HEADER HYDROLASE/RNA/DNA 06-OCT-25 9YK5 TITLE 100K X-RAY STRUCTURE OF MIXED METAL D132N BACILLUS HALODURANS RNASE H1 TITLE 2 COMPLEX WITH RNA/DNA DUPLEX 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(*UP*CP*GP*AP*CP*A)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*AP*TP*GP*TP*CP*G)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALALKALIBACTERIUM HALODURANS; SOURCE 3 ORGANISM_TAXID: 86665; SOURCE 4 GENE: RNHA, BH0863; 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: HALALKALIBACTERIUM HALODURANS; SOURCE 10 ORGANISM_TAXID: 86665; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HALALKALIBACTERIUM HALODURANS; SOURCE 14 ORGANISM_TAXID: 86665 KEYWDS RNA HYDROLASE, NUCLEIC ACID BINDING, RNA/DNA HYBRID, MIXED METAL KEYWDS 2 COMPLEX, HYDROLASE, HYDROLASE-RNA-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.KOVALEVSKY,O.GERLITS REVDAT 1 18-MAR-26 9YK5 0 JRNL AUTH O.GERLITS,A.COLLINS,A.KOVALEVSKY JRNL TITL STRUCTURAL INSIGHTS INTO RNASE H CATALYTIC MECHANISM FROM JRNL TITL 2 ROOM-TEMPERATURE X-RAY AND NEUTRON CRYSTALLOGRAPHY OF APO- JRNL TITL 3 AND RNA/DNA HYBRID-BOUND ENZYME JRNL REF CURR RES STRUCT BIOL V. 11 00188 2026 JRNL REFN ESSN 2665-928X JRNL DOI 10.1016/J.CRSTBI.2026.100188 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.D.ADAMS,M.MUSTYAKIMOV,P.V.AFONINE,P.LANGAN REMARK 1 TITL GENERALIZED X-RAY AND NEUTRON CRYSTALLOGRAPHIC ANALYSIS: REMARK 1 TITL 2 MORE ACCURATE AND COMPLETE STRUCTURES FOR BIOLOGICAL REMARK 1 TITL 3 MACROMOLECULES REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH O.GERLITS,A.COLLINS,A.KOVALEVSKY REMARK 1 TITL STRUCTURAL INSIGHTS INTO RNASE H CATALYTIC MECHANISM FROM REMARK 1 TITL 2 ROOM-TEMPERATURE X-RAY AND NEUTRON CRYSTALLOGRAPHY OF APO- REMARK 1 TITL 3 AND RNA/DNA HYBRID-BOUND ENZYME REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12893 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.255 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 649 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 26.2000 - 3.4200 0.98 2502 111 0.2102 0.2205 REMARK 3 2 3.4200 - 2.7100 1.00 2449 141 0.2390 0.2396 REMARK 3 3 2.7100 - 2.3700 1.00 2443 125 0.2664 0.3075 REMARK 3 4 2.3700 - 2.1600 1.00 2428 125 0.2715 0.2810 REMARK 3 5 2.1500 - 2.0000 0.99 2422 147 0.3247 0.3745 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.240 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 : 0.006 1396 REMARK 3 ANGLE : 0.820 1946 REMARK 3 CHIRALITY : 0.038 219 REMARK 3 PLANARITY : 0.005 203 REMARK 3 DIHEDRAL : 16.140 271 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 9YK5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000300712. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12959 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 61.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.68600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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 (%): 48.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 0.2 M NACL, AND 12 REMARK 280 -16% PEG 10,000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 41.30950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.60850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.30950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.60850 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: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SER A 58 REMARK 465 ALA A 59 REMARK 465 LYS A 60 REMARK 465 ARG A 195 REMARK 465 LYS A 196 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 A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 95.0 REMARK 620 3 HOH A 303 O 95.8 89.2 REMARK 620 4 HOH A 