HEADER HYDROLASE/DNA 20-JAN-11 3QEB TITLE CRYSTAL STRUCTURE OF HUMAN EXONUCLEASE 1 EXO1 (WT) IN COMPLEX WITH DNA TITLE 2 AND MN2+ (COMPLEX III) 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(*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 3QEB 1 REMARK LINK REVDAT 2 04-MAY-11 3QEB 1 JRNL REVDAT 1 20-APR-11 3QEB 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. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.2_432) 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 9214 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 438 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 31.0316 - 4.3249 1.00 3233 164 0.2057 0.2465 REMARK 3 2 4.3249 - 3.4343 0.99 3030 141 0.2299 0.2912 REMARK 3 3 3.4343 - 3.0000 0.83 2513 133 0.2914 0.3250 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.06 REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 50.46 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 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) : 11.21010 REMARK 3 B22 (A**2) : 11.21010 REMARK 3 B33 (A**2) : -22.42030 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 : 0.001 3236 REMARK 3 ANGLE : 0.412 4450 REMARK 3 CHIRALITY : 0.025 501 REMARK 3 PLANARITY : 0.001 500 REMARK 3 DIHEDRAL : 16.815 1251 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): -5.3126 24.7232 -17.3397 REMARK 3 T TENSOR REMARK 3 T11: 0.4348 T22: 0.8096 REMARK 3 T33: 0.7404 T12: 0.0070 REMARK 3 T13: 0.1027 T23: -0.3666 REMARK 3 L TENSOR REMARK 3 L11: 0.0320 L22: 1.4410 REMARK 3 L33: 1.1784 L12: 0.2273 REMARK 3 L13: -0.0943 L23: -0.3075 REMARK 3 S TENSOR REMARK 3 S11: -0.0510 S12: 0.2756 S13: 0.1811 REMARK 3 S21: -0.4394 S22: -0.1254 S23: -0.1251 REMARK 3 S31: 0.2316 S32: 0.0217 S33: 0.1878 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN Z AND RESID 29:86) REMARK 3 ORIGIN FOR THE GROUP (A): -10.3007 19.2326 1.2595 REMARK 3 T TENSOR REMARK 3 T11: 0.8056 T22: 0.5114 REMARK 3 T33: 0.5907 T12: -0.2142 REMARK 3 T13: 0.0387 T23: -0.0266 REMARK 3 L TENSOR REMARK 3 L11: 2.1851 L22: 2.9742 REMARK 3 L33: 3.2203 L12: 0.1244 REMARK 3 L13: -1.2568 L23: -0.9993 REMARK 3 S TENSOR REMARK 3 S11: 0.0541 S12: -0.0284 S13: 0.3137 REMARK 3 S21: 1.0235 S22: 0.2489 S23: -0.3573 REMARK 3 S31: 0.8838 S32: -0.4090 S33: -0.2052 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN Z AND RESID 87:130) REMARK 3 ORIGIN FOR THE GROUP (A): -26.9037 24.6375 6.2920 REMARK 3 T TENSOR REMARK 3 T11: 0.3789 T22: 0.7253 REMARK 3 T33: 1.6961 T12: -0.0628 REMARK 3 T13: 0.1199 T23: -0.1402 REMARK 3 L TENSOR REMARK 3 L11: 0.4387 L22: 4.6466 REMARK 3 L33: 3.8289 L12: -1.4191 REMARK 3 L13: 0.1622 L23: -1.1178 REMARK 3 S TENSOR REMARK 3 S11: -0.9256 S12: 0.3060 S13: 0.6064 REMARK 3 S21: 0.5298 S22: -0.0102 S23: 1.9893 REMARK 3 S31: -0.1976 S32: -0.9841 S33: 0.8202 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN Z AND RESID 131:233) REMARK 3 ORIGIN FOR THE GROUP (A): -5.0226 31.2370 -9.8332 REMARK 3 T TENSOR REMARK 3 T11: 0.3293 T22: 0.3171 REMARK 3 T33: 0.3437 T12: 0.0631 REMARK 3 T13: 0.0235 T23: -0.1665 REMARK 3 L TENSOR REMARK 3 L11: 2.0319 L22: 2.5314 REMARK 3 L33: 4.2242 L12: 0.1003 REMARK 3 L13: 0.4360 L23: 1.3106 REMARK 3 S TENSOR REMARK 3 S11: 0.1317 S12: 0.2311 S13: -0.3899 REMARK 3 S21: -0.0931 S22: 0.0391 S23: -0.3928 REMARK 3 S31: -0.1084 S32: -0.4040 S33: -0.1138 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN Z AND RESID 234:276) REMARK 3 ORIGIN FOR THE GROUP (A): -13.3425 53.1887 -16.2909 REMARK 3 T TENSOR REMARK 3 T11: 1.2692 T22: 0.7894 REMARK 3 T33: 0.4428 T12: 0.2953 REMARK 3 T13: -0.0203 T23: 0.0461 REMARK 3 L TENSOR REMARK 3 L11: 5.0528 L22: 4.1807 REMARK 3 L33: 0.5094 L12: 0.0532 REMARK 3 L13: 0.1640 L23: -1.4524 REMARK 3 S TENSOR REMARK 3 S11: 0.0067 S12: 1.4317 S13: 0.5641 REMARK 3 S21: -1.1107 S22: 0.1605 S23: 0.0945 REMARK 3 S31: -1.7269 S32: -0.6812 S33: -0.0884 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN Z AND RESID 277:346) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2469 36.4393 6.4651 REMARK 3 T TENSOR REMARK 3 T11: 0.5355 T22: 0.5974 REMARK 3 T33: 0.4255 T12: 0.0352 REMARK 3 T13: -0.0510 T23: -0.0754 REMARK 3 L TENSOR REMARK 3 L11: 0.9195 L22: 1.9841 REMARK 3 L33: 2.4350 L12: -0.9123 REMARK 3 L13: 0.6586 L23: 0.8497 REMARK 3 S TENSOR REMARK 3 S11: 0.0400 S12: -0.3665 S13: 0.0352 REMARK 3 S21: 0.1135 S22: 0.2484 S23: -0.3622 REMARK 3 S31: -0.1420 S32: 0.4021 S33: -0.2982 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A) REMARK 3 ORIGIN FOR THE GROUP (A): -27.4885 32.5252 -15.3413 REMARK 3 T TENSOR REMARK 3 T11: 1.5887 T22: 0.8658 REMARK 3 T33: 1.1958 T12: 0.4107 REMARK 3 T13: 0.3380 T23: 0.3741 REMARK 3 L TENSOR REMARK 3 L11: 4.8427 L22: 1.3117 REMARK 3 L33: 9.6340 L12: -1.7314 REMARK 3 L13: 5.7830 L23: -0.6923 REMARK 3 S TENSOR REMARK 3 S11: 0.7676 S12: 0.3543 S13: -1.5036 REMARK 3 S21: 1.3260 S22: 0.2699 S23: 1.5908 REMARK 3 S31: -0.9425 S32: 0.9604 S33: -0.8168 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN B) REMARK 3 ORIGIN FOR THE GROUP (A): -27.4504 34.3807 -16.3352 REMARK 3 T TENSOR REMARK 3 T11: 1.4604 T22: 0.8104 REMARK 3 T33: 1.2346 T12: 0.1448 REMARK 3 T13: 0.0767 T23: 0.3795 REMARK 3 L TENSOR REMARK 3 L11: 1.1609 L22: 9.0072 REMARK 3 L33: 8.9539 L12: 0.4720 REMARK 3 L13: 0.9497 L23: -1.7813 REMARK 3 S TENSOR REMARK 3 S11: 0.2237 S12: 0.4146 S13: -0.8750 REMARK 3 S21: -0.3250 S22: 2.1062 S23: 2.0357 REMARK 3 S31: 0.8637 S32: 0.5026 S33: -2.1295 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 3QEB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063536. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-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) : 1.00 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 : 11100 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 83.3 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) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.9 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 (%): 49.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6K, MES, 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 91.44150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.20300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.20300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 137.16225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.20300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.20300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.72075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.20300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.20300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 137.16225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.20300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.20300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.72075 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 91.44150 