PDB Short entry for 4B20 HEADER HYDROLASE 12-JUL-12 4B20 TITLE STRUCTURAL BASIS OF DNA LOOP RECOGNITION BY ENDONUCLEASE V COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE V; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEOXYINOSINE 3'ENDONUCLEASE, DEOXYRIBONUCLEASE V, DNASE V; COMPND 5 EC: 3.1.21.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'; COMPND 9 CHAIN: C, F; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'; COMPND 12 CHAIN: D, G SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.ROSNES,A.D.ROWE,R.J.FORSTROM,I.ALSETH,M.BJORAS,B.DALHUS REVDAT 1 17-APR-13 4B20 0 JRNL AUTH I.ROSNES,A.D.ROWE,E.S.VIK,R.J.FORSTROM,I.ALSETH,M.BJORAS, JRNL AUTH 2 B.DALHUS JRNL TITL STRUCTURAL BASIS OF DNA LOOP RECOGNITION BY ENDONUCLEASE V. JRNL REF STRUCTURE V. 21 257 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23313664 JRNL DOI 10.1016/J.STR.2012.12.007 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.0 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 17361 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.2274 REMARK 3 FREE R VALUE : 0.2906 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.3 REMARK 3 FREE R VALUE TEST SET COUNT : 843 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.85 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1283 REMARK 3 BIN R VALUE (WORKING SET) : 0.41 REMARK 3 BIN FREE R VALUE : 0.35 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.7 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 63 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3580 REMARK 3 NUCLEIC ACID ATOMS : 629 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.6 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -33.456 REMARK 3 B22 (A**2) : 28.833 REMARK 3 B33 (A**2) : 4.623 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.68 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.59 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.0073 REMARK 3 BOND ANGLES (DEGREES) : 1.349 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.45 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.204 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.27 ; 1.5 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.18 ; 2.0 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.74 ; 2.0 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.80 ; 2.5 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.330552 REMARK 3 BSOL : 41.4369 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:INOSIN.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : INOSIN.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CNS_TOPPAR:ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4B20 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUL-12. REMARK 100 THE PDBE ID CODE IS EBI-53330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD(MX-225) REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19328 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.75 REMARK 200 RESOLUTION RANGE LOW (A) : 60.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.9 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.60 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.5 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.61550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.68500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 97.49650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.61550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.68500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 97.49650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.61550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 67.68500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 