HEADER HYDROLASE/DNA/RNA 05-JUN-18 6DMV TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 IN COMPLEX TITLE 2 WITH AN RNA/DNA HYBRID: SOAKED FOR 40 S IN 2 MM MG2+ AND 200 MM K+ AT TITLE 3 21 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE H; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*AP*CP*AP*U)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'-R(P*CP*G)-3'); COMPND 13 CHAIN: b; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 17 CHAIN: C; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 5 GENE: RNHA, BH0863; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 14 ORGANISM_TAXID: 86665; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 18 ORGANISM_TAXID: 86665; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 22 ORGANISM_TAXID: 86665 KEYWDS PROTEIN-RNA-DNA COMPLEX, DOUBLE HELIX, RNA HYDROLYSIS, IN CRYSTALLO KEYWDS 2 CATALYSIS, METAL DEPENDENT CATALYSIS, MONOVALENT CATIONS, DIVALENT KEYWDS 3 CATIONS, HYDROLASE, HYDROLASE-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 4 11-OCT-23 6DMV 1 REMARK REVDAT 3 27-APR-22 6DMV 1 SPRSDE LINK REVDAT 2 18-DEC-19 6DMV 1 REMARK LINK REVDAT 1 15-AUG-18 6DMV 0 JRNL AUTH N.L.SAMARA,W.YANG JRNL TITL CATION TRAFFICKING PROPELS RNA HYDROLYSIS. JRNL REF NAT. STRUCT. MOL. BIOL. V. 25 715 2018 JRNL REFN ESSN 1545-9985 JRNL PMID 30076410 JRNL DOI 10.1038/S41594-018-0099-4 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 28094 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1409 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 19.8828 - 3.2708 0.98 2777 161 0.1283 0.1535 REMARK 3 2 3.2708 - 2.5979 0.99 2744 161 0.1597 0.1674 REMARK 3 3 2.5979 - 2.2701 1.00 2777 117 0.1610 0.1582 REMARK 3 4 2.2701 - 2.0627 1.00 2750 153 0.1574 0.2041 REMARK 3 5 2.0627 - 1.9150 1.00 2778 136 0.1716 0.1978 REMARK 3 6 1.9150 - 1.8022 0.99 2732 129 0.2116 0.2261 REMARK 3 7 1.8022 - 1.7120 0.99 2723 150 0.2106 0.2378 REMARK 3 8 1.7120 - 1.6375 0.99 2718 152 0.2320 0.2375 REMARK 3 9 1.6375 - 1.5745 1.00 2730 147 0.2585 0.3132 REMARK 3 10 1.5745 - 1.5202 0.71 1956 103 0.2891 0.3302 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) : 22.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1453 REMARK 3 ANGLE : 1.025 2011 REMARK 3 CHIRALITY : 0.056 219 REMARK 3 PLANARITY : 0.006 210 REMARK 3 DIHEDRAL : 18.873 828 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 61:66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.480 -3.769 19.182 REMARK 3 T TENSOR REMARK 3 T11: 0.2382 T22: 0.4743 REMARK 3 T33: 0.3518 T12: 0.1009 REMARK 3 T13: 0.0450 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 8.6765 L22: 5.1840 REMARK 3 L33: 6.9840 L12: -3.8408 REMARK 3 L13: -3.2361 L23: -2.5699 REMARK 3 S TENSOR REMARK 3 S11: 0.3969 S12: 0.9158 S13: 0.0151 REMARK 3 S21: -0.5694 S22: -0.8440 S23: -0.8431 REMARK 3 S31: -0.1506 S32: 1.6273 S33: 0.4853 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 67:87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.967 -6.383 16.685 REMARK 3 T TENSOR REMARK 3 T11: 0.2098 T22: 0.2020 REMARK 3 T33: 0.2144 T12: 0.0037 REMARK 3 T13: -0.0129 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 5.9173 L22: 2.2465 REMARK 3 L33: 4.0118 L12: -2.0949 REMARK 3 L13: 4.9844 L23: -1.8380 REMARK 3 S TENSOR REMARK 3 S11: 0.4201 S12: 0.2962 S13: -0.4113 REMARK 3 S21: -0.2046 S22: -0.2418 S23: 0.1273 REMARK 3 S31: 0.4420 S32: 0.0968 S33: -0.2866 