HEADER HYDROLASE 18-JAN-16 5HNF TITLE CRYSTAL STRUCTURE OF PYRENE- AND PHENANTHRENE-MODIFIED DNA IN COMPLEX TITLE 2 WITH THE BPUJ1 ENDONUCLEASE BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESTRICTION ENDONUCLEASE R.BPUJI; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*(YPE)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3'); COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*(YPF)P*C)-3'); COMPND 11 CHAIN: M; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PUMILUS; SOURCE 3 ORGANISM_TAXID: 1408; SOURCE 4 GENE: BPUJIR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS PHENANTHRENE, PYRENE, DNA, ENDONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PROBST,W.AESCHIMANN,T.-T.-H.CHAU,S.M.LANGENEGGER,A.STOCKER,R.HAENER REVDAT 3 10-JAN-24 5HNF 1 REMARK REVDAT 2 14-SEP-16 5HNF 1 JRNL REVDAT 1 17-AUG-16 5HNF 0 JRNL AUTH M.PROBST,W.AESCHIMANN,T.T.CHAU,S.M.LANGENEGGER,A.STOCKER, JRNL AUTH 2 R.HANER JRNL TITL STRUCTURAL INSIGHT INTO DNA-ASSEMBLED OLIGOCHROMOPHORES: JRNL TITL 2 CRYSTALLOGRAPHIC ANALYSIS OF PYRENE- AND JRNL TITL 3 PHENANTHRENE-MODIFIED DNA IN COMPLEX WITH BPUJI JRNL TITL 4 ENDONUCLEASE. JRNL REF NUCLEIC ACIDS RES. V. 44 7079 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27422870 JRNL DOI 10.1093/NAR/GKW644 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 61042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5615 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 43.9476 - 4.8029 0.98 3784 206 0.1633 0.1722 REMARK 3 2 4.8029 - 3.8129 0.98 3819 194 0.1499 0.1417 REMARK 3 3 3.8129 - 3.3311 0.92 3554 186 0.1451 0.1670 REMARK 3 4 3.3311 - 3.0266 0.86 3356 174 0.1504 0.1870 REMARK 3 5 3.0266 - 2.8097 0.93 3579 186 0.1674 0.2042 REMARK 3 6 2.8097 - 2.6441 0.96 3686 195 0.1672 0.2090 REMARK 3 7 2.6441 - 2.5117 0.96 3755 197 0.1690 0.1999 REMARK 3 8 2.5117 - 2.4024 0.94 3651 195 0.1715 0.1955 REMARK 3 9 2.4024 - 2.3099 0.95 3613 196 0.1688 0.2202 REMARK 3 10 2.3099 - 2.2302 0.95 3717 196 0.1668 0.2220 REMARK 3 11 2.2302 - 2.1605 0.96 3709 193 0.1699 0.1976 REMARK 3 12 2.1605 - 2.0987 0.96 3665 190 0.1607 0.1879 REMARK 3 13 2.0987 - 2.0435 0.95 3691 194 0.1646 0.1791 REMARK 3 14 2.0435 - 1.9936 0.95 3645 190 0.1619 0.2027 REMARK 3 15 1.9936 - 1.9483 0.95 3732 203 0.1695 0.1791 REMARK 3 16 1.9483 - 1.9068 0.90 3410 184 0.1814 0.2209 REMARK 3 17 1.9068 - 1.8687 0.89 3483 181 0.1820 0.2172 REMARK 3 18 1.8687 - 1.8334 0.90 3457 186 0.1855 0.2058 REMARK 3 19 1.8334 - 1.8007 0.90 3501 178 0.1865 0.1962 REMARK 3 20 1.8007 - 1.7701 0.90 3473 180 0.1943 0.2078 REMARK 3 21 1.7701 - 1.7416 0.92 3546 189 0.2032 0.2215 REMARK 3 22 1.7416 - 1.7148 0.91 3537 185 0.2108 0.2500 REMARK 3 23 1.7148 - 1.6896 0.92 3538 181 0.2137 0.2368 REMARK 3 24 1.6896 - 1.6658 0.91 3604 194 0.2132 0.2420 REMARK 3 25 1.6658 - 1.6433 0.91 3496 181 0.2206 0.2749 REMARK 3 26 1.6433 - 1.6219 0.92 3575 183 0.2294 0.2299 REMARK 3 27 1.6219 - 1.6016 0.91 3478 181 0.2327 0.2860 REMARK 3 28 1.6016 - 1.5823 0.91 3549 188 0.2505 0.2984 REMARK 3 29 1.5823 - 1.5639 0.90 3465 186 0.2470 0.2925 REMARK 3 30 