HEADER DNA BINDING PROTEIN/DNA 24-APR-03 1P51 TITLE ANABAENA HU-DNA COCRYSTAL STRUCTURE (AHU6) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP COMPND 3 *T)-3'; COMPND 4 CHAIN: E, F, I, H; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA-BINDING PROTEIN HU; COMPND 8 CHAIN: A, B, C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED DNA WITH A 5' PHOSPHATE SOURCE 4 MODIFICATION; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ANABAENA SP.; SOURCE 7 ORGANISM_TAXID: 1167; SOURCE 8 GENE: HUP OR HANA OR ASR3935; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: RJ1878 LACKS FUNCTIONAL HU GENES; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET21A (PETAHU) KEYWDS PROTEIN-DNA COMPLEX, DNA BENDING, HU, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.K.SWINGER,K.M.LEMBERG,Y.ZHANG,P.A.RICE REVDAT 5 16-AUG-23 1P51 1 REMARK REVDAT 4 13-JUL-11 1P51 1 VERSN REVDAT 3 24-FEB-09 1P51 1 VERSN REVDAT 2 29-JUL-03 1P51 1 JRNL HEADER REVDAT 1 13-MAY-03 1P51 0 JRNL AUTH K.K.SWINGER,K.M.LEMBERG,Y.ZHANG,P.A.RICE JRNL TITL FLEXIBLE DNA BENDING IN HU-DNA COCRYSTAL STRUCTURES JRNL REF EMBO J. V. 22 3749 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12853489 JRNL DOI 10.1093/EMBOJ/CDG351 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.4 REMARK 3 NUMBER OF REFLECTIONS : 16900 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) : 0.291 REMARK 3 R VALUE (WORKING SET) : 0.286 REMARK 3 FREE R VALUE : 0.338 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1828 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 140 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2767 REMARK 3 NUCLEIC ACID ATOMS : 1556 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 72 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.44000 REMARK 3 B22 (A**2) : -0.62000 REMARK 3 B33 (A**2) : 2.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.477 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.417 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.487 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.821 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.751 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4535 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6435 ; 0.927 ; 2.404 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 364 ; 3.511 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 664 ; 0.046 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2832 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1770 ; 0.175 ; 0.200 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): 186 ; 0.124 ; 0.200 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): 48 ; 0.157 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.136 ; 0.200 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): 1831 ; 0.431 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2939 ; 0.810 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2704 ; 0.894 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3496 ; 1.668 ; 4.500 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 53 REMARK 3 RESIDUE RANGE : B 1 B 53 REMARK 3 RESIDUE RANGE : A 76 A 92 REMARK 3 RESIDUE RANGE : B 76 B 92 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8298 5.3820 17.2572 REMARK 3 T TENSOR REMARK 3 T11: 0.2892 T22: 0.2728 REMARK 3 T33: 0.3185 T12: 0.0010 REMARK 3 T13: 0.0253 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 1.3324 L22: 1.9985 REMARK 3 L33: 1.1348 L12: -0.1824 REMARK 3 L13: -0.6087 L23: -0.7982 REMARK 3 S TENSOR REMARK 3 S11: -0.0561 S12: -0.1089 S13: -0.1360 REMARK 3 S21: -0.1734 S22: -0.0574 S23: 0.0377 REMARK 3 S31: 0.1103 S32: 0.0258 S33: 0.1135 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 53 REMARK 3 RESIDUE RANGE : D 1 D 53 REMARK 3 RESIDUE RANGE : C 76 C 92 REMARK 3 RESIDUE RANGE : D 76 D 92 REMARK 3 ORIGIN FOR THE GROUP (A): 7.7777 27.0397 59.9312 REMARK 3 T TENSOR REMARK 3 T11: 0.2417 T22: 0.2628 REMARK 3 T33: 0.4342 T12: -0.0113 REMARK 3 T13: -0.0045 T23: -0.0355 REMARK 3 L TENSOR REMARK 3 L11: 4.8240 L22: 1.7330 REMARK 3 L33: 0.7836 L12: -0.7030 REMARK 3 L13: 0.5186 L23: 0.0590 REMARK 3 S TENSOR REMARK 3 S11: 0.0714 S12: -0.1070 S13: 0.7545 REMARK 3 S21: -0.0201 S22: -0.0559 S23: -0.2528 REMARK 3 S31: -0.0024 S32: -0.0520 S33: -0.0155 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 54 A 75 REMARK 3 ORIGIN FOR THE GROUP (A): 21.2179 30.5111 28.5245 REMARK 3 T TENSOR REMARK 3 T11: 0.4645 T22: 0.2807 REMARK 3 T33: 0.3498 T12: -0.0386 REMARK 3 T13: -0.0658 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 0.8123 L22: 2.0218 REMARK 3 L33: -3.7609 L12: -3.1444 REMARK 3 L13: -3.1692 L23: 0.6734 REMARK 3 S TENSOR REMARK 3 S11: 0.0759 S12: -0.0218 S13: 0.2115 REMARK 3 S21: 0.4048 S22: 0.1900 S23: -0.3798 REMARK 3 S31: 0.5375 S32: 0.2416 S33: -0.2659 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 54 B 75 REMARK 3 ORIGIN FOR THE GROUP (A): -5.4766 32.1591 11.2270 REMARK 3 T TENSOR REMARK 3 T11: 0.3408 T22: 0.3342 REMARK 3 T33: 0.2477 T12: -0.0075 REMARK 3 T13: -0.0218 T23: -0.0361 REMARK 3 L TENSOR REMARK 3 L11: 4.3538 L22: -0.0045 REMARK 3 L33: 3.8106 L12: 1.3031 REMARK 3 L13: -2.0520 L23: 0.9620 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: 0.1810 S13: -0.0600 REMARK 3 S21: -0.3051 S22: 0.0258 S23: 0.0592 REMARK 3 S31: -0.1621 S32: -0.2890 S33: -0.0288 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 : C 54 C 75 REMARK 3 ORIGIN FOR THE GROUP (A): 20.7561 0.7458 52.0494 REMARK 3 T TENSOR REMARK 3 T11: 0.4473 T22: 0.2415 REMARK 3 T33: 0.2749 T12: 0.0507 REMARK 3 T13: -0.0007 T23: 0.0519 REMARK 3 L TENSOR REMARK 3 L11: 5.7687 L22: -3.5416 REMARK 3 L33: 0.4349 L12: -0.1685 REMARK 3 L13: 2.9875 L23: -2.0305 REMARK 3 S TENSOR REMARK 3 S11: 0.0157 S12: 0.2033 S13: 0.3075 REMARK 3 S21: -0.1793 S22: -0.0125 S23: 0.4080 REMARK 3 S31: 0.1706 S32: 0.7276 S33: -0.0032 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 : D 54 D 75 REMARK 3 ORIGIN FOR