HEADER HYDROLASE/RNA/DNA 09-JUN-18 6DPG TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS RIBONUCLEASE H1 E188A IN TITLE 2 COMPLEX WITH AN RNA/DNA HYBRID: REACTION IN 4 MM MN2+ AND 200 MM K+ TITLE 3 FOR 240 S AT 21 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: RNASE H; COMPND 6 EC: 3.1.26.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-R(*AP*CP*AP*U)-3' PORTION OF CLEAVED RNA 5'- COMPND 11 R(*AP*CP*AP*UP*CP*G)-3'; COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-R(P*CP*G)-3' PORTION OF CLEAVED RNA 5'- COMPND 16 R(*AP*CP*AP*UP*CP*G)-3'; COMPND 17 CHAIN: b; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 4; COMPND 20 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3'); COMPND 21 CHAIN: C; COMPND 22 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 86665; SOURCE 4 GENE: RNHA, BH0863; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-RNA-DNA COMPLEX, DOUBLE HELIX, RNA HYDROLYSIS, IN CRYSTALLO KEYWDS 2 CATALYSIS, METAL DEPENDENT CATALYSIS, MONOVALENT CATIONS, DIVALENT KEYWDS 3 CATIONS, HYDROLASE-RNA-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.L.SAMARA,W.YANG REVDAT 2 11-OCT-23 6DPG 1 LINK REVDAT 1 15-AUG-18 6DPG 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. 1.38 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 37148 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1798 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 19.9566 - 3.2385 0.94 2771 141 0.1418 0.1549 REMARK 3 2 3.2385 - 2.5722 0.99 2830 149 0.1529 0.1603 REMARK 3 3 2.5722 - 2.2476 0.98 2821 116 0.1550 0.1503 REMARK 3 4 2.2476 - 2.0423 0.98 2767 144 0.1547 0.1709 REMARK 3 5 2.0423 - 1.8960 0.98 2788 144 0.1590 0.2197 REMARK 3 6 1.8960 - 1.7843 0.97 2712 160 0.1596 0.1832 REMARK 3 7 1.7843 - 1.6950 0.97 2736 146 0.1586 0.1825 REMARK 3 8 1.6950 - 1.6213 0.96 2743 134 0.1745 0.1917 REMARK 3 9 1.6213 - 1.5589 0.96 2722 136 0.1947 0.2454 REMARK 3 10 1.5589 - 1.5051 0.95 2652 142 0.2255 0.2872 REMARK 3 11 1.5051 - 1.4581 0.95 2674 152 0.2456 0.2855 REMARK 3 12 1.4581 - 1.4164 0.95 2712 118 0.2875 0.3020 REMARK 3 13 1.4164 - 1.3791 0.86 2422 116 0.3074 0.3707 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.88 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 : 0.007 1537 REMARK 3 ANGLE : 1.030 2116 REMARK 3 CHIRALITY : 0.069 234 REMARK 3 PLANARITY : 0.006 216 REMARK 3 DIHEDRAL : 22.205 610 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 21.7770 0.3799 16.8170 REMARK 3 T TENSOR REMARK 3 T11: 0.1767 T22: 0.1410 REMARK 3 T33: 0.1470 T12: 0.0171 REMARK 3 T13: 0.0046 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 2.2068 L22: 1.3355 REMARK 3 L33: 3.9772 L12: -0.3185 REMARK 3 L13: 0.9680 L23: 0.1165 REMARK 3 S TENSOR REMARK 3 S11: 0.0798 S12: 0.0427 S13: -0.0217 REMARK 3 S21: -0.1526 S22: -0.0803 S23: 0.0150 REMARK 3 S31: -0.0923 S32: -0.0366 S33: -0.0052 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES REFINED IN PHENIX AND REMARK 3 NUCLEIC ACID AND PROTEIN RESIDUES BUILT IN COOT REMARK 4 REMARK 4 6DPG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000235032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-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 : 22-ID 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 300 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 : 37154 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 19.