1.5639 - 1.5464 0.68 2690 143 0.2511 0.2604 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.440 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) : 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 : 0.011 2906 REMARK 3 ANGLE : 1.236 4000 REMARK 3 CHIRALITY : 0.058 420 REMARK 3 PLANARITY : 0.007 448 REMARK 3 DIHEDRAL : 18.612 1122 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 101 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.6311 -31.7278 30.9002 REMARK 3 T TENSOR REMARK 3 T11: 0.0892 T22: 0.1305 REMARK 3 T33: 0.1056 T12: 0.0125 REMARK 3 T13: -0.0012 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 1.1377 L22: 0.8022 REMARK 3 L33: 0.7874 L12: -0.2396 REMARK 3 L13: -0.0332 L23: 0.0469 REMARK 3 S TENSOR REMARK 3 S11: -0.0518 S12: -0.1923 S13: -0.0646 REMARK 3 S21: 0.0748 S22: 0.0346 S23: -0.0820 REMARK 3 S31: 0.0083 S32: 0.1457 S33: -0.0020 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 102 THROUGH 176 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.3430 -19.5628 17.0798 REMARK 3 T TENSOR REMARK 3 T11: 0.1126 T22: 0.0672 REMARK 3 T33: 0.0820 T12: 0.0009 REMARK 3 T13: 0.0037 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.6301 L22: 0.4490 REMARK 3 L33: 0.4560 L12: -0.4904 REMARK 3 L13: -0.0091 L23: 0.0788 REMARK 3 S TENSOR REMARK 3 S11: 0.0325 S12: 0.0750 S13: 0.0921 REMARK 3 S21: -0.0509 S22: -0.0388 S23: -0.0007 REMARK 3 S31: -0.1343 S32: 0.0231 S33: -0.1071 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 177 THROUGH 248 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.4580 -24.3665 15.8277 REMARK 3 T TENSOR REMARK 3 T11: 0.1214 T22: 0.1198 REMARK 3 T33: 0.1010 T12: 0.0120 REMARK 3 T13: -0.0197 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.8898 L22: 0.4840 REMARK 3 L33: 0.4093 L12: -0.3408 REMARK 3 L13: -0.1427 L23: -0.1319 REMARK 3 S TENSOR REMARK 3 S11: -0.0052 S12: 0.1182 S13: -0.0623 REMARK 3 S21: -0.0402 S22: -0.0404 S23: 0.0629 REMARK 3 S31: -0.0213 S32: -0.0998 S33: -0.0119 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 249 THROUGH 281 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.1677 -14.4298 24.2310 REMARK 3 T TENSOR REMARK 3 T11: 0.1253 T22: 0.1378 REMARK 3 T33: 0.1963 T12: -0.0225 REMARK 3 T13: -0.0215 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.2544 L22: 0.3574 REMARK 3 L33: 0.2331 L12: -0.0962 REMARK 3 L13: 0.2294 L23: 0.0067 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: -0.0185 S13: 0.3428 REMARK 3 S21: 0.0992 S22: 0.0042 S23: -0.0231 REMARK 3 S31: -0.0746 S32: 0.1259 S33: -0.0053 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 101 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.6856 -38.9424 16.3805 REMARK 3 T TENSOR REMARK 3 T11: 0.1232 T22: 0.1434 REMARK 3 T33: 0.1822 T12: 0.0053 REMARK 3 T13: 0.0256 T23: -0.0176 REMARK 3 L TENSOR REMARK 3 L11: 0.2060 L22: 0.2852 REMARK 3 L33: 0.2174 L12: -0.2253 REMARK 3 L13: -0.0095 L23: -0.1348 REMARK 3 S TENSOR REMARK 3 S11: -0.0234 S12: -0.0571 S13: -0.1735 REMARK 3 S21: -0.0960 S22: -0.0511 S23: -0.2188 REMARK 3 S31: 0.0614 S32: 0.0709 