THE GROUP (A): -5.7610 2.0301 69.3889 REMARK 3 T TENSOR REMARK 3 T11: 0.3211 T22: 0.2886 REMARK 3 T33: 0.3101 T12: 0.0399 REMARK 3 T13: 0.0323 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 2.4041 L22: 4.7171 REMARK 3 L33: 4.9840 L12: 1.8847 REMARK 3 L13: 4.1565 L23: -0.8202 REMARK 3 S TENSOR REMARK 3 S11: 0.2123 S12: -0.0649 S13: 0.2357 REMARK 3 S21: -0.0776 S22: 0.0550 S23: 0.1214 REMARK 3 S31: 0.4746 S32: 0.1753 S33: -0.2673 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 2 E 5 REMARK 3 RESIDUE RANGE : F 16 F 18 REMARK 3 ORIGIN FOR THE GROUP (A): 12.4969 24.8779 38.4396 REMARK 3 T TENSOR REMARK 3 T11: 0.4957 T22: 0.1403 REMARK 3 T33: 0.4133 T12: -0.0195 REMARK 3 T13: -0.0379 T23: 0.2246 REMARK 3 L TENSOR REMARK 3 L11: 1.3820 L22: -0.7263 REMARK 3 L33: 8.7836 L12: 0.4081 REMARK 3 L13: -3.5390 L23: 0.8352 REMARK 3 S TENSOR REMARK 3 S11: 0.6462 S12: -0.7433 S13: 0.3504 REMARK 3 S21: -0.0064 S22: -0.5371 S23: 0.1724 REMARK 3 S31: -0.1249 S32: 0.4080 S33: -0.1091 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 6 E 15 REMARK 3 RESIDUE RANGE : F 6 F 15 REMARK 3 ORIGIN FOR THE GROUP (A): 7.7542 33.0003 20.1204 REMARK 3 T TENSOR REMARK 3 T11: 0.4024 T22: 0.3776 REMARK 3 T33: 0.2937 T12: 0.0566 REMARK 3 T13: -0.0494 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.3373 L22: -2.1982 REMARK 3 L33: 2.4037 L12: 1.3161 REMARK 3 L13: 1.6508 L23: -0.5400 REMARK 3 S TENSOR REMARK 3 S11: 0.1449 S12: 0.0625 S13: -0.1077 REMARK 3 S21: 0.0923 S22: -0.0614 S23: -0.1468 REMARK 3 S31: -0.0744 S32: -0.0801 S33: -0.0835 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 16 E 18 REMARK 3 RESIDUE RANGE : F 2 F 5 REMARK 3 ORIGIN FOR THE GROUP (A): 2.5288 29.0493 -0.6332 REMARK 3 T TENSOR REMARK 3 T11: 0.4112 T22: 0.5318 REMARK 3 T33: 0.2695 T12: 0.0390 REMARK 3 T13: -0.0349 T23: -0.0199 REMARK 3 L TENSOR REMARK 3 L11: -4.1065 L22: 10.7907 REMARK 3 L33: 4.8841 L12: -10.9281 REMARK 3 L13: -4.1435 L23: 3.6279 REMARK 3 S TENSOR REMARK 3 S11: 0.5468 S12: 0.7105 S13: -0.3362 REMARK 3 S21: -0.1443 S22: -0.2493 S23: -0.6014 REMARK 3 S31: -0.1406 S32: -0.2549 S33: -0.2975 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : I 2 I 5 REMARK 3 RESIDUE RANGE : H 16 H 18 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0689 4.6570 40.6155 REMARK 3 T TENSOR REMARK 3 T11: 0.3858 T22: 0.4154 REMARK 3 T33: 0.1937 T12: -0.0073 REMARK 3 T13: 0.0540 T23: -0.0570 REMARK 3 L TENSOR REMARK 3 L11: 11.3236 L22: 8.9380 REMARK 3 L33: -0.7317 L12: -10.8578 REMARK 3 L13: 6.2540 L23: -6.0160 REMARK 3 S TENSOR REMARK 3 S11: 0.1819 S12: 0.7231 S13: -0.1545 REMARK 3 S21: -0.1361 S22: -0.1297 S23: 0.6000 REMARK 3 S31: 0.2820 S32: 0.4575 S33: -0.0521 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : I 6 I 15 REMARK 3 RESIDUE RANGE : H 6 H 15 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8106 -0.3182 61.0571 REMARK 3 T TENSOR REMARK 3 T11: 0.3993 T22: 0.3448 REMARK 3 T33: 0.3118 T12: 0.0130 REMARK 3 T13: 0.0543 