0.4032 REMARK 3 S TENSOR REMARK 3 S11: -0.1753 S12: 0.8249 S13: -0.1061 REMARK 3 S21: -0.0624 S22: 0.2123 S23: -0.0773 REMARK 3 S31: -0.1944 S32: 0.3945 S33: -0.1725 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN Z AND RESID 87:130) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1608 -8.8792 -5.7690 REMARK 3 T TENSOR REMARK 3 T11: 0.6751 T22: 0.8666 REMARK 3 T33: 1.0559 T12: 0.0935 REMARK 3 T13: -0.3934 T23: 0.2875 REMARK 3 L TENSOR REMARK 3 L11: 0.8857 L22: 3.0453 REMARK 3 L33: 0.8222 L12: -0.4584 REMARK 3 L13: -0.6103 L23: -0.5384 REMARK 3 S TENSOR REMARK 3 S11: -0.3550 S12: 0.3265 S13: 0.0375 REMARK 3 S21: -0.7600 S22: -0.4422 S23: 0.1472 REMARK 3 S31: -0.6706 S32: 0.1131 S33: 0.4646 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN Z AND RESID 131:233) REMARK 3 ORIGIN FOR THE GROUP (A): 3.3205 -30.7911 10.2204 REMARK 3 T TENSOR REMARK 3 T11: 0.4698 T22: 0.5295 REMARK 3 T33: 0.4618 T12: 0.0577 REMARK 3 T13: -0.1882 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 2.6489 L22: 1.8596 REMARK 3 L33: 4.1377 L12: 0.0575 REMARK 3 L13: 0.6592 L23: 0.3049 REMARK 3 S TENSOR REMARK 3 S11: -0.1428 S12: -0.2190 S13: -0.0968 REMARK 3 S21: 0.2089 S22: 0.1332 S23: -0.1632 REMARK 3 S31: 0.0255 S32: -0.1508 S33: -0.0031 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN Z AND RESID 234:276) REMARK 3 ORIGIN FOR THE GROUP (A): -19.3054 -23.5132 16.7621 REMARK 3 T TENSOR REMARK 3 T11: 0.6697 T22: 1.8315 REMARK 3 T33: 0.9164 T12: 0.2927 REMARK 3 T13: -0.0593 T23: -0.1849 REMARK 3 L TENSOR REMARK 3 L11: 0.2631 L22: 3.1996 REMARK 3 L33: 2.4180 L12: 0.0302 REMARK 3 L13: 0.0406 L23: 1.7388 REMARK 3 S TENSOR REMARK 3 S11: -0.5356 S12: -1.2480 S13: 0.6124 REMARK 3 S21: 0.7069 S22: 0.0309 S23: 1.2454 REMARK 3 S31: -0.2924 S32: -1.7339 S33: 0.6063 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN Z AND RESID 277:346) REMARK 3 ORIGIN FOR THE GROUP (A): -1.4758 -38.5234 -5.9089 REMARK 3 T TENSOR REMARK 3 T11: 0.7663 T22: 0.4849 REMARK 3 T33: 0.4956 T12: -0.0718 REMARK 3 T13: -0.0819 T23: -0.1070 REMARK 3 L TENSOR REMARK 3 L11: 3.5048 L22: 0.1096 REMARK 3 L33: 3.8559 L12: 0.0424 REMARK 3 L13: 0.8196 L23: 0.6887 REMARK 3 S TENSOR REMARK 3 S11: -0.2918 S12: 0.5451 S13: -0.1743 REMARK 3 S21: -0.3953 S22: 0.1806 S23: -0.0364 REMARK 3 S31: 0.4484 S32: -0.5874 S33: 0.0778 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A) REMARK 3 ORIGIN FOR THE GROUP (A): 2.8127 -9.6750 13.3209 REMARK 3 T TENSOR REMARK 3 T11: 0.8052 T22: 1.6165 REMARK 3 T33: 1.5077 T12: 0.3714 REMARK 3 T13: 0.4998 T23: 0.1430 REMARK 3 L TENSOR REMARK 3 L11: 2.9462 L22: 0.0337 REMARK 3 L33: 6.1165 L12: 0.5144 REMARK 3 L13: 3.5289 L23: 0.6789 REMARK 3 S TENSOR REMARK 3 S11: 1.6477 S12: -1.2765 S13: 3.1457 REMARK 3 S21: 0.1263 S22: 