HEADER HYDROLASE/DNA 23-APR-13 4KB1 TITLE CRYSTAL STRUCTURE OF RNASE T IN COMPLEX WITH A BLUGE DNA (TWO TITLE 2 NUCLEOTIDE INSERTION CT ) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE T; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RNASE T; COMPND 5 SYNONYM: EXORIBONUCLEASE T, RNASE T; COMPND 6 EC: 3.1.13.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: BULGE DNA; COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: B1652, JW1644, RNT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIPL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS DNAQ, DEDD, EXONUCLEASE, DNA REPAIR, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.-Y.HSIAO,H.S.YUAN REVDAT 3 20-SEP-23 4KB1 1 REMARK SEQADV LINK REVDAT 2 28-MAY-14 4KB1 1 JRNL REVDAT 1 05-MAR-14 4KB1 0 JRNL AUTH Y.Y.HSIAO,W.H.FANG,C.C.LEE,Y.P.CHEN,H.S.YUAN JRNL TITL STRUCTURAL INSIGHTS INTO DNA REPAIR BY RNASE T--AN JRNL TITL 2 EXONUCLEASE PROCESSING 3' END OF STRUCTURED DNA IN REPAIR JRNL TITL 3 PATHWAYS. JRNL REF PLOS BIOL. V. 12 01803 2014 JRNL REFN ISSN 1544-9173 JRNL PMID 24594808 JRNL DOI 10.1371/JOURNAL.PBIO.1001803 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 63562 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3222 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 28.6250 - 5.1097 0.94 2547 140 0.1808 0.1940 REMARK 3 2 5.1097 - 4.0594 0.99 2632 156 0.1450 0.1445 REMARK 3 3 4.0594 - 3.5473 0.99 2628 152 0.1500 0.1510 REMARK 3 4 3.5473 - 3.2235 0.99 2643 156 0.1645 0.1812 REMARK 3 5 3.2235 - 2.9927 0.99 2623 144 0.1835 0.1972 REMARK 3 6 2.9927 - 2.8164 0.99 2618 127 0.1929 0.2244 REMARK 3 7 2.8164 - 2.6755 0.99 2688 122 0.1971 0.2089 REMARK 3 8 2.6755 - 2.5591 0.99 2602 145 0.2011 0.2193 REMARK 3 9 2.5591 - 2.4606 0.99 2649 131 0.1939 0.1983 REMARK 3 10 2.4606 - 2.3758 0.99 2642 136 0.1897 0.2232 REMARK 3 11 2.3758 - 2.3015 0.99 2638 154 0.1899 0.2205 REMARK 3 12 2.3015 - 2.2357 1.00 2585 155 0.1916 0.2199 REMARK 3 13 2.2357 - 2.1769 1.00 2656 120 0.1952 0.2597 REMARK 3 14 2.1769 - 2.1238 1.00 2641 150 0.1926 0.2146 REMARK 3 15 2.1238 - 2.0756 0.99 2622 126 0.1961 0.2488 REMARK 3 16 2.0756 - 2.0314 0.99 2610 137 0.1976 0.2008 REMARK 3 17 2.0314 - 1.9908 0.99 2594 153 0.2057 0.2253 REMARK 3 18 1.9908 - 1.9532 0.99 2633 136 0.2156 0.2437 REMARK 3 19 1.9532 - 1.9183 0.99 2654 149 0.2218 0.2654 REMARK 3 20 1.9183 - 1.8858 0.99 2607 131 0.2194 0.2472 REMARK 3 21 1.8858 - 1.8554 0.99 2588 151 0.2255 0.2419 REMARK 3 22 1.8554 - 1.8269 0.99 2641 112 0.2394 0.2811 REMARK 3 23 1.8269 - 1.8000 0.99 2599 139 0.2560 0.2962 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.730 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 : 0.004 4060 REMARK 3 ANGLE : 0.864 5656 REMARK 3 CHIRALITY : 0.057 631 REMARK 3 PLANARITY : 0.003 617 REMARK 3 DIHEDRAL : 18.885 1502 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 4KB1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000079114. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-11 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 : 65372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 27.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.41100 REMARK 200 FOR SHELL : 2.870 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: 3NGY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.10% W/V N-OCTYL- -D-GLUCOSIDE, 0.1 M REMARK 280 SODIUM CITRATE TRIBASIC DEHYDRATE, 22% POLYETHYLENE GLYCOL 3350, REMARK 280 PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 40.92200 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 ALA B 212 REMARK 465 GLU B 213 REMARK 465 GLU B 214 REMARK 465 VAL B 215 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 656 O HOH A 661 1.82 REMARK 500 O HOH B 561 O HOH B 567 1.82 REMARK 500 O HOH B 548 O HOH B 551 1.82 REMARK 500 O HOH A 583 O HOH A 604 1.82 REMARK 500 O HOH B 559 O HOH B 602 1.86 REMARK 500 O HOH C 227 O HOH C 242 1.88 REMARK 500 O HOH B 565 O HOH B 585 1.91 REMARK 500 O HOH A 622 O HOH C 241 1.92 REMARK 500 O HOH C 226 O HOH C 240 1.93 REMARK 500 O HOH A 481 O HOH A 552 1.96 REMARK 500 O HOH A 613 O HOH A 665 1.97 REMARK 500 O HOH A 603 O HOH A 621 1.98 REMARK 500 O2 DC D 4 O HOH D 215 1.98 REMARK 500 O HOH B 537 O HOH B 547 2.00 REMARK 500 O HOH A 617 O HOH A 618 2.01 REMARK 500 O HOH B 584 O HOH B 613 2.03 REMARK 500 O HOH A 505 O HOH A 662 2.04 REMARK 500 O HOH B 506 O HOH B 623 2.05 REMARK 500 NH1 ARG B 114 O HOH B 563 2.05 REMARK 500 O HOH A 573 O HOH A 604 2.08 REMARK 500 O HOH A 602 O HOH A 606 2.08 REMARK 500 O HOH A 549 O HOH A 580 2.09 REMARK 500 O LEU B 7 O HOH B 527 2.11 REMARK 500 O HOH A 637 O HOH A 668 2.12 REMARK 500 O HIS B 181 O HOH B 462 2.12 REMARK 500 O HOH A 577 O HOH A 588 2.12 REMARK 500 O2 DC D 16 O HOH D 205 2.13 REMARK 500 O HOH A 596 O HOH A 599 2.13 REMARK 500 O HOH A 543 O HOH A 546 2.14 REMARK 500 O HOH A 598 O HOH A 632 2.15 REMARK 500 O HOH C 210 O HOH C 229 2.15 REMARK 500 O HOH A 474 O HOH A 644 2.17 REMARK 500 O HOH A 590 O HOH A 591 2.17 REMARK 500 OD1 ASN B 123 O HOH B 602 2.19 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 O HOH A 639 O HOH B 583 2655 1.93 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 DT C 9 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG C 13 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG C 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT D 9 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT D 9 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT D 17 O4' - C1' - N1 ANGL. DEV. = 2.0 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 38.27 38.50 REMARK 500 ASP A 55 -87.93 -110.80 REMARK 500 PHE A 146 -25.36 -146.28 REMARK 500 ARG B 15 40.85 38.84 REMARK 500 ASP B 55 -86.87 -113.36 REMARK 500 PHE B 146 -25.90 -140.80 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 C 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 23 OD2 REMARK 620 2 HOH A 402 O 100.0 REMARK 620 3 HOH A 415 O 78.4 81.4 REMARK 620 4 HOH A 424 O 89.3 94.7 166.2 REMARK 620 5 DT C 17 O3' 155.9 100.8 92.9 100.9 REMARK 620 6 DC C 18 OP1 97.8 160.7 94.9 93.0 60.