HEADER HYDROLASE/DNA 05-APR-13 4K1G TITLE STRUCTURE OF E. COLI NFO(ENDO IV)-H69A MUTANT BOUND TO A CLEAVED DNA TITLE 2 DUPLEX CONTAINING A ALPHADA:T BASEPAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE 4; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ENDODEOXYRIBONUCLEASE IV, ENDONUCLEASE IV; COMPND 5 EC: 3.1.21.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*CP*GP*TP*CP*C)-3'); COMPND 10 CHAIN: E, M; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)- COMPND 14 3'); COMPND 15 CHAIN: F, N; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3'); COMPND 19 CHAIN: H, O; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: NFO, B2159, JW2146; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 4; SOURCE 13 SYNTHETIC: YES KEYWDS DNA ENDONUCLEASE IV, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.MORERA,A.VIGOUROUX REVDAT 3 20-SEP-23 4K1G 1 REMARK SEQADV LINK REVDAT 2 12-MAR-14 4K1G 1 JRNL REVDAT 1 31-JUL-13 4K1G 0 JRNL AUTH A.MAZOUZI,A.VIGOUROUX,B.AIKESHEV,P.J.BROOKS,M.K.SAPARBAEV, JRNL AUTH 2 S.MORERA,A.A.ISHCHENKO JRNL TITL INSIGHT INTO MECHANISMS OF 3'-5' EXONUCLEASE ACTIVITY AND JRNL TITL 2 REMOVAL OF BULKY 8,5'-CYCLOPURINE ADDUCTS BY JRNL TITL 3 APURINIC/APYRIMIDINIC ENDONUCLEASES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 E3071 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23898172 JRNL DOI 10.1073/PNAS.1305281110 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 70976 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 + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3550 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.95 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.13 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 4628 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2201 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4396 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE : 0.2423 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.01 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 232 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 : 4366 REMARK 3 NUCLEIC ACID ATOMS : 1182 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.80840 REMARK 3 B22 (A**2) : -3.45760 REMARK 3 B33 (A**2) : -3.35070 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.199 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.122 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5827 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 8129 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2248 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 122 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 728 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5827 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 779 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 6808 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.12 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.31 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.98 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4K1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078770. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 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 : SIIII REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71003 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 41.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: PDB ENTRY 2NQJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS HCL, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 56.23000 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 56.23000 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 58.97500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.33000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 58.97500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.33000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.23000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 58.97500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.33000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.23000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 58.97500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 68.33000 REMARK 290 SMTRY3 8 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 300 REMARK: AUTHORS STATE THAT THE QUATERNARY STRUCTURE IS A PROTEIN REMARK 300 MONOMER-DOUBLE STRANDED DNA COMPLEX. ONE OF THE DNA STRANDS IS REMARK 300 CLEAVED BETWEEN THE BASE 306 AND THE BASE 307. 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: 4080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -118.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, F, H 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, M, N, O 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 VAL A 284 REMARK 465 ALA A 285 REMARK 465 THR B 280 REMARK 465 GLU B 281 REMARK 465 LYS B 282 REMARK 465 ALA B 283 REMARK 465 VAL B 284 REMARK 465 ALA B 285 REMARK 465 DC N 331 REMARK 465 DG O 315 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 H 307 P DA H 307 OP3 -0.118 REMARK 500 DC M 306 O3' DC M 306 C3' -0.046 REMARK 500 DA O 307 P DA O 307 OP3 -0.124 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 DG E 301 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG E 301 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DC E 305 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC E 306 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC F 331 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT F 333 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 DT F 333 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 DC F 334 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 DT F 336 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT F 339 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 DG F 341 C3' - O3' - P ANGL. DEV. = 11.9 DEGREES REMARK 500 DC F 343 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC F 345 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA H 307 C1' - O4' - C4' ANGL. DEV. = -15.2 DEGREES REMARK 500 DA H 307 C3' - C2' - C1' ANGL. DEV. = -13.7 DEGREES REMARK 500 DA H 307 O4' - C1' - N9 ANGL. DEV. = 19.5 DEGREES REMARK 500 DC H 311 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA H 313 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC H 314 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG M 301 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DC M 305 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC M 306 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG N 332 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG N 332 N9 - C1' - C2' ANGL. DEV. = 8.5 DEGREES REMARK 500 DG N 332 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG N 332 C3' - O3' - P ANGL. DEV. = 15.2 DEGREES REMARK 500 DT N 333 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC N 334 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT N 339 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DG N 341 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG N 341 C3' - O3' - P ANGL. DEV. = 12.9 DEGREES REMARK 500 DC N 343 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC N 343 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DC N 345 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA O 307 C1' - O4' - C4' ANGL. DEV. = -12.3 DEGREES REMARK 500 DA O 307 C3' - C2' - C1' ANGL. DEV. = -14.2 DEGREES REMARK 500 DA O 307 N9 - C1' - C2' ANGL. DEV. = 8.9 DEGREES REMARK 500 DA O 307 O4' - C1' - N9 ANGL. DEV. = 17.0 DEGREES REMARK 500 DA O 307 N9 - C4 - C5 ANGL. DEV. = -2.9 DEGREES REMARK 500 DA O 307 N1 - C6 - N6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA O 307 C8 - N9 - C1' ANGL. DEV. = -11.9 DEGREES REMARK 500 DA O 307 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 DC O 308 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC O 314 O4' - C1' - N1 ANGL. DEV. = 3.3 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 LEU A 190 11.13 -143.84 REMARK 500 LEU B 190 14.18 -140.54 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 145 OE2 REMARK 620 2 ASP A 179 OD1 91.9 REMARK 620 3 HIS A 216 ND1 92.1 124.9 REMARK 620 4 GLU A 261 OE1 176.2 89.7 89.8 REMARK 620 5 HOH A 508 O 82.2 135.1 99.8 94.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 182 NE2 REMARK 620 2 ASP A 229 OD1 102.1 REMARK 620 3 ASP A 229 OD2 89.4 55.2 REMARK 620 4 HIS A 231 NE2 124.2 