S33: -0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'M' AND (RESID 201 THROUGH 211 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.3764 -38.2714 17.3650 REMARK 3 T TENSOR REMARK 3 T11: 0.1316 T22: 0.1293 REMARK 3 T33: 0.1655 T12: -0.0051 REMARK 3 T13: 0.0173 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.1227 L22: 0.2758 REMARK 3 L33: 0.4719 L12: -0.1601 REMARK 3 L13: 0.1069 L23: 0.0321 REMARK 3 S TENSOR REMARK 3 S11: -0.1955 S12: 0.1053 S13: 0.0373 REMARK 3 S21: -0.1413 S22: 0.1004 S23: -0.0605 REMARK 3 S31: 0.0620 S32: 0.1191 S33: -0.0006 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 5HNF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217293. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00004 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61076 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.546 REMARK 200 RESOLUTION RANGE LOW (A) : 43.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.170 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.12 REMARK 200 R MERGE FOR SHELL (I) : 0.37500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.030 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: 2VLA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM CITRATE, PEG 3350, PH 7.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 82.86150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.63900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 82.86150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.63900 REMARK 290 SMTRY3 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, L, M 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 419 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 282 REMARK 465 HIS A 283 REMARK 465 LYS A 284 REMARK 465 SER A 285 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 OP1 DG M 207 O HOH M 301 2.09 REMARK 500 O HOH A 593 O HOH A 598 2.10 REMARK 500 O HOH L 225 O HOH M 337 2.13 REMARK 500 NZ LYS A 174 O HOH A 301 2.16 REMARK 500 OD1 ASN A 281 O HOH A 302 2.17 REMARK 500 O HOH A 477 O HOH A 592 2.18 REMARK 500 O HOH A 302 O HOH A 571 2.18 REMARK 500 OD1 ASN A 50 O HOH A 303 2.19 REMARK 500 O HOH A 657 O HOH A 659 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 DG L 109 O3' DG L 109 C3' -0.039 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 GLU A 85 -10.25 71.15 REMARK 500 GLU A 85 -12.59 73.36 REMARK 500 GLN A 134 103.86 -162.08 REMARK 500 VAL A 164 -71.47 -121.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 667 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH L 254 DISTANCE = 6.76 ANGSTROMS DBREF 5HNF A 1 285 UNP A3FMN7 A3FMN7_BACPU 1 285 DBREF 5HNF L 101 111 PDB 5HNF 5HNF 101 111 DBREF 5HNF M 201 211 PDB 5HNF 5HNF 201 211 SEQADV 5HNF GLY A -2 UNP A3FMN7 EXPRESSION TAG SEQADV 5HNF SER A -1 UNP A3FMN7 EXPRESSION TAG SEQADV 5HNF HIS A 0 UNP A3FMN7 EXPRESSION TAG SEQRES 1 A 288 GLY SER HIS MET ASN TYR ASN PRO GLU GLU GLN PHE ARG SEQRES 2 A 288 CYS THR ILE ILE ARG GLY LYS ALA LYS ASN MET LEU ASP SEQRES 3 A 288 ASN LEU LEU PRO ALA TYR ALA ASN ILE ILE ASP ASP ILE SEQRES 4 A 288 CYS