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 25 OE1 REMARK 620 2 ASP A 186 OD2 123.7 REMARK 620 3 HOH A 502 O 75.4 98.5 REMARK 620 4 DC C 18 OP1 112.9 121.5 81.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 23 OD1 REMARK 620 2 HOH B 412 O 86.0 REMARK 620 3 HOH B 424 O 88.9 173.6 REMARK 620 4 HOH B 426 O 100.1 85.8 91.3 REMARK 620 5 DT D 17 O3' 155.7 89.6 96.7 103.4 REMARK 620 6 DC D 18 OP1 98.6 95.1 89.4 161.3 58.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 25 OE1 REMARK 620 2 ASP B 186 OD2 128.1 REMARK 620 3 DC D 18 OP1 120.8 107.5 REMARK 620 N 1 2 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VA3 RELATED DB: PDB REMARK 900 RELATED ID: 3VA0 RELATED DB: PDB REMARK 900 RELATED ID: 3V9Z RELATED DB: PDB REMARK 900 RELATED ID: 3V9X RELATED DB: PDB REMARK 900 RELATED ID: 3V9W RELATED DB: PDB REMARK 900 RELATED ID: 3NGY RELATED DB: PDB REMARK 900 RELATED ID: 4KAZ RELATED DB: PDB REMARK 900 RELATED ID: 4KB0 RELATED DB: PDB DBREF 4KB1 A 1 215 UNP P30014 RNT_ECOLI 1 215 DBREF 4KB1 B 1 215 UNP P30014 RNT_ECOLI 1 215 DBREF 4KB1 C 1 18 PDB 4KB1 4KB1 1 18 DBREF 4KB1 D 1 18 PDB 4KB1 4KB1 1 18 SEQADV 4KB1 MET A -19 UNP P30014 INITIATING METHIONINE SEQADV 4KB1 GLY A -18 UNP P30014 EXPRESSION TAG SEQADV 4KB1 SER A -17 UNP P30014 EXPRESSION TAG SEQADV 4KB1 SER A -16 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS A -15 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS A -14 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS A -13 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS A -12 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS A -11 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS A -10 UNP P30014 EXPRESSION TAG SEQADV 4KB1 SER A -9 UNP P30014 EXPRESSION TAG SEQADV 4KB1 SER A -8 UNP P30014 EXPRESSION TAG SEQADV 4KB1 GLY A -7 UNP P30014 EXPRESSION TAG SEQADV 4KB1 LEU A -6 UNP P30014 EXPRESSION TAG SEQADV 4KB1 VAL A -5 UNP P30014 EXPRESSION TAG SEQADV 4KB1 PRO A -4 UNP P30014 EXPRESSION TAG SEQADV 4KB1 ARG A -3 UNP P30014 EXPRESSION TAG SEQADV 4KB1 GLY A -2 UNP P30014 EXPRESSION TAG SEQADV 4KB1 SER A -1 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS A 0 UNP P30014 EXPRESSION TAG SEQADV 4KB1 MET B -19 UNP P30014 INITIATING METHIONINE SEQADV 4KB1 GLY B -18 UNP P30014 EXPRESSION TAG SEQADV 4KB1 SER B -17 UNP P30014 EXPRESSION TAG SEQADV 4KB1 SER B -16 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS B -15 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS B -14 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS B -13 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS B -12 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS B -11 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS B -10 UNP P30014 EXPRESSION TAG SEQADV 4KB1 SER B -9 UNP P30014 EXPRESSION TAG SEQADV 4KB1 SER B -8 UNP P30014 EXPRESSION TAG SEQADV 4KB1 GLY B -7 UNP