0.6962 S23: -1.2196 REMARK 3 S31: -1.9793 S32: -0.1069 S33: -1.7078 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN B) REMARK 3 ORIGIN FOR THE GROUP (A): -0.4234 -9.2790 14.9819 REMARK 3 T TENSOR REMARK 3 T11: 0.9792 T22: 1.5450 REMARK 3 T33: 1.3162 T12: 0.1513 REMARK 3 T13: 0.3273 T23: 0.0145 REMARK 3 L TENSOR REMARK 3 L11: 7.2819 L22: 7.9131 REMARK 3 L33: 4.2083 L12: -3.5900 REMARK 3 L13: -5.5229 L23: 2.2680 REMARK 3 S TENSOR REMARK 3 S11: 0.1837 S12: -1.7001 S13: 1.7981 REMARK 3 S21: -0.2616 S22: 2.0766 S23: -0.8108 REMARK 3 S31: 1.0963 S32: 0.0940 S33: -1.9841 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 3QEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.200 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16451 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, PEG 6K, PH 6.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 90.90000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.90500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.90500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 136.35000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.90500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.90500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.45000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.90500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.90500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 136.35000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.90500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.90500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.45000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 90.90000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z, 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 Z 1 REMARK 465 MET Z 347 REMARK 465 PRO Z 348 REMARK 465 ALA Z 349 REMARK 465 HIS Z 350 REMARK 465 SER Z 351 REMARK 465 ARG Z 352 REMARK 465 DT A 23 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 DC A 11 P DC A 11 OP3 -0.127 REMARK 500 DC A 11 O3' DG A 12 P -0.118 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 TYR Z 149 N - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 DC A 11 C3' - O3' - P ANGL. DEV. = 13.6 DEGREES REMARK 500 DG A 12 O3' - P - OP2 ANGL. DEV. = -17.3 DEGREES REMARK 500 DG A 12 O3' - P - OP1 ANGL. DEV. = 8.6 DEGREES REMARK 500 DG A 12 C3' - O3' - P ANGL. DEV. = 15.0 DEGREES REMARK 500 DC A 13 O3' - P - O5' ANGL. DEV. = 12.9 DEGREES REMARK 500 DC A 13 O3' - P - OP2 ANGL. DEV. = -16.1 DEGREES REMARK 500 DT A 14 C3' - O3' - P ANGL. DEV. = -10.8 DEGREES REMARK 500 DA A 15 O3' - P - OP1 ANGL. DEV. = 13.0 DEGREES REMARK 500 DA A 15 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA A 15 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA A 15 C3' - O3' - P ANGL. DEV. = 17.4 DEGREES REMARK 500 DG A 16 O3' - P - O5' ANGL. DEV. = 12.1 DEGREES REMARK 500 DG B 3 O4' - C1' - N9 ANGL. DEV. = 2.2 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 SER Z 84 -5.34 85.44 REMARK 500 ARG Z 108 47.41 -107.57 REMARK 500 GLU Z 109 -16.26 -143.55 REMARK 500 TYR Z 149 -66.36 -132.93 REMARK 500 ASP Z 173 32.01 -77.24 REMARK 500 LYS Z 185 19.80 53.38 REMARK 500 VAL Z 267 98.78 -66.09 REMARK 500 ILE Z 291 -71.69 -72.64 REMARK 500 ARG Z 293 37.83 78.15 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 BA Z 354 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP Z 30 OD2 REMARK 620 2 ASP Z 152 OD2 88.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA Z 353 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP Z 152 OD1 REMARK 620 2 ASP Z 171 OD2 88.2 REMARK 620 3 ASP Z 173 OD1 54.4 75.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA Z 355 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER Z 222 O REMARK 620 2 SER Z 229 OG 61.9 REMARK 620 3 DT A 14 OP2 136.6 112.0 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA Z 353 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA Z 354 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA Z 355 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA Z 356 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QE9 RELATED DB: PDB REMARK 900 RELATED ID: 3QEB RELATED DB: PDB DBREF 3QEA Z 1 352 UNP Q9UQ84 EXO1_HUMAN 1 352 DBREF 3QEA A 11 23 PDB 3QEA 3QEA 11 23 DBREF 3QEA B 1 10 PDB 3QEA 3QEA 1 10 SEQRES 1 Z 352 MET GLY ILE GLN GLY LEU LEU GLN PHE ILE LYS GLU ALA SEQRES 2 Z 352 SER GLU PRO ILE HIS VAL ARG LYS TYR LYS GLY GLN VAL SEQRES 3 Z 352 VAL ALA VAL ASP THR TYR CYS TRP LEU HIS LYS GLY ALA SEQRES 4 Z 352 ILE ALA CYS ALA GLU LYS LEU ALA LYS GLY GLU PRO THR SEQRES 5 Z 352 ASP ARG TYR VAL GLY PHE CYS MET LYS PHE VAL ASN MET SEQRES 6 Z 352 LEU LEU SER HIS GLY ILE LYS PRO ILE LEU VAL PHE ASP SEQRES 7 Z 352 GLY CYS THR LEU PRO SER LYS LYS GLU VAL GLU ARG SER SEQRES 8 Z 352 ARG ARG GLU ARG ARG GLN ALA ASN LEU LEU LYS GLY LYS SEQRES 9 Z 352 GLN LEU LEU ARG GLU GLY LYS VAL SER GLU ALA ARG GLU SEQRES 10 Z 352 CYS PHE THR ARG SER ILE ASN ILE THR HIS ALA MET ALA SEQRES 11 Z 352 HIS LYS VAL ILE LYS ALA ALA ARG SER GLN GLY VAL ASP SEQRES 12 Z 352 CYS LEU VAL ALA PRO TYR GLU ALA ASP ALA GLN LEU ALA SEQRES 13 Z 352 TYR LEU ASN LYS ALA GLY ILE VAL GLN ALA ILE ILE THR SEQRES 14 Z 352 GLU ASP SER ASP LEU LEU ALA PHE GLY CYS LYS LYS VAL SEQRES 15 Z 352 ILE LEU LYS MET ASP GLN PHE GLY ASN GLY LEU GLU ILE SEQRES 16 Z 352 ASP GLN ALA ARG LEU GLY MET CYS ARG GLN LEU GLY ASP SEQRES 17 Z 352 VAL PHE THR GLU GLU LYS PHE ARG TYR MET CYS ILE LEU SEQRES 18 Z 352 SER GLY CYS ASP TYR LEU SER SER LEU ARG GLY