310 O 93.0 91.8 171.0 REMARK 620 5 A B 6 OP1 98.1 165.8 95.0 82.0 REMARK 620 6 HOH B 105 O 173.0 87.7 77.7 93.4 80.0 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 OE2 118.6 REMARK 620 3 ASN A 132 OD1 128.8 101.8 REMARK 620 4 C B 5 O3' 125.0 82.4 88.3 REMARK 620 5 A B 6 OP1 72.2 113.6 120.2 53.1 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9YJL RELATED DB: PDB REMARK 900 9YJL IS WILD-TYPE PROTEIN IN THE APO-FORM REMARK 900 RELATED ID: 9YJM RELATED DB: PDB REMARK 900 9YJM IS SAME MUTANT IN APO-FORM REMARK 900 RELATED ID: 9YK1 RELATED DB: PDB REMARK 900 9YK1 IS SAME MUTANT WITH RNA/DNA DUPLEX REMARK 900 RELATED ID: 9YK3 RELATED DB: PDB REMARK 900 9YK3 IS SAME MUTANT WITH COMPLEMENTARY RNA/DNA DUPLEX DBREF 9YK5 A 59 196 UNP Q9KEI9 RNH1_HALH5 59 196 DBREF 9YK5 B 1 6 PDB 9YK5 9YK5 1 6 DBREF 9YK5 C 1 6 PDB 9YK5 9YK5 1 6 SEQADV 9YK5 SER A 58 UNP Q9KEI9 EXPRESSION TAG SEQADV 9YK5 ASN A 132 UNP Q9KEI9 ASP 132 ENGINEERED MUTATION SEQRES 1 A 139 SER ALA LYS GLU GLU ILE ILE TRP GLU SER LEU SER VAL SEQRES 2 A 139 ASP VAL GLY SER GLN GLY ASN PRO GLY ILE VAL GLU TYR SEQRES 3 A 139 LYS GLY VAL ASP THR LYS THR GLY GLU VAL LEU PHE GLU SEQRES 4 A 139 ARG GLU PRO ILE PRO ILE GLY THR ASN ASN MET GLY GLU SEQRES 5 A 139 PHE LEU ALA ILE VAL HIS GLY LEU ARG TYR LEU LYS GLU SEQRES 6 A 139 ARG ASN SER ARG LYS PRO ILE TYR SER ASN SER GLN THR SEQRES 7 A 139 ALA ILE LYS TRP VAL LYS ASP LYS LYS ALA LYS SER THR SEQRES 8 A 139 LEU VAL ARG ASN GLU GLU THR ALA LEU ILE TRP LYS LEU SEQRES 9 A 139 VAL ASP GLU ALA GLU GLU TRP LEU ASN THR HIS THR TYR SEQRES 10 A 139 GLU THR PRO ILE LEU LYS TRP GLN THR ASP LYS TRP GLY SEQRES 11 A 139 GLU ILE LYS ALA ASP TYR GLY ARG LYS SEQRES 1 B 6 U C G A C A SEQRES 1 C 6 DA DT DG DT DC DG HET MN A 201 1 HET MG A 202 1 HET PO3 C 101 4 HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM PO3 PHOSPHITE ION FORMUL 4 MN MN 2+ FORMUL 5 MG MG 2+ FORMUL 6 PO3 O3 P 3- FORMUL 7 HOH *31(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 HIS A 172 1 18 HELIX 4 AA4 GLN A 182 GLY A 187 1 6 SHEET 1 AA1 3 VAL A 93 GLU A 96 0 SHEET 2 AA1 3 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA1 3 ILE A 100 GLY A 103 -1 O ILE A 100 N VAL A 81 SHEET 1 AA2 5 VAL A 93 GLU A 96 0 SHEET 2 AA2 5 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA2 5 LEU A 68 GLN A 75 -1 N GLY A 73 O GLU A 82 SHEET 4 AA2 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA2 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 LINK O3' DG C 6 P PO3 C 101 1555 1555 1.61 LINK OD2 ASP A 71 MN MN A 201 1555 1555 2.10 LINK OD1 ASP A 71 MG MG A 202 1555 1555 2.23 LINK OE2 GLU A 109 MG MG A 202 1555 1555 2.24 LINK OD1 ASN A 132 MG MG A 202 1555 1555 2.24 LINK OD1 ASP A 192 MN MN A 201 1555 1555 2.18 LINK MN MN A 201 O HOH A 303 1555 1555 2.22 LINK MN MN A 201 O HOH A 310 1555 1555 2.10 LINK MN MN A 201 OP1 A B 6 1555 1555 2.13 LINK MN MN A 201 O HOH B 105 1555 1555 2.68 LINK MG MG A 202 O3' C B 5 1555 1555 2.85 LINK MG MG A 202 OP1 A B 6 1555 1555 2.72 CISPEP 1 ASN A 77 PRO A 78 0 0.32 CRYST1 82.619 37.217 62.310 90.00 96.61 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 0.012104 0.000000 0.001403 0.00000 SCALE2 0.000000 0.026870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016156 0.00000 CONECT 91 1343 CONECT 92 1342 CONECT 378 1343 CONECT 573 1343 CONECT 1076 1342 CONECT 1185 1343 CONECT 1198 1342 1343 CONECT 1327 1344 CONECT 1342 92 1076 1198 1350 CONECT 1342 1357 1373 CONECT 1343 91 378 573 1185 CONECT 1343 1198 CONECT 1344 1327 1345 1346 1347 CONECT 1345 1344 CONECT 1346 1344 CONECT 1347 1344 CONECT 1350 1342 CONECT 1357 1342 CONECT 1373 1342 MASTER 258 0 3 4 8 0 0 6 1371 3 19 13 END