P30014 EXPRESSION TAG SEQADV 4KB1 LEU B -6 UNP P30014 EXPRESSION TAG SEQADV 4KB1 VAL B -5 UNP P30014 EXPRESSION TAG SEQADV 4KB1 PRO B -4 UNP P30014 EXPRESSION TAG SEQADV 4KB1 ARG B -3 UNP P30014 EXPRESSION TAG SEQADV 4KB1 GLY B -2 UNP P30014 EXPRESSION TAG SEQADV 4KB1 SER B -1 UNP P30014 EXPRESSION TAG SEQADV 4KB1 HIS B 0 UNP P30014 EXPRESSION TAG 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 GLU 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 GLU 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 18 DG DG DC DC DC DT DC DT DT DT DA DG DG SEQRES 2 C 18 DG DC DC DT DC SEQRES 1 D 18 DG DG DC DC DC DT DC DT DT DT DA DG DG SEQRES 2 D 18 DG DC DC DT DC HET MG A 301 1 HET MG B 301 1 HET MG C 101 1 HET MG D 101 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG 4(MG 2+) FORMUL 9 HOH *569(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 SER A 182 LEU A 204 1 23 HELIX 8 8 PRO A 208 GLU A 213 1 6 HELIX 9 9 GLY B 9 PHE B 14 1 6 HELIX 10 10 GLN B 71 GLY B 79 1 9 HELIX 11 11 SER B 91 GLY B 111 1 21 HELIX 12 12 ALA B 122 ALA B 136 1 15 HELIX 13 13 THR B 151 GLY B 160 1 10 HELIX 14 14 VAL B 163 ALA B 171 1 9 HELIX 15 15 SER B 182 LEU B 204 1 23 SHEET 1 A 5 LEU A 52 HIS A 61 0 SHEET 2 A 5 LEU A 36 MET A 46 -1 N THR A 43 O ASP A 55 SHEET 3 A 5 PHE A 17 THR A 26 -1 N GLU A 25 O LEU A 37 SHEET 4 A 5 ARG A 114 ALA A 119 1 O ARG A 114 N TYR A 18 SHEET 5 A 5 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 VAL B 118 N VAL B 20 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 C 101 1555 1555 2.28 LINK OE1 GLU A 25 MG MG A 301 1555 1555 2.37 LINK OD2 ASP A 186 MG MG A 301 1555 1555 2.32 LINK MG MG A 301 O HOH A 502 1555 1555 2.50 LINK MG MG A 301 OP1 DC C 18 1555 1555 2.10 LINK O HOH A 402 MG MG C 101 1555 1555 2.45 LINK O HOH A 415 MG MG C 101 1555 1555 2.33 LINK O HOH A 424 MG MG C 101 1555 1555 2.33 LINK OD1 ASP B 23 MG MG D 101 1555 1555 2.39 LINK OE1 GLU B 25 MG MG B 301 1555 1555 2.18 LINK OD2 ASP B 186 MG MG B 301 1555 1555 2.23 LINK MG MG B 301 OP1 DC D 18 1555 1555 2.06 LINK O HOH B 412 MG MG D 101 1555 1555 2.23 LINK O HOH B 424 MG MG D 101 1555 1555 2.37 LINK O HOH B 426 MG MG D 101 1555 1555 2.23 LINK O3' DT C 17 MG MG C 101 1555 1555 2.43 LINK OP1 DC C 18 MG MG C 101 1555 1555 2.47 LINK O3' DT D 17 MG MG D 101 1555 1555 2.44 LINK OP1 DC D 18 MG MG D 101 1555 1555 2.61 CISPEP 1 TRP A 207 PRO A 208 0 -2.35 CISPEP 2 TRP B 207 PRO B 208 0 -1.17 SITE 1 AC1 6 ASP A 23 GLU A 25 ASP A 186 HOH A 502 SITE 2 AC1 6 DC C 18 MG C 101 SITE 1 AC2 5 ASP B 23 GLU B 25 ALA B 180 ASP B 186 SITE 2 AC2 5 DC D 18 SITE 1 AC3 7 ASP A 23 MG A 301 HOH A 402 HOH A 415 SITE 2 AC3 7 HOH A 424 DT C 17 DC C 18 SITE 1 AC4 6 ASP B 23 HOH B 412 HOH B 424 HOH B 426 SITE 2 AC4 6 DT D 17 DC D 18 CRYST1 60.556 81.844 73.744 90.00 105.71 90.00 P 1 21 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 0.016514 0.000000 0.004645 0.00000 SCALE2 0.000000 0.012218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014087 0.00000