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 88:96 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.184 -11.521 23.886 REMARK 3 T TENSOR REMARK 3 T11: 0.2373 T22: 0.1941 REMARK 3 T33: 0.3328 T12: 0.0650 REMARK 3 T13: 0.0069 T23: 0.0492 REMARK 3 L TENSOR REMARK 3 L11: 4.9960 L22: 7.9322 REMARK 3 L33: 8.4788 L12: -3.1847 REMARK 3 L13: -5.3110 L23: 0.2891 REMARK 3 S TENSOR REMARK 3 S11: -0.3614 S12: -0.5066 S13: -1.3972 REMARK 3 S21: 0.0254 S22: 0.0689 S23: -0.4540 REMARK 3 S31: 0.8161 S32: 0.4330 S33: 0.1884 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 97:141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.338 0.777 21.995 REMARK 3 T TENSOR REMARK 3 T11: 0.1183 T22: 0.0896 REMARK 3 T33: 0.1495 T12: 0.0155 REMARK 3 T13: 0.0202 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 4.0706 L22: 1.2133 REMARK 3 L33: 4.3564 L12: -0.3746 REMARK 3 L13: 2.1984 L23: 0.4544 REMARK 3 S TENSOR REMARK 3 S11: 0.0674 S12: -0.1557 S13: -0.0177 REMARK 3 S21: -0.0984 S22: -0.0621 S23: 0.0136 REMARK 3 S31: -0.0667 S32: -0.2453 S33: 0.0020 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 142:155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.475 7.754 16.544 REMARK 3 T TENSOR REMARK 3 T11: 0.3791 T22: 0.5135 REMARK 3 T33: 0.3168 T12: 0.3136 REMARK 3 T13: -0.0673 T23: -0.1365 REMARK 3 L TENSOR REMARK 3 L11: 2.9727 L22: 1.6372 REMARK 3 L33: 1.9737 L12: 0.6220 REMARK 3 L13: 2.0989 L23: -0.3137 REMARK 3 S TENSOR REMARK 3 S11: 0.4032 S12: 0.0982 S13: 0.4764 REMARK 3 S21: -0.2885 S22: -0.4532 S23: 0.4412 REMARK 3 S31: -0.8333 S32: -0.7563 S33: 0.1596 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 156:186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.112 4.575 22.712 REMARK 3 T TENSOR REMARK 3 T11: 0.1627 T22: 0.0774 REMARK 3 T33: 0.1311 T12: 0.0276 REMARK 3 T13: 0.0114 T23: 0.0392 REMARK 3 L TENSOR REMARK 3 L11: 3.7033 L22: 2.4432 REMARK 3 L33: 4.3935 L12: -0.7070 REMARK 3 L13: 0.5891 L23: 1.3167 REMARK 3 S TENSOR REMARK 3 S11: 0.0724 S12: -0.0680 S13: 0.2319 REMARK 3 S21: -0.1021 S22: -0.1055 S23: -0.0716 REMARK 3 S31: -0.1956 S32: -0.0827 S33: 0.0123 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 187:195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.817 -9.678 12.414 REMARK 3 T TENSOR REMARK 3 T11: 0.4718 T22: 0.3565 REMARK 3 T33: 0.2261 T12: 0.0266 REMARK 3 T13: -0.0071 T23: -0.0913 REMARK 3 L TENSOR REMARK 3 L11: 3.4253 L22: 9.3284 REMARK 3 L33: 7.4022 L12: 0.6158 REMARK 3 L13: -5.0232 L23: -0.2729 REMARK 3 S TENSOR REMARK 3 S11: -0.3704 S12: 1.1214 S13: -0.9397 REMARK 3 S21: -0.7577 S22: 0.1006 S23: 0.1082 REMARK 3 S31: 1.3481 S32: -0.3900 S33: 0.2122 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN B AND RESID 1:4 ) OR ( CHAIN B AND RESID 5:6 REMARK 3 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.778 1.336 4.510 REMARK 3 T TENSOR REMARK 3 T11: 0.3086 T22: 0.2306 REMARK 3 T33: 0.1395 T12: 0.0689 REMARK 3 T13: 0.0281 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 7.0216 L22: 8.5855 REMARK 3 L33: 3.1432 L12: 0.6640 REMARK 3 L13: 2.1835 L23: -0.2623 REMARK 3 S TENSOR REMARK 3 S11: -0.0528 S12: 0.4469 S13: -0.0477 REMARK 3 S21: -0.7342 S22: -0.1586 S23: -0.3064 REMARK 3 S31: 0.1138 S32: 0.2464 S33: 0.1953 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.370 3.684 3.145 REMARK 3 T TENSOR REMARK 3 T11: 0.4125 T22: 0.2147 REMARK 3 T33: 0.1722 T12: 0.1038 REMARK 3 T13: -0.0424 