97.49650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.61550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 67.68500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 97.49650 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 APPLY THE FOLLOWING TO CHAINS: A, D, 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, G, F 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, 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 BIOMT1 2 -1.000000 0.000000 0.000000 55.23100 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, G, F 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 BIOMT1 2 -1.000000 0.000000 0.000000 55.23100 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 270.74000 REMARK 350 BIOMT3 2 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 PHE A 225 REMARK 465 PHE B 225 REMARK 465 DG C 1 REMARK 465 DC D 17 REMARK 465 DG F 1 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 LEU A 224 CA C O CB CG CD1 CD2 REMARK 470 LEU B 224 CA C O CB CG CD1 CD2 REMARK 470 DC C 2 P OP1 OP2 REMARK 470 DC F 2 P OP1 OP2 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 DA D 8 OP3 DA D 8 P -0.078 REMARK 500 DA G 8 OP3 DA G 8 P -0.076 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 TYR A 3 -176.91 -178.82 REMARK 500 HIS A 7 -172.77 -177.52 REMARK 500 PRO A 13 -49.42 -23.93 REMARK 500 GLU A 68 147.03 -171.57 REMARK 500 GLU A 72 115.38 -172.81 REMARK 500 PRO A 82 127.98 -38.60 REMARK 500 GLU A 131 67.68 32.70 REMARK 500 LEU A 142 -50.45 -127.34 REMARK 500 ASP A 151 34.75 -91.89 REMARK 500 ARG A 153 -25.19 -23.98 REMARK 500 VAL A 189 -70.16 -55.21 REMARK 500 LYS A 222 -100.38 -142.74 REMARK 500 LEU B 67 -42.17 -142.87 REMARK 500 GLU B 72 111.09 -176.99 REMARK 500 LEU B 120 83.76 -164.56 REMARK 500 ARG B 153 149.80 -39.42 REMARK 500 CYS B 154 28.84 49.74 REMARK 500 LYS B 222 77.37 -114.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG C 7 0.08 SIDE CHAIN REMARK 500 DG F 7 0.06 SIDE CHAIN 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 A1224 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 43 OD1 REMARK 620 2 ASP A 110 OD2 77.8 REMARK 620 3 DG C 7 O3' 121.2 92.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1224 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 43 OD1 REMARK 620 2 ASP B 110 OD2 104.0 REMARK 620 3 DG F 7 O3' 169.8 80.1 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 A1224 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1224 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W35 RELATED DB: PDB REMARK 900 STRUCTURES OF ENDONUCLEASE V WITH DNA REVEAL INITIATION REMARK 900 OF DEAMINATED ADENINE REPAIR REMARK 900 RELATED ID: 2W36 RELATED DB: PDB REMARK 900 STRUCTURES OF ENDONUCLEASE V WITH DNA REVEAL INITIATION REMARK 900 OF DEAMINATED ADENINE REPAIR DBREF 4B20 A 1 225 UNP Q9X2H9 NFI_THEMA 1 225 DBREF 4B20 B 1 225 UNP Q9X2H9 NFI_THEMA 1 225 DBREF 4B20 C 1 7 PDB 4B20 4B20 1 7 DBREF 4B20 D 8 17 PDB 4B20 4B20 8 17 DBREF 4B20 F 1 7 PDB 4B20 4B20 1 7 DBREF 4B20 G 8 17 PDB 4B20 4B20 8 17 SEQRES 1 A 225 MET ASP TYR ARG GLN LEU HIS ARG TRP ASP LEU PRO PRO SEQRES 2 A 225 GLU GLU ALA ILE LYS VAL GLN ASN GLU LEU ARG LYS LYS SEQRES 3 A 225 ILE LYS LEU THR PRO TYR GLU GLY GLU PRO GLU TYR VAL SEQRES 4 A 225 ALA GLY VAL ASP LEU SER PHE PRO GLY LYS GLU GLU GLY SEQRES 5 A 225 LEU ALA VAL ILE VAL VAL LEU GLU TYR PRO SER PHE LYS SEQRES 6 A 225 ILE LEU GLU VAL VAL SER GLU ARG GLY GLU ILE THR PHE SEQRES 7 A 225 PRO TYR ILE PRO GLY LEU LEU ALA PHE ARG GLU GLY PRO SEQRES 8 A 225 LEU PHE LEU LYS ALA TRP GLU LYS LEU ARG THR LYS PRO SEQRES 9 A 225 ASP VAL VAL VAL PHE ASP GLY GLN GLY LEU ALA HIS PRO SEQRES 10 A 225 ARG LYS LEU GLY ILE ALA SER HIS MET GLY LEU PHE ILE SEQRES 11 A 225 GLU ILE PRO THR ILE GLY VAL ALA LYS SER ARG LEU TYR SEQRES 12 A 225 GLY THR PHE LYS MET