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: -0.2713 L22: -2.1532 REMARK 3 L33: 3.0841 L12: -0.1199 REMARK 3 L13: -1.0482 L23: -0.2888 REMARK 3 S TENSOR REMARK 3 S11: 0.2961 S12: -0.0450 S13: 0.0785 REMARK 3 S21: 0.1146 S22: 0.0203 S23: 0.0326 REMARK 3 S31: -0.1105 S32: -0.0222 S33: -0.3164 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : I 16 I 18 REMARK 3 RESIDUE RANGE : H 2 H 5 REMARK 3 ORIGIN FOR THE GROUP (A): 1.1297 8.7167 79.4664 REMARK 3 T TENSOR REMARK 3 T11: 0.3759 T22: 0.4754 REMARK 3 T33: 0.3449 T12: -0.0501 REMARK 3 T13: 0.0693 T23: 0.1557 REMARK 3 L TENSOR REMARK 3 L11: 4.9999 L22: 9.7298 REMARK 3 L33: -4.8230 L12: 5.6818 REMARK 3 L13: 3.4039 L23: 11.5854 REMARK 3 S TENSOR REMARK 3 S11: -0.4904 S12: 0.5455 S13: -0.0204 REMARK 3 S21: -0.1451 S22: 0.3518 S23: -0.0662 REMARK 3 S31: 0.3260 S32: -0.2265 S33: 0.1385 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DATA IS ANISOTROPIC WITH LIMITS REMARK 3 2.5 X 2.5 X 2.8. DATA WERE TRUNCATED REMARK 3 TO AN ELLIPSOID AND REFLECTIONS REMARK 3 WITH AN AVERAGE (I/SIGI) RATIO LESS THAN REMARK 3 2 WERE REMOVED. THE COMPLETENESS REMARK 3 ABOVE IS UNDERESTIMATED. WHEN THE REMARK 3 TRUNCATION IS FACTORED IN, DATA REMARK 3 IN REFINEMENT ARE 91% COMPLETE. REMARK 4 REMARK 4 1P51 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000019015. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : GE 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23324 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.10700 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) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 46.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.35900 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: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1P71 WITH NONIDENTICAL SIDECHAINS PRUNED REMARK 200 BACK TO A COMMON ATOM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000 MONOMETHYL ETHER, GLYCEROL, REMARK 280 TRIS, JEFFAMINE, POTASSIUM CHLORIDE, CALCIUM CHLORIDE, SODIUM REMARK 280 AZIDE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 53.91800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE FUNCTIONAL COMPLEX IS A PROTEIN HOMODIMER REMARK 300 BOUND TO A DNA DUPLEX. THE ASSYMETRIC UNIT REMARK 300 CONTAINS TWO COPIES OF THE FUNCTIONAL REMARK 300 COMPLEX. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, H, C, D 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 LYS A 93 REMARK 465 ALA A 94 REMARK 465 LYS B 93 REMARK 465 ALA B 94 REMARK 465 LYS C 93 REMARK 465 ALA C 94 REMARK 465 LYS D 93 REMARK 465 ALA D 94 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 PRO D 92 O 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 DC E 3 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA E 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG E 17 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC E 18 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA E 19 