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 2.8945 L22: 2.4914 REMARK 3 L33: 6.0427 L12: -1.9987 REMARK 3 L13: -3.2747 L23: 0.5956 REMARK 3 S TENSOR REMARK 3 S11: 0.0362 S12: 0.3327 S13: -0.1078 REMARK 3 S21: -0.8402 S22: -0.4376 S23: 0.3069 REMARK 3 S31: -0.4510 S32: -0.3861 S33: 0.3938 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 6DMV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-BM-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28103 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 19.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: 6DMN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG3350, 20% GLYCEROL, 200 MM KI, REMARK 280 AND 25 MM CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 40.71100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.90150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.71100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.90150 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, b, C 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 GLY A 55 REMARK 465 SER A 56 REMARK 465 HIS A 57 REMARK 465 MET A 58 REMARK 465 ALA A 59 REMARK 465 LYS A 60 REMARK 465 LYS A 196 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 A B 1 O2' REMARK 470 G b 6 O2' 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 C 2 O3' DG C 2 C3' -0.037 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 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.5 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 LYS A 146 59.32 -91.82 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 444 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A 445 DISTANCE = 6.38 ANGSTROMS 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 96.9 REMARK 620 3 HOH A 312 O 170.0 74.0 REMARK 620 4 HOH A 333 O 88.8 94.6 87.8 REMARK 620 5 HOH A 356 O 94.4 93.2 90.4 171.2 REMARK 620 6 C b 5 OP1 103.4 159.6 85.9 87.9 83.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 104.6 REMARK 620 3 ASP A 132 OD1 140.0 93.0 REMARK 620 4 ASP A 132 OD2 114.8 138.6 48.3 REMARK 620 5 U B 4 O3' 135.4 79.3 82.6 81.3 REMARK 620 6 C b 5 OP1 82.8 107.5 125.9 89.9 54.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 203 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 192 OD1 REMARK 620 2 ARG A 195 O 147.7 REMARK 620 3 HOH A 310 O 63.9 83.9 REMARK 620 4 HOH A 312 O 51.4 116.4 61.3 REMARK 620 5 HOH A 333 O 54.8 152.8 113.1 60.8 REMARK 620 6 G b 6 OP2 106.4 98.2 134.7 78.1 54.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 109 O REMARK 620 2 DT C 4 O4 160.9 REMARK 620 3 DG C 5 O6 90.1 77.5 REMARK 620 4 HOH C 206 O 105.3 88.0 84.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6DMN RELATED DB: PDB DBREF 6DMV A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DMV B 1 4 PDB 6DMV 6DMV 1 4 DBREF 6DMV b 5 6 PDB 6DMV 6DMV 5 6 DBREF 6DMV C 1 6 PDB 6DMV 6DMV 1 6 SEQADV 6DMV GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DMV SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DMV HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DMV MET A 58 UNP Q9KEI9 EXPRESSION TAG SEQRES 1 A 142 GLY SER HIS MET ALA LYS GLU GLU ILE ILE TRP GLU SER SEQRES 2 A 142 LEU SER VAL ASP VAL GLY SER GLN GLY ASN PRO GLY ILE SEQRES 3 A 142 VAL GLU TYR LYS GLY VAL ASP THR LYS THR GLY GLU VAL SEQRES 4 A 142 LEU PHE GLU ARG GLU PRO ILE PRO ILE GLY THR ASN ASN SEQRES 5 A 142 MET GLY GLU PHE LEU ALA