ILE GLY SEQRES 19 Z 352 LEU ALA LYS ALA CYS LYS VAL LEU ARG LEU ALA ASN ASN SEQRES 20 Z 352 PRO ASP ILE VAL LYS VAL ILE LYS LYS ILE GLY HIS TYR SEQRES 21 Z 352 LEU LYS MET ASN ILE THR VAL PRO GLU ASP TYR ILE ASN SEQRES 22 Z 352 GLY PHE ILE ARG ALA ASN ASN THR PHE LEU TYR GLN LEU SEQRES 23 Z 352 VAL PHE ASP PRO ILE LYS ARG LYS LEU ILE PRO LEU ASN SEQRES 24 Z 352 ALA TYR GLU ASP ASP VAL ASP PRO GLU THR LEU SER TYR SEQRES 25 Z 352 ALA GLY GLN TYR VAL ASP ASP SER ILE ALA LEU GLN ILE SEQRES 26 Z 352 ALA LEU GLY ASN LYS ASP ILE ASN THR PHE GLU GLN ILE SEQRES 27 Z 352 ASP ASP TYR ASN PRO ASP THR ALA MET PRO ALA HIS SER SEQRES 28 Z 352 ARG SEQRES 1 A 13 DC DG DC DT DA DG DT DC DG DA DC DA DT SEQRES 1 B 10 DT DC DG DA DC DT DA DG DC DG HET BA Z 353 1 HET BA Z 354 1 HET BA Z 355 1 HET BA Z 356 1 HETNAM BA BARIUM ION FORMUL 4 BA 4(BA 2+) FORMUL 8 HOH *6(H2 O) HELIX 1 1 GLY Z 5 ILE Z 10 1 6 HELIX 2 2 ARG Z 20 LYS Z 23 5 4 HELIX 3 3 THR Z 31 ALA Z 41 1 11 HELIX 4 4 CYS Z 42 LYS Z 48 1 7 HELIX 5 5 ASP Z 53 HIS Z 69 1 17 HELIX 6 6 LYS Z 85 LEU Z 107 1 23 HELIX 7 7 GLU Z 114 THR Z 120 1 7 HELIX 8 8 ARG Z 121 ILE Z 123 5 3 HELIX 9 9 THR Z 126 SER Z 139 1 14 HELIX 10 10 GLU Z 150 ALA Z 161 1 12 HELIX 11 11 ASP Z 171 GLY Z 178 5 8 HELIX 12 12 ALA Z 198 CYS Z 203 5 6 HELIX 13 13 THR Z 211 CYS Z 224 1 14 HELIX 14 14 GLY Z 234 ALA Z 245 1 12 HELIX 15 15 ASP Z 249 LYS Z 255 1 7 HELIX 16 16 LYS Z 256 LEU Z 261 1 6 HELIX 17 17 PRO Z 268 GLN Z 285 1 18 HELIX 18 18 ASP Z 306 GLY Z 314 5 9 HELIX 19 19 ASP Z 318 LEU Z 327 1 10 SHEET 1 A 7 SER Z 14 HIS Z 18 0 SHEET 2 A 7 ASN Z 191 ASP Z 196 -1 O GLU Z 194 N GLU Z 15 SHEET 3 A 7 LYS Z 181 LEU Z 184 -1 N VAL Z 182 O ILE Z 195 SHEET 4 A 7 ALA Z 166 ILE Z 168 1 N ILE Z 167 O ILE Z 183 SHEET 5 A 7 VAL Z 26 ASP Z 30 1 N ASP Z 30 O ILE Z 168 SHEET 6 A 7 LYS Z 72 PHE Z 77 1 O LYS Z 72 N VAL Z 27 SHEET 7 A 7 ASP Z 143 VAL Z 146 1 O LEU Z 145 N LEU Z 75 SHEET 1 B 2 LEU Z 286 ASP Z 289 0 SHEET 2 B 2 LYS Z 294 PRO Z 297 -1 O ILE Z 296 N VAL Z 287 LINK OD2 ASP Z 30 BA BA Z 354 1555 1555 3.28 LINK OD1 ASP Z 152 BA BA Z 353 1555 1555 3.28 LINK OD2 ASP Z 152 BA BA Z 354 1555 1555 3.15 LINK OD2 ASP Z 171 BA BA Z 353 1555 1555 3.40 LINK OD1 ASP Z 173 BA BA Z 353 1555 1555 3.46 LINK O SER Z 222 BA BA Z 355 1555 1555 3.21 LINK OG SER Z 229 BA BA Z 355 1555 1555 3.20 LINK BA BA Z 355 OP2 DT A 14 1555 1555 3.45 SITE 1 AC1 3 ASP Z 152 ASP Z 171 ASP Z 173 SITE 1 AC2 2 ASP Z 30 ASP Z 152 SITE 1 AC3 4 DT A 14 SER Z 222 SER Z 229 ILE Z 233 SITE 1 AC4 1 ARG Z 243 CRYST1 71.810 71.810 181.800 90.00 90.00 90.00 P 43 21 2 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 0.013926 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013926 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005501 0.00000