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA F 4 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DT F 7 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA F 10 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG F 17 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG I 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT I 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT I 12 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG I 17 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC I 18 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT I 20 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA H 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG H 17 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC H 18 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT H 20 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 ASP A 40 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 40 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP C 40 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP D 40 CB - CG - OD2 ANGL. DEV. = 5.6 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 PHE A 47 -75.65 -70.14 REMARK 500 ASN A 66 -6.06 67.34 REMARK 500 PHE B 47 -72.30 -75.63 REMARK 500 ASN B 66 -3.15 65.74 REMARK 500 PHE C 47 -77.65 -68.80 REMARK 500 ASN C 66 -2.52 71.06 REMARK 500 PHE D 47 -81.92 -73.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B8Z RELATED DB: PDB REMARK 900 THERMOTOGA MARITIMA HU PROTEIN ALONE REMARK 900 RELATED ID: 1IHF RELATED DB: PDB REMARK 900 E. COLI IHF BOUND TO DNA REMARK 900 RELATED ID: 1P71 RELATED DB: PDB REMARK 900 ANABAENA HU BOUND TO TR3 DNA REMARK 900 RELATED ID: 1P78 RELATED DB: PDB REMARK 900 ANABAENA HU BOUND TO AHU2 DNA DBREF 1P51 A 1 94 UNP P05514 DBH_ANASP 1 94 DBREF 1P51 B 1 94 UNP P05514 DBH_ANASP 1 94 DBREF 1P51 C 1 94 UNP P05514 DBH_ANASP 1 94 DBREF 1P51 D 1 94 UNP P05514 DBH_ANASP 1 94 DBREF 1P51 E 2 20 PDB 1P51 1P51 2 20 DBREF 1P51 F 2 20 PDB 1P51 1P51 2 20 DBREF 1P51 I 2 20 PDB 1P51 1P51 2 20 DBREF 1P51 H 2 20 PDB 1P51 1P51 2 20 SEQRES 1 E 19 DG DC DA DT DA DT DC DA DA DT DT DT DG SEQRES 2 E 19 DT DT DG DC DA DT SEQRES 1 F 19 DG DC DA DT DA DT DC DA DA DT DT DT DG SEQRES 2 F 19 DT DT DG DC DA DT SEQRES 1 I 19 DG DC DA DT DA DT DC DA DA DT DT DT DG SEQRES 2 I 19 DT DT DG DC DA DT SEQRES 1 H 19 DG DC DA DT DA DT DC DA DA DT DT DT DG SEQRES 2 H 19 DT DT DG DC DA DT SEQRES 1 A 94 MET ASN LYS GLY GLU LEU VAL ASP ALA VAL ALA GLU LYS SEQRES 2 A 94 ALA SER VAL THR LYS LYS GLN ALA ASP ALA VAL LEU THR SEQRES 3 A 94 ALA ALA LEU GLU THR ILE ILE GLU ALA VAL SER SER GLY SEQRES 4 A 94 ASP LYS VAL THR LEU VAL GLY PHE GLY SER PHE GLU SER SEQRES 5 A 94 ARG GLU ARG LYS ALA ARG GLU GLY ARG ASN PRO LYS THR SEQRES 6 A 94 ASN GLU LYS MET GLU ILE PRO ALA THR ARG VAL PRO ALA SEQRES 7 A 94 PHE SER ALA GLY LYS LEU PHE ARG GLU LYS VAL ALA PRO SEQRES 8 A 94 PRO LYS ALA SEQRES 1 B 94 MET ASN LYS GLY GLU LEU VAL ASP ALA VAL ALA GLU LYS SEQRES 2 B 94 