PRO CYS ASP LYS ALA SER PHE VAL LYS ASP PHE ASN SEQRES 5 A 288 ASN ARG LEU ILE GLU ILE LEU GLY GLU GLU THR THR LYS SEQRES 6 A 288 LYS THR LEU ASP ASN HIS ARG THR GLU ILE ALA GLY LYS SEQRES 7 A 288 LEU PHE GLY MET PHE TYR GLU ASP ASP GLU VAL ILE PHE SEQRES 8 A 288 PRO SER GLY ARG THR ASN LYS TYR ILE GLU ASP SER ASP SEQRES 9 A 288 GLN PRO ALA PHE PHE LYS ASP ILE CYS PHE LYS PHE GLN SEQRES 10 A 288 PHE PRO ASN GLY MET ASP LYS LEU ASP LYS VAL ILE GLU SEQRES 11 A 288 LYS VAL GLY ALA LYS ILE GLN ILE ARG GLN PHE PRO TYR SEQRES 12 A 288 ILE LEU GLN VAL LEU LEU THR ALA ASP ASN ASN ASN ILE SEQRES 13 A 288 GLN LEU SER LYS ASP ASP ILE ALA TYR TYR VAL LEU ASN SEQRES 14 A 288 SER LEU GLN VAL LEU GLN GLY LYS ILE LYS PRO ILE GLU SEQRES 15 A 288 VAL ILE GLU LYS ILE ILE GLU ASP ARG SER ASN ASP ILE SEQRES 16 A 288 THR LYS LYS VAL ARG HIS PRO GLY LYS GLU THR SER TYR SEQRES 17 A 288 SER MET GLN HIS ILE ARG GLU GLN LEU ASN TYR LEU GLU SEQRES 18 A 288 LEU ALA ASN LEU ILE ARG ILE ASP GLY ASN LEU VAL LYS SEQRES 19 A 288 LEU ASN TYR ARG GLU ALA GLU ASN ILE ASN TYR ILE ALA SEQRES 20 A 288 GLN PHE TRP GLY ASN LYS PRO GLU PHE ASN ALA TYR LYS SEQRES 21 A 288 TYR ASP PHE THR SER GLU ASP ASP LYS LYS SER PHE PHE SEQRES 22 A 288 LYS ASP TRP GLN GLN TYR TYR SER ASN VAL ASN SER HIS SEQRES 23 A 288 LYS SER SEQRES 1 L 11 DG YPE DA DC DC DC DG DT DG DG DA SEQRES 1 M 11 DT DC DC DA DC DG DG DG DT YPF DC HET YPE L 102 29 HET YPF M 210 27 HETNAM YPE 4-[8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL]BUT-3-YN-1-YL HETNAM 2 YPE DIHYDROGEN PHOSPHATE HETNAM YPF 4-[6-(4-OXIDANYLBUT-1-YNYL)PHENANTHREN-3-YL]BUT-3-YNYL HETNAM 2 YPF DIHYDROGEN PHOSPHATE FORMUL 2 YPE C24 H19 O5 P FORMUL 3 YPF C22 H19 O5 P FORMUL 4 HOH *479(H2 O) HELIX 1 AA1 MET A 21 CYS A 37 1 17 HELIX 2 AA2 LYS A 41 GLY A 57 1 17 HELIX 3 AA3 THR A 61 ILE A 72 1 12 HELIX 4 AA4 SER A 90 SER A 100 1 11 HELIX 5 AA5 ASP A 101 PHE A 113 1 13 HELIX 6 AA6 LYS A 121 ALA A 131 1 11 HELIX 7 AA7 ARG A 136 ASN A 151 1 16 HELIX 8 AA8 LYS A 157 VAL A 164 1 8 HELIX 9 AA9 SER A 167 GLN A 172 1 6 HELIX 10 AB1 LYS A 176 ASN A 190 1 15 HELIX 11 AB2 GLU A 202 ALA A 220 1 19 HELIX 12 AB3 GLU A 236 GLN A 245 1 10 HELIX 13 AB4 PHE A 246 ASN A 249 5 4 HELIX 14 AB5 ASN A 254 TYR A 258 5 5 HELIX 15 AB6 SER A 262 ASN A 279 1 18 SHEET 1 AA1 3 CYS A 39 ASP A 40 0 SHEET 2 AA1 3 VAL A 86 PRO A 89 -1 O ILE A 87 N CYS A 39 SHEET 3 AA1 3 PHE A 80 ASP A 83 -1 N ASP A 83 O VAL A 86 SHEET 1 AA2 3 LEU A 155 SER A 156 0 SHEET 2 AA2 3 LEU A 229 LEU A 232 -1 O VAL A 230 N LEU A 155 SHEET 3 AA2 3 ILE A 223 ASP A 226 -1 N ARG A 224 O LYS A 231 LINK O3' DG L 101 PBA YPE L 102 1555 1555 1.59 LINK OAZ YPE L 102 P DA L 103 1555 1555 1.60 LINK O3' DT M 209 PBA YPF M 210 1555 1555 1.58 LINK OAZ YPF M 210 P DC M 211 1555 1555 1.59 CISPEP 1 CYS A 37 PRO A 38 0 5.02 CISPEP 2 PHE A 115 PRO A 116 0 -5.39 CRYST1 165.723 59.278 44.048 90.00 94.20 90.00 C 1 2 1 4 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 0.006034 0.000000 0.000443 0.00000 SCALE2 0.000000 0.016870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022764 0.00000