ILE VAL HIS GLY LEU ARG TYR SEQRES 6 A 142 LEU LYS GLU ARG ASN SER ARG LYS PRO ILE TYR SER ASP SEQRES 7 A 142 SER GLN THR ALA ILE LYS TRP VAL LYS ASP LYS LYS ALA SEQRES 8 A 142 LYS SER THR LEU VAL ARG ASN GLU GLU THR ALA LEU ILE SEQRES 9 A 142 TRP LYS LEU VAL ASP GLU ALA GLU GLU TRP LEU ASN THR SEQRES 10 A 142 HIS THR TYR GLU THR PRO ILE LEU LYS TRP GLN THR ASP SEQRES 11 A 142 LYS TRP GLY GLU ILE LYS ALA ASP TYR GLY ARG LYS SEQRES 1 B 4 A C A U SEQRES 1 b 2 C G SEQRES 1 C 6 DC DG DA DT DG DT HET MG A 201 1 HET MG A 202 1 HET K A 203 1 HET IOD A 204 1 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HET GOL A 208 6 HET GOL A 209 6 HET EDO A 210 4 HET EDO A 211 4 HET GOL A 212 6 HET GOL A 213 6 HET K C 101 1 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K 2(K 1+) FORMUL 8 IOD 4(I 1-) FORMUL 12 GOL 4(C3 H8 O3) FORMUL 14 EDO 2(C2 H6 O2) FORMUL 19 HOH *175(H2 O) HELIX 1 AA1 THR A 104 ARG A 123 1 20 HELIX 2 AA2 SER A 133 LYS A 143 1 11 HELIX 3 AA3 THR A 155 ASN A 170 1 16 HELIX 4 AA4 GLN A 182 GLY A 187 1 6 SHEET 1 AA1 5 VAL A 93 GLY A 103 0 SHEET 2 AA1 5 GLY A 79 ASP A 87 -1 N VAL A 81 O ILE A 100 SHEET 3 AA1 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 AA1 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA1 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 LINK O3' U B 4 P C b 5 1555 1555 1.60 LINK OD2 ASP A 71 MG MG A 201 1555 1555 1.96 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.11 LINK OE1 GLU A 109 MG MG A 202 1555 1555 2.45 LINK OD1 ASP A 132 MG MG A 202 1555 1555 2.35 LINK OD2 ASP A 132 MG MG A 202 1555 1555 2.87 LINK OD1 ASP A 192 MG MG A 201 1555 1555 2.06 LINK OD1 ASP A 192 K K A 203 1555 1555 3.26 LINK O ARG A 195 K K A 203 1555 1555 2.87 LINK MG MG A 201 O HOH A 312 1555 1555 2.26 LINK MG MG A 201 O HOH A 333 1555 1555 1.94 LINK MG MG A 201 O HOH A 356 1555 1555 2.08 LINK MG MG A 201 OP1 C b 5 1555 1555 2.16 LINK MG MG A 202 O3' U B 4 1555 1555 2.81 LINK MG MG A 202 OP1 C b 5 1555 1555 2.56 LINK K K A 203 O HOH A 310 1555 1555 2.94 LINK K K A 203 O HOH A 312 1555 1555 2.56 LINK K K A 203 O HOH A 333 1555 1555 3.13 LINK K K A 203 OP2 G b 6 1555 1555 2.84 LINK O HOH B 109 K A K C 101 1555 1555 3.00 LINK O4 DT C 4 K A K C 101 1555 1555 3.16 LINK O6 DG C 5 K A K C 101 1555 1555 2.61 LINK K A K C 101 O HOH C 206 1555 1555 3.14 CISPEP 1 ASN A 77 PRO A 78 0 0.69 SITE 1 AC1 6 ASP A 71 ASP A 192 HOH A 312 HOH A 333 SITE 2 AC1 6 HOH A 356 C b 5 SITE 1 AC2 5 ASP A 71 GLU A 109 ASP A 132 U B 4 SITE 2 AC2 5 C b 5 SITE 1 AC3 6 ASP A 192 GLY A 194 ARG A 195 HOH A 310 SITE 2 AC3 6 HOH A 312 G b 6 SITE 1 AC4 1 TYR A 83 SITE 1 AC5 3 ILE A 64 HOH A 412 HOH A 445 SITE 1 AC6 1 HOH A 434 SITE 1 AC7 6 GLY A 76 ASN A 77 PRO A 78 HOH A 316 SITE 2 AC7 6 DG C 2 DA C 3 SITE 1 AC8 6 HIS A 115 ARG A 118 ASN A 170 GOL A 213 SITE 2 AC8 6 HOH A 398 HOH A 417 SITE 1 AC9 6 LYS A 143 THR A 173 TYR A 174 HOH A 301 SITE 2 AC9 6 HOH A 303 HOH A 400 SITE 1 AD1 3 LYS A 89 GLU A 153 HOH A 360 SITE 1 AD2 5 THR A 148 HOH A 309 HOH A 348 DT C 4 SITE 2 AD2 5 DG C 5 SITE 1 AD3 8 HIS A 115 ARG A 118 ARG A 123 GLU A 167 SITE 2 AD3 8 ASN A 170 GOL A 209 HOH A 302 HOH A 366 SITE 1 AD4 4 HOH B 109 DT C 4 DG C 5 HOH C 208 CRYST1 81.422 37.803 61.986 90.00 96.31 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 0.012282 0.000000 0.001359 0.00000 SCALE2 0.000000 0.026453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016231 0.00000