HEADER HYDROLASE/DNA 14-JUN-10 3NGZ TITLE CRYSTAL STRUCTURE OF RNASE T IN COMPLEX WITH A NON-PREFERRED SSDNA TITLE 2 (GC) WITH ONE MG IN THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE T; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RNASE T, EXORIBONUCLEASE T; COMPND 5 EC: 3.1.13.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(P*GP*C)-3'; COMPND 10 CHAIN: C, D; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: SSDNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: JM109 / ATCC 53323; SOURCE 5 GENE: RNT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: RIPL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS EXORIBONUCLEASE, RNA PROCESSING, RNA MATURATION, PROTEIN-DNA KEYWDS 2 INTERACTIONS, PROTEIN-DNA COMPLEX, EXO-NUCLEASE, HYDROLASE-DNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.-Y.HSIAO,H.S.YUAN REVDAT 4 01-NOV-23 3NGZ 1 REMARK SEQADV LINK REVDAT 3 21-DEC-11 3NGZ 1 JRNL VERSN REVDAT 2 23-FEB-11 3NGZ 1 JRNL REVDAT 1 16-FEB-11 3NGZ 0 JRNL AUTH Y.-Y.HSIAO,C.-C.YANG,C.L.LIN,J.L.J.LIN,Y.DUH,H.S.YUAN JRNL TITL STRUCTURAL BASIS FOR RNA TRIMMING BY RNASE T IN STABLE RNA JRNL TITL 2 3'-END MATURATION JRNL REF NAT.CHEM.BIOL. V. 7 236 2011 JRNL REFN ISSN 1552-4450 JRNL PMID 21317904 JRNL DOI 10.1038/NCHEMBIO.524 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 28628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.780 REMARK 3 FREE R VALUE TEST SET COUNT : 2227 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 28.4621 - 5.2812 0.97 1756 139 0.2050 0.2406 REMARK 3 2 5.2812 - 4.1962 0.98 1693 145 0.1701 0.2188 REMARK 3 3 4.1962 - 3.6670 0.99 1680 131 0.1674 0.2234 REMARK 3 4 3.6670 - 3.3323 0.98 1631 154 0.1849 0.2147 REMARK 3 5 3.3323 - 3.0937 0.99 1668 139 0.1902 0.2428 REMARK 3 6 3.0937 - 2.9115 0.99 1651 142 0.2055 0.2644 REMARK 3 7 2.9115 - 2.7658 0.99 1625 125 0.1958 0.3052 REMARK 3 8 2.7658 - 2.6455 1.00 1663 145 0.2064 0.2643 REMARK 3 9 2.6455 - 2.5438 0.99 1667 116 0.2024 0.2830 REMARK 3 10 2.5438 - 2.4560 0.98 1599 150 0.1944 0.2851 REMARK 3 11 2.4560 - 2.3793 1.00 1639 148 0.1954 0.2902 REMARK 3 12 2.3793 - 2.3113 0.99 1600 158 0.1926 0.2651 REMARK 3 13 2.3113 - 2.2505 0.99 1632 114 0.2004 0.3019 REMARK 3 14 2.2505 - 2.1956 0.99 1657 131 0.2161 0.2819 REMARK 3 15 2.1956 - 2.1457 1.00 1581 148 0.2110 0.2929 REMARK 3 16 2.1457 - 2.1000 0.99 1659 142 0.2180 0.3295 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 : 0.32 REMARK 3 B_SOL : 41.33 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.67330 REMARK 3 B22 (A**2) : -5.89600 REMARK 3 B33 (A**2) : -3.77730 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 3331 REMARK 3 ANGLE : 0.985 4533 REMARK 3 CHIRALITY : 0.069 501 REMARK 3 PLANARITY : 0.003 583 REMARK 3 DIHEDRAL : 15.773 1169 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 3NGZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059816. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU 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 : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28759 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12000 REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43700 REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 3NGY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% V/V 2-PROPANOL, 0.1M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE PH 5.5, 20% PEG 4000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 48.37350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.79250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.37350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.79250 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, 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 ASN A 4 REMARK 465 ALA A 5 REMARK 465 GLN A 6 REMARK 465 LEU A 7 REMARK 465 VAL A 215 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ASP B 3 REMARK 465 ASN B 4 REMARK 465 ALA B 5 REMARK 465 GLN B 6 REMARK 465 LEU B 7 REMARK 465 GLU B 214 REMARK 465 VAL B 215 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 GLU A 214 CG CD OE1 OE2 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 D 1 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG D 1 O4' - C1' - N9 ANGL. DEV. = 2.2 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 ARG A 15 46.75 33.39 REMARK 500 ASP A 55 -91.09 -114.63 REMARK 500 PHE A 146 -19.67 -145.80 REMARK 500 ASP B 55 -92.07 -120.50 REMARK 500 PHE B 146 -20.80 -143.51 REMARK 500 REMARK 500 REMARK: NULL 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 A1000 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 23 OD2 REMARK 620 2 HOH A1001 O 81.7 REMARK 620 3 HOH A1002 O 80.9 162.4 REMARK 620 4 HOH A1004 O 79.3 89.2 84.8 REMARK 620 5 HOH C1003 O 172.0 99.5 97.4 92.8 REMARK 620 6 HOH C1005 O 84.9 92.6 88.7 163.7 102.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B2000 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 23 OD1 REMARK 620 2 HOH B2002 O 80.6 REMARK 620 3 HOH B2003 O 81.5 160.6 REMARK 620 4 HOH B2005 O 76.5 84.6 83.9 REMARK 620 5 HOH D2001 O 171.3 100.8 95.8 95.0 REMARK 620 6 HOH D2004 O 89.2 87.9 99.4 164.8 99.4 REMARK 620 N 1 2 3 4 5 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 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 217 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NGY RELATED DB: PDB REMARK 900 RNASE T (E92G MUTANT) REMARK 900 RELATED ID: 3NH0 RELATED DB: PDB REMARK 900 RNASE T IN COMPLEX WITH A NON-PREFERRED SSDNA (AAC) REMARK 900 RELATED ID: 3NH1 RELATED DB: PDB REMARK 900 RNASE T IN COMPLEX WITH A PREFERRED SSDNA (TAGG) WITH TWO MG IN THE REMARK 900 ACTIVE SITE REMARK 900 RELATED ID: 3NH2 RELATED DB: PDB REMARK 900 RNASE T IN COMPLEX WITH A STEM DNA WITH A 3' OVERHANG DBREF 3NGZ A 1 215 UNP P30014 RNT_ECOLI 1 215 DBREF 3NGZ B 1 215 UNP P30014 RNT_ECOLI 1 215 DBREF 3NGZ C 1 2 PDB 3NGZ 3NGZ 1 2 DBREF 3NGZ D 1 2 PDB 3NGZ 3NGZ 1 2 SEQADV 3NGZ MET A -19 UNP P30014 EXPRESSION TAG SEQADV 3NGZ GLY A -18 UNP P30014 EXPRESSION TAG SEQADV 3NGZ SER A -17 UNP P30014 EXPRESSION TAG SEQADV 3NGZ SER A -16 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS A -15 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS A -14 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS A -13 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS A -12 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS A -11 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS A -10 UNP P30014 EXPRESSION TAG SEQADV 3NGZ SER A -9 UNP P30014 EXPRESSION