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: 2730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 DA A 22 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 DT B 1 P DT B 1 OP3 -0.128 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 SER Z 84 CB - CA - C ANGL. DEV. = 14.7 DEGREES REMARK 500 LYS Z 85 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 DG A 16 O4' - C1' - N9 ANGL. DEV. = 3.2 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 TYR Z 22 38.01 -92.43 REMARK 500 VAL Z 112 -60.21 -92.18 REMARK 500 TYR Z 149 -69.05 -144.55 REMARK 500 VAL Z 209 44.68 -94.82 REMARK 500 ARG Z 231 109.58 -54.36 REMARK 500 LYS Z 262 15.25 59.42 REMARK 500 ASN Z 264 70.67 -100.10 REMARK 500 VAL Z 287 -158.86 -112.62 REMARK 500 ILE Z 291 -62.94 -122.42 REMARK 500 LEU Z 310 51.18 -107.79 REMARK 500 THR Z 345 -90.76 -110.97 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 MN Z 353 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP Z 152 OD2 REMARK 620 2 HOH Z 356 O 104.9 REMARK 620 3 HOH Z 359 O 89.0 96.4 REMARK 620 4 DT B 1 OP1 98.5 92.4 166.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN Z 354 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP Z 152 OD1 REMARK 620 2 ASP Z 171 OD2 66.9 REMARK 620 3 ASP Z 173 OD2 112.6 98.8 REMARK 620 4 HOH Z 355 O 173.4 108.0 71.7 REMARK 620 5 DT B 1 OP1 83.5 93.2 162.8 92.9 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 MN Z 353 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN Z 354 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QE9 RELATED DB: PDB REMARK 900 RELATED ID: 3QEA RELATED DB: PDB DBREF 3QEB Z 1 352 UNP Q9UQ84 EXO1_HUMAN 1 352 DBREF 3QEB A 11 23 PDB 3QEB 3QEB 11 23 DBREF 3QEB B 1 10 PDB 3QEB 3QEB 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 MN Z 353 1 HET MN Z 354 1 HETNAM MN MANGANESE (II) ION FORMUL 4 MN 2(MN 2+) FORMUL 6 HOH *16(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 ALA Z 47 1 6 HELIX 5 5 ASP Z 53 HIS Z 69 1 17 HELIX 6 6 LEU Z 82 LYS Z 85 5 4 HELIX 7 7 LYS Z 86 LEU Z 106 1 21 HELIX 8 8 LEU Z 107 GLU Z 109 5 3 HELIX 9 9 VAL Z 112 ARG Z 121 1 10 HELIX 10 10 THR Z 126 GLN Z 140 1 15 HELIX 11 11 GLU Z 150 ALA Z 161 1 12 HELIX 12 12 SER Z 172 GLY Z 178 1 7 HELIX 13 13 ALA Z 198 CYS Z 203 5 6 HELIX 14 14 THR Z 211 SER Z 222 1 12 HELIX 15 15 GLY Z 234 ALA Z 245 1 12 HELIX 16 16 ASP Z 249 LYS Z 256 1 8 HELIX 17 17 LYS Z 256 LYS Z 262 1 7 HELIX 18 18 PRO Z 268 GLN Z 285 1 18 HELIX 19 19 ASP Z 306 GLY Z 314 5 9 HELIX 20 20 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 LEU Z 184 O LEU Z 193 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 ILE Z 74 N VAL Z 27 SHEET 7 A 7 ASP Z 143 VAL Z 146 1 O LEU Z 145 N LEU Z 75 LINK OD2 ASP Z 152 MN MN Z 353 1555 1555 2.42 LINK OD1 ASP Z 152 MN MN Z 354 1555 1555 2.51 LINK OD2 ASP Z 171 MN MN Z 354 1555 1555 2.52 LINK OD2 ASP Z 173 MN MN Z 354 1555 1555 2.57 LINK MN MN Z 353 O HOH Z 356 1555 1555 2.51 LINK MN MN Z 353 O HOH Z 359 1555 1555 2.33 LINK MN MN Z 353 OP1 DT B 1 1555 1555 2.30 LINK MN MN Z 354 O HOH Z 355 1555 1555 2.62 LINK MN MN Z 354 OP1 DT B 1 1555 1555 2.30 SITE 1 AC1 4 DT B 1 ASP Z 152 HOH Z 356 HOH Z 359 SITE 1 AC2 5 DT B 1 ASP Z 152 ASP Z 171 ASP Z 173 SITE 2 AC2 5 HOH Z 355 CRYST1 70.406 70.406 182.883 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 0.014203 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014203 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005468 0.00000