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.1 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: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDBID 1ZBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.99 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 40.82250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.82200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.82250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.82200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL 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: 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 O HOH A 421 O HOH A 434 2.09 REMARK 500 O HOH A 361 O HOH A 417 2.11 REMARK 500 O HOH A 302 O HOH A 416 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 66 O3 GOL A 210 2656 1.26 REMARK 500 HE2 HIS A 115 OE2 GLU A 167 4546 1.54 REMARK 500 OE2 GLU A 153 HZ2 LYS A 190 3455 1.55 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 C b 5 P C b 5 OP3 -0.129 REMARK 500 C b 5 P C b 5 OP3 -0.106 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 438 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A 439 DISTANCE = 7.34 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 MN A 211 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 ASP A 192 OD1 99.2 REMARK 620 3 HOH A 321 O 90.3 90.3 REMARK 620 4 HOH A 324 O 87.2 82.9 172.3 REMARK 620 5 C b 5 OP3 157.4 102.5 95.7 89.4 REMARK 620 6 C b 5 OP1 96.6 163.5 84.9 102.6 62.4 REMARK 620 7 C b 5 OP1 95.9 163.5 83.1 104.4 63.4 1.9 REMARK 620 8 C b 5 OP1 91.2 169.2 86.9 100.4 67.4 5.7 6.0 REMARK 620 9 HOH b 203 O 171.5 87.5 94.9 88.5 15.0 77.2 78.1 82.3 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 212 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD1 REMARK 620 2 GLU A 109 OE1 95.9 REMARK 620 3 ASP A 132 OD1 123.6 102.8 REMARK 620 4 ASP A 132 OD2 98.1 152.9 50.2 REMARK 620 5 U B 4 O3' 147.7 81.1 88.1 98.6 REMARK 620 6 C b 5 OP3 148.4 83.3 86.9 96.4 2.3 REMARK 620 7 C b 5 OP1 93.8 116.0 122.5 86.1 60.1 59.3 REMARK 620 8 C b 5 OP1 92.2 119.0 121.5 83.6 62.6 61.7 3.3 REMARK 620 9 C b 5 OP1 90.4 113.8 126.8 89.3 62.5 61.8 4.4 5.8 REMARK 620 N 1 2 3 4 5 6 7 8 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 163 OD1 REMARK 620 2 GLU A 166 OE1 104.9 REMARK 620 3 HOH A 304 O 163.8 91.3 REMARK 620 4 HOH A 403 O 86.2 103.8 90.0 REMARK 620 5 HOH A 409 O 104.5 150.3 59.3 74.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN b 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 384 O REMARK 620 2 HOH A 395 O 87.5 REMARK 620 3 C b 5 OP3 97.3 174.4 REMARK 620 4 G b 6 OP2 80.9 102.1 81.5 REMARK 620 5 HOH b 206 O 90.3 93.5 83.7 161.7 REMARK 620 6 HOH b 207 O 158.6 71.8 103.6 97.5 96.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 4 O5' REMARK 620 2 C b 5 OP2 100.7 REMARK 620 N 1 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 DG C 5 O6 REMARK 620 2 HOH C 207 O 85.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN b 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 101 DBREF 6DPG A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 6DPG B 1 4 PDB 6DPG 6DPG 1 4 DBREF 6DPG b 5 6 PDB 6DPG 6DPG 5 6 DBREF 6DPG C 1 6 PDB 6DPG 6DPG 1 6 SEQADV 6DPG GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPG SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPG HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPG MET A 58 UNP Q9KEI9 EXPRESSION TAG SEQADV 6DPG ALA A 188 UNP Q9KEI9 GLU 188 ENGINEERED MUTATION 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 ALA 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 MN A 201 1 HET IOD A 202 1 HET IOD A 203 1 HET IOD A 204 1 HET GOL A 205 6 HET EDO A 206 4 HET EDO A 207 4 HET EDO A 208 4 HET EDO A 209 4 HET GOL A 210 6 HET MN A 211 1 HET MN A 212 1 HET K B 101 1 HET MN b 101 1 HET K C 101 1 HETNAM MN MANGANESE (II) ION HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM K POTASSIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MN 4(MN 2+) FORMUL 6 IOD 3(I 1-) FORMUL 9 GOL 2(C3 H8 O3) FORMUL 10 EDO 4(C2 H6 O2) FORMUL 17 K 2(K 1+) FORMUL 20 HOH *174(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'A U B 4 P A C b 5 1555 1555 1.61 LINK OD2 ASP A 71 MN MN A 211 1555 1555 2.15 LINK OD1 ASP A 71 MN MN A 212 1555 1555 2.05 LINK OE1 GLU A 109 MN MN A 212 1555 1555 2.04 LINK OD1 ASP A 132 MN MN A 212 1555 1555 2.06 LINK OD2 ASP A 132 MN MN A 212 1555 1555 2.80 LINK OD1 ASP A 163 MN MN A 201 1555 1555 2.68 LINK OE1 GLU A 166 MN MN A 201 1555 1555 2.02 LINK OD1 ASP A 192 MN MN A 211 1555 1555 2.16 LINK MN MN A 201 O HOH A 304 1555 1555 1.98 LINK MN MN A 201 O HOH A 403 1555 1555 2.00 LINK MN MN A 201 O HOH A 409 1555 1555 2.21 LINK MN MN A 211 O HOH A 321 1555 1555 2.15 LINK MN MN A 211 O HOH A 324 1555 1555 2.16 LINK MN MN A 211 OP3B C b 5 1555 1555 2.15 LINK MN MN A 211 OP1A C b 5 1555 1555 2.32 LINK MN MN A 211 OP1B C b 5 1555 1555 2.23 LINK MN MN A 211 OP1C C b 5 1555 1555 2.37 LINK MN MN A 211 O CHOH b 203 1555 1555 2.16 LINK MN MN A 212 O3'A U B 4 1555 1555 2.65 LINK MN MN A 212 OP3C C b 5 1555 1555 2.41 LINK MN MN A 212 OP1A C b 5 1555 1555 2.14 LINK MN MN A 212 OP1B C b 5 1555 1555 2.15 LINK MN MN A 212 OP1C C b 5 1555 1555 1.96 LINK O BHOH A 384 MN B MN b 101 1555 1555 2.21 LINK O HOH A 395 MN B MN b 101 1555 1555 2.19 LINK O5'B U B 4 K B K B 101 1555 1555 3.27 LINK K B K B 101 OP2B C b 5 1555 1555 2.58 LINK OP3B C b 5 MN B MN b 101 1555 1555 2.21 LINK OP2 G b 6 MN B MN b 101 1555 1555 2.39 LINK MN B MN b 101 O HOH b 206 1555 1555 2.26 LINK MN B MN b 101 O HOH b 207 1555 1555 2.17 LINK O6 DG C 5 K A K C 101 1555 1555 2.60 LINK K A K C 101 O HOH C 207 1555 1555 2.97 CISPEP 1 ASN A 77 PRO A 78 0 0.43 SITE 1 AC1 7 LYS A 144 ASP A 163 GLU A 166 HOH A 304 SITE 2 AC1 7 HOH A 308 HOH A 403 HOH A 409 SITE 1 AC2 1 TYR A 83 SITE 1 AC3 3 ILE A 64 HOH A 436 HOH A 438 SITE 1 AC4 6 GLY A 76 ASN A 77 PRO A 78 HOH A 358 SITE 2 AC4 6 DG C 2 DA C 3 SITE 1 AC5 4 LYS A 143 THR A 173 TYR A 174 HOH A 354 SITE 1 AC6 4 THR A 148 HOH A 311 DT C 4 DG C 5 SITE 1 AC7 4 GLU A 62 EDO A 209 HOH A 404 HOH A 430 SITE 1 AC8 6 GLU A 62 ILE A 63 TRP A 65 ARG A 151 SITE 2 AC8 6 EDO A 208 HOH A 388 SITE 1 AC9 6 GLU A 66 SER A 125 LYS A 127 HOH A 314 SITE 2 AC9 6 HOH A 366 HOH A 369 SITE 1 AD1 6 ASP A 71 ASP A 192 HOH A 321 HOH A 324 SITE 2 AD1 6 C b 5 HOH b 203 SITE 1 AD2 5 ASP A 71 GLU A 109 ASP A 132 U B 4 SITE 2 AD2 5 C b 5 SITE 1 AD3 4 ASP A 132 U B 4 C b 5 HOH b 208 SITE 1 AD4 7 HOH A 384 HOH A 395 C b 5 G b 6 SITE 2 AD4 7 HOH b 203 HOH b 206 HOH b 207 SITE 1 AD5 4 DT C 4 DG C 5 HOH C 207 HOH C 209 CRYST1 81.645 37.644 61.962 90.00 96.64 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 0.012248 0.000000 0.001426 0.00000 SCALE2 0.000000 0.026565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016248 0.00000