TAG SEQADV 3NGZ SER A -8 UNP P30014 EXPRESSION TAG SEQADV 3NGZ GLY A -7 UNP P30014 EXPRESSION TAG SEQADV 3NGZ LEU A -6 UNP P30014 EXPRESSION TAG SEQADV 3NGZ VAL A -5 UNP P30014 EXPRESSION TAG SEQADV 3NGZ PRO A -4 UNP P30014 EXPRESSION TAG SEQADV 3NGZ ARG A -3 UNP P30014 EXPRESSION TAG SEQADV 3NGZ GLY A -2 UNP P30014 EXPRESSION TAG SEQADV 3NGZ SER A -1 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS A 0 UNP P30014 EXPRESSION TAG SEQADV 3NGZ GLY A 92 UNP P30014 GLU 92 ENGINEERED MUTATION SEQADV 3NGZ MET B -19 UNP P30014 EXPRESSION TAG SEQADV 3NGZ GLY B -18 UNP P30014 EXPRESSION TAG SEQADV 3NGZ SER B -17 UNP P30014 EXPRESSION TAG SEQADV 3NGZ SER B -16 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS B -15 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS B -14 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS B -13 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS B -12 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS B -11 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS B -10 UNP P30014 EXPRESSION TAG SEQADV 3NGZ SER B -9 UNP P30014 EXPRESSION TAG SEQADV 3NGZ SER B -8 UNP P30014 EXPRESSION TAG SEQADV 3NGZ GLY B -7 UNP P30014 EXPRESSION TAG SEQADV 3NGZ LEU B -6 UNP P30014 EXPRESSION TAG SEQADV 3NGZ VAL B -5 UNP P30014 EXPRESSION TAG SEQADV 3NGZ PRO B -4 UNP P30014 EXPRESSION TAG SEQADV 3NGZ ARG B -3 UNP P30014 EXPRESSION TAG SEQADV 3NGZ GLY B -2 UNP P30014 EXPRESSION TAG SEQADV 3NGZ SER B -1 UNP P30014 EXPRESSION TAG SEQADV 3NGZ HIS B 0 UNP P30014 EXPRESSION TAG SEQADV 3NGZ GLY B 92 UNP P30014 GLU 92 ENGINEERED MUTATION SEQRES 1 A 235 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 235 LEU VAL PRO ARG GLY SER HIS MET SER ASP ASN ALA GLN SEQRES 3 A 235 LEU THR GLY LEU CYS ASP ARG PHE ARG GLY PHE TYR PRO SEQRES 4 A 235 VAL VAL ILE ASP VAL GLU THR ALA GLY PHE ASN ALA LYS SEQRES 5 A 235 THR ASP ALA LEU LEU GLU ILE ALA ALA ILE THR LEU LYS SEQRES 6 A 235 MET ASP GLU GLN GLY TRP LEU MET PRO ASP THR THR LEU SEQRES 7 A 235 HIS PHE HIS VAL GLU PRO PHE VAL GLY ALA ASN LEU GLN SEQRES 8 A 235 PRO GLU ALA LEU ALA PHE ASN GLY ILE ASP PRO ASN ASP SEQRES 9 A 235 PRO ASP ARG GLY ALA VAL SER GLY TYR GLU ALA LEU HIS SEQRES 10 A 235 GLU ILE PHE LYS VAL VAL ARG LYS GLY ILE LYS ALA SER SEQRES 11 A 235 GLY CYS ASN ARG ALA ILE MET VAL ALA HIS ASN ALA ASN SEQRES 12 A 235 PHE ASP HIS SER PHE MET MET ALA ALA ALA GLU ARG ALA SEQRES 13 A 235 SER LEU LYS ARG ASN PRO PHE HIS PRO PHE ALA THR PHE SEQRES 14 A 235 ASP THR ALA ALA LEU ALA GLY LEU ALA LEU GLY GLN THR SEQRES 15 A 235 VAL LEU SER LYS ALA CYS GLN THR ALA GLY MET ASP PHE SEQRES 16 A 235 ASP SER THR GLN ALA HIS SER ALA LEU TYR ASP THR GLU SEQRES 17 A 235 ARG THR ALA VAL LEU PHE CYS GLU ILE VAL ASN ARG TRP SEQRES 18 A 235 LYS ARG LEU GLY GLY TRP PRO LEU SER ALA ALA GLU GLU SEQRES 19 A 235 VAL SEQRES 1 B 235 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 235 LEU VAL PRO ARG GLY SER HIS MET SER ASP ASN ALA GLN SEQRES 3 B 235 LEU THR GLY LEU CYS ASP ARG PHE ARG GLY PHE TYR PRO SEQRES 4 B 235 VAL VAL ILE ASP VAL GLU THR ALA GLY PHE ASN ALA LYS SEQRES 5 B 235 THR ASP ALA LEU LEU GLU ILE ALA ALA ILE THR LEU LYS SEQRES 6 B 235 MET ASP GLU GLN GLY TRP LEU MET PRO ASP THR THR LEU SEQRES 7 B 235 HIS PHE HIS VAL