ALA SER VAL THR LYS LYS GLN ALA ASP ALA VAL LEU THR SEQRES 3 B 94 ALA ALA LEU GLU THR ILE ILE GLU ALA VAL SER SER GLY SEQRES 4 B 94 ASP LYS VAL THR LEU VAL GLY PHE GLY SER PHE GLU SER SEQRES 5 B 94 ARG GLU ARG LYS ALA ARG GLU GLY ARG ASN PRO LYS THR SEQRES 6 B 94 ASN GLU LYS MET GLU ILE PRO ALA THR ARG VAL PRO ALA SEQRES 7 B 94 PHE SER ALA GLY LYS LEU PHE ARG GLU LYS VAL ALA PRO SEQRES 8 B 94 PRO LYS ALA SEQRES 1 C 94 MET ASN LYS GLY GLU LEU VAL ASP ALA VAL ALA GLU LYS SEQRES 2 C 94 ALA SER VAL THR LYS LYS GLN ALA ASP ALA VAL LEU THR SEQRES 3 C 94 ALA ALA LEU GLU THR ILE ILE GLU ALA VAL SER SER GLY SEQRES 4 C 94 ASP LYS VAL THR LEU VAL GLY PHE GLY SER PHE GLU SER SEQRES 5 C 94 ARG GLU ARG LYS ALA ARG GLU GLY ARG ASN PRO LYS THR SEQRES 6 C 94 ASN GLU LYS MET GLU ILE PRO ALA THR ARG VAL PRO ALA SEQRES 7 C 94 PHE SER ALA GLY LYS LEU PHE ARG GLU LYS VAL ALA PRO SEQRES 8 C 94 PRO LYS ALA SEQRES 1 D 94 MET ASN LYS GLY GLU LEU VAL ASP ALA VAL ALA GLU LYS SEQRES 2 D 94 ALA SER VAL THR LYS LYS GLN ALA ASP ALA VAL LEU THR SEQRES 3 D 94 ALA ALA LEU GLU THR ILE ILE GLU ALA VAL SER SER GLY SEQRES 4 D 94 ASP LYS VAL THR LEU VAL GLY PHE GLY SER PHE GLU SER SEQRES 5 D 94 ARG GLU ARG LYS ALA ARG GLU GLY ARG ASN PRO LYS THR SEQRES 6 D 94 ASN GLU LYS MET GLU ILE PRO ALA THR ARG VAL PRO ALA SEQRES 7 D 94 PHE SER ALA GLY LYS LEU PHE ARG GLU LYS VAL ALA PRO SEQRES 8 D 94 PRO LYS ALA FORMUL 9 HOH *72(H2 O) HELIX 1 1 ASN A 2 ALA A 14 1 13 HELIX 2 2 THR A 17 SER A 38 1 22 HELIX 3 3 GLY A 82 ALA A 90 1 9 HELIX 4 4 ASN B 2 ALA B 14 1 13 HELIX 5 5 THR B 17 SER B 38 1 22 HELIX 6 6 GLY B 82 ALA B 90 1 9 HELIX 7 7 ASN C 2 ALA C 14 1 13 HELIX 8 8 THR C 17 SER C 38 1 22 HELIX 9 9 GLY C 82 ALA C 90 1 9 HELIX 10 10 ASN D 2 ALA D 14 1 13 HELIX 11 11 THR D 17 SER D 38 1 22 HELIX 12 12 GLY D 82 ALA D 90 1 9 SHEET 1 A 3 VAL A 42 LEU A 44 0 SHEET 2 A 3 GLY A 48 ARG A 55 -1 O GLY A 48 N LEU A 44 SHEET 3 A 3 THR A 74 ALA A 81 -1 O THR A 74 N ARG A 55 SHEET 1 B 2 ARG A 58 ARG A 61 0 SHEET 2 B 2 LYS A 68 ILE A 71 -1 O MET A 69 N GLY A 60 SHEET 1 C 3 VAL B 42 LEU B 44 0 SHEET 2 C 3 GLY B 48 ARG B 55 -1 O PHE B 50 N VAL B 42 SHEET 3 C 3 THR B 74 ALA B 81 -1 O VAL B 76 N ARG B 53 SHEET 1 D 2 ARG B 58 ARG B 61 0 SHEET 2 D 2 LYS B 68 ILE B 71 -1 O MET B 69 N GLY B 60 SHEET 1 E 3 VAL C 42 LEU C 44 0 SHEET 2 E 3 GLY C 48 ARG C 55 -1 O GLY C 48 N LEU C 44 SHEET 3 E 3 THR C 74 ALA C 81 -1 O THR C 74 N ARG C 55 SHEET 1 F 2 ARG C 58 ARG C 61 0 SHEET 2 F 2 LYS C 68 ILE C 71 -1 O MET C 69 N GLY C 60 SHEET 1 G 3 VAL D 42 LEU D 44 0 SHEET 2 G 3 GLY D 48 ARG D 55 -1 O PHE D 50 N VAL D 42 SHEET 3 G 3 THR D 74 ALA D 81 -1 O THR D 74 N ARG D 55 SHEET 1 H 2 ARG D 58 ARG D 61 0 SHEET 2 H 2 LYS D 68 ILE D 71 -1 O MET D 69 N GLY D 60 CRYST1 37.646 107.836 83.464 90.00 92.25 90.00 P 1 21 1 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 0.026563 0.000000 0.001044 0.00000 SCALE2 0.000000 0.009273 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011990 0.00000