PRO GLU ASP LYS ARG CYS SER TRP SEQRES 13 A 225 SER TYR LEU TYR ASP GLY GLU GLU ILE ILE GLY CYS VAL SEQRES 14 A 225 ILE ARG THR LYS GLU GLY SER ALA PRO ILE PHE VAL SER SEQRES 15 A 225 PRO GLY HIS LEU MET ASP VAL GLU SER SER LYS ARG LEU SEQRES 16 A 225 ILE LYS ALA PHE THR LEU PRO GLY ARG ARG ILE PRO GLU SEQRES 17 A 225 PRO THR ARG LEU ALA HIS ILE TYR THR GLN ARG LEU LYS SEQRES 18 A 225 LYS GLY LEU PHE SEQRES 1 B 225 MET ASP TYR ARG GLN LEU HIS ARG TRP ASP LEU PRO PRO SEQRES 2 B 225 GLU GLU ALA ILE LYS VAL GLN ASN GLU LEU ARG LYS LYS SEQRES 3 B 225 ILE LYS LEU THR PRO TYR GLU GLY GLU PRO GLU TYR VAL SEQRES 4 B 225 ALA GLY VAL ASP LEU SER PHE PRO GLY LYS GLU GLU GLY SEQRES 5 B 225 LEU ALA VAL ILE VAL VAL LEU GLU TYR PRO SER PHE LYS SEQRES 6 B 225 ILE LEU GLU VAL VAL SER GLU ARG GLY GLU ILE THR PHE SEQRES 7 B 225 PRO TYR ILE PRO GLY LEU LEU ALA PHE ARG GLU GLY PRO SEQRES 8 B 225 LEU PHE LEU LYS ALA TRP GLU LYS LEU ARG THR LYS PRO SEQRES 9 B 225 ASP VAL VAL VAL PHE ASP GLY GLN GLY LEU ALA HIS PRO SEQRES 10 B 225 ARG LYS LEU GLY ILE ALA SER HIS MET GLY LEU PHE ILE SEQRES 11 B 225 GLU ILE PRO THR ILE GLY VAL ALA LYS SER ARG LEU TYR SEQRES 12 B 225 GLY THR PHE LYS MET PRO GLU ASP LYS ARG CYS SER TRP SEQRES 13 B 225 SER TYR LEU TYR ASP GLY GLU GLU ILE ILE GLY CYS VAL SEQRES 14 B 225 ILE ARG THR LYS GLU GLY SER ALA PRO ILE PHE VAL SER SEQRES 15 B 225 PRO GLY HIS LEU MET ASP VAL GLU SER SER LYS ARG LEU SEQRES 16 B 225 ILE LYS ALA PHE THR LEU PRO GLY ARG ARG ILE PRO GLU SEQRES 17 B 225 PRO THR ARG LEU ALA HIS ILE TYR THR GLN ARG LEU LYS SEQRES 18 B 225 LYS GLY LEU PHE SEQRES 1 C 7 DG DC DG DA DC DA DG SEQRES 1 D 10 DA DT DC DT DT DG DT DC DG DC SEQRES 1 F 7 DG DC DG DA DC DA DG SEQRES 1 G 10 DA DT DC DT DT DG DT DC DG DC HET MG A1224 1 HET MG B1224 1 HETNAM MG MAGNESIUM ION FORMUL 7 MG 2(MG 2+) FORMUL 8 HOH *79(H2 O) HELIX 1 1 PRO A 12 ARG A 24 1 13 HELIX 2 2 LYS A 25 ILE A 27 5 3 HELIX 3 3 LEU A 85 GLU A 98 1 14 HELIX 4 4 GLY A 121 GLU A 131 1 11 HELIX 5 5 ASP A 188 PHE A 199 1 12 HELIX 6 6 PRO A 207 LEU A 220 1 14 HELIX 7 7 PRO B 12 ARG B 24 1 13 HELIX 8 8 LYS B 25 ILE B 27 5 3 HELIX 9 9 LEU B 85 LEU B 100 1 16 HELIX 10 10 GLY B 121 GLU B 131 1 11 HELIX 11 11 ASP B 188 PHE B 199 1 12 HELIX 12 12 PRO B 207 LEU B 220 1 14 SHEET 1 AA 8 LYS A 65 GLU A 75 0 SHEET 2 AA 8 GLU A 51 GLU A 60 -1 O GLY A 52 N GLY A 74 SHEET 3 AA 8 TYR A 38 GLY A 48 -1 O VAL A 39 N LEU A 59 SHEET 4 AA 8 VAL A 106 PHE A 109 1 O VAL A 106 N ALA A 40 SHEET 5 AA 8 THR A 134 ALA A 138 1 O ILE A 135 N PHE A 109 SHEET 6 AA 8 ILE A 179 PRO A 183 -1 O PHE A 180 N ALA A 138 SHEET 7 AA 8 GLU A 164 ILE A 170 -1 O CYS A 168 N VAL A 181 SHEET 8 AA 8 TRP A 156 ASP A 161 -1 O SER A 157 N VAL A 169 SHEET 1 BA 8 ILE B 66 GLU B 75 0 SHEET 2 BA 8 GLU B 51 GLU B 60 -1 O GLY B 52 N GLY B 74 SHEET 3 BA 8 TYR B 38 GLY B 48 -1 O VAL B 39 N LEU B 59 SHEET 4 BA 8 VAL B 106 ASP B 110 1 O VAL B 106 N ALA B 40 SHEET 5 BA 8 THR B 134 ALA B 138 1 O ILE B 135 N PHE B 109 SHEET 6 BA 8 ILE B 179 PRO B 183 -1 O PHE B 180 N ALA B 138 SHEET 7 BA 8 ILE B 165 ARG B 171 -1 O CYS B 168 N VAL B 181 SHEET 8 BA 8 SER B 155 TYR B 160 -1 O SER B 155 N ARG B 171 LINK MG MG A1224 OD1 ASP A 43 1555 1555 2.30 LINK MG MG A1224 OD2 ASP A 110 1555 1555 2.19 LINK MG MG A1224 O3' DG C 7 1555 1555 2.09 LINK MG MG B1224 OD2 ASP B 110 1555 1555 1.99 LINK MG MG B1224 O3' DG F 7 1555 1555 2.01 LINK MG MG B1224 OD1 ASP B 43 1555 1555 2.00 CISPEP 1 TYR A 61 PRO A 62 0 0.02 CISPEP 2 TYR B 61 PRO B 62 0 0.10 SITE 1 AC1 4 ASP A 43 ASP A 110 DG C 7 DA D 8 SITE 1 AC2 3 ASP B 43 ASP B 110 DG F 7 CRYST1 55.231 135.370 194.993 90.00 90.00 90.00 I 2 2 2 16 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 0.018106 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005128 0.00000