GLU PRO PHE VAL GLY ALA ASN LEU GLN SEQRES 8 B 235 PRO GLU ALA LEU ALA PHE ASN GLY ILE ASP PRO ASN ASP SEQRES 9 B 235 PRO ASP ARG GLY ALA VAL SER GLY TYR GLU ALA LEU HIS SEQRES 10 B 235 GLU ILE PHE LYS VAL VAL ARG LYS GLY ILE LYS ALA SER SEQRES 11 B 235 GLY CYS ASN ARG ALA ILE MET VAL ALA HIS ASN ALA ASN SEQRES 12 B 235 PHE ASP HIS SER PHE MET MET ALA ALA ALA GLU ARG ALA SEQRES 13 B 235 SER LEU LYS ARG ASN PRO PHE HIS PRO PHE ALA THR PHE SEQRES 14 B 235 ASP THR ALA ALA LEU ALA GLY LEU ALA LEU GLY GLN THR SEQRES 15 B 235 VAL LEU SER LYS ALA CYS GLN THR ALA GLY MET ASP PHE SEQRES 16 B 235 ASP SER THR GLN ALA HIS SER ALA LEU TYR ASP THR GLU SEQRES 17 B 235 ARG THR ALA VAL LEU PHE CYS GLU ILE VAL ASN ARG TRP SEQRES 18 B 235 LYS ARG LEU GLY GLY TRP PRO LEU SER ALA ALA GLU GLU SEQRES 19 B 235 VAL SEQRES 1 C 2 DG DC SEQRES 1 D 2 DG DC HET MG A1000 1 HET CO A 217 1 HET MG B2000 1 HET CO B 217 1 HETNAM MG MAGNESIUM ION HETNAM CO COBALT (II) ION FORMUL 5 MG 2(MG 2+) FORMUL 6 CO 2(CO 2+) FORMUL 9 HOH *584(H2 O) HELIX 1 1 GLY A 9 PHE A 14 1 6 HELIX 2 2 GLN A 71 GLY A 79 1 9 HELIX 3 3 SER A 91 GLY A 111 1 21 HELIX 4 4 ALA A 122 ALA A 136 1 15 HELIX 5 5 THR A 151 GLY A 160 1 10 HELIX 6 6 VAL A 163 ALA A 171 1 9 HELIX 7 7 ASP A 176 ALA A 180 5 5 HELIX 8 8 SER A 182 LEU A 204 1 23 HELIX 9 9 SER A 210 GLU A 214 5 5 HELIX 10 10 GLY B 9 PHE B 14 1 6 HELIX 11 11 GLN B 71 GLY B 79 1 9 HELIX 12 12 ASP B 84 GLY B 88 5 5 HELIX 13 13 SER B 91 GLY B 111 1 21 HELIX 14 14 ALA B 122 SER B 137 1 16 HELIX 15 15 THR B 151 GLY B 160 1 10 HELIX 16 16 VAL B 163 ALA B 171 1 9 HELIX 17 17 ASP B 176 ALA B 180 5 5 HELIX 18 18 SER B 182 LEU B 204 1 23 SHEET 1 A 6 ALA A 89 VAL A 90 0 SHEET 2 A 6 LEU A 52 VAL A 62 1 N HIS A 61 O VAL A 90 SHEET 3 A 6 LEU A 36 MET A 46 -1 N LEU A 37 O VAL A 62 SHEET 4 A 6 PHE A 17 THR A 26 -1 N GLU A 25 O LEU A 37 SHEET 5 A 6 ARG A 114 ALA A 119 1 O ARG A 114 N TYR A 18 SHEET 6 A 6 PHE A 143 ASP A 150 1 O PHE A 149 N MET A 117 SHEET 1 B 5 LEU B 52 HIS B 61 0 SHEET 2 B 5 LEU B 36 MET B 46 -1 N THR B 43 O ASP B 55 SHEET 3 B 5 PHE B 17 THR B 26 -1 N GLU B 25 O LEU B 37 SHEET 4 B 5 ARG B 114 ALA B 119 1 O ARG B 114 N TYR B 18 SHEET 5 B 5 PHE B 143 ASP B 150 1 O PHE B 149 N MET B 117 LINK OD2 ASP A 23 MG MG A1000 1555 1555 2.43 LINK MG MG A1000 O HOH A1001 1555 1555 2.35 LINK MG MG A1000 O HOH A1002 1555 1555 2.28 LINK MG MG A1000 O HOH A1004 1555 1555 2.42 LINK MG MG A1000 O HOH C1003 1555 1555 2.22 LINK MG MG A1000 O HOH C1005 1555 1555 2.44 LINK OD1 ASP B 23 MG MG B2000 1555 1555 2.46 LINK MG MG B2000 O HOH B2002 1555 1555 2.33 LINK MG MG B2000 O HOH B2003 1555 1555 2.22 LINK MG MG B2000 O HOH B2005 1555 1555 2.44 LINK MG MG B2000 O HOH D2001 1555 1555 2.24 LINK MG MG B2000 O HOH D2004 1555 1555 2.36 CISPEP 1 TRP A 207 PRO A 208 0 -2.68 CISPEP 2 TRP B 207 PRO B 208 0 -5.93 SITE 1 AC1 6 ASP A 23 HOH A1001 HOH A1002 HOH A1004 SITE 2 AC1 6 HOH C1003 HOH C1005 SITE 1 AC2 2 ARG A 135 HOH A 227 SITE 1 AC3 6 ASP B 23 HOH B2002 HOH B2003 HOH B2005 SITE 2 AC3 6 HOH D2001 HOH D2004 SITE 1 AC4 2 ARG B 135 HOH B 233 CRYST1 96.747 105.585 47.180 90.00 90.00 90.00 P 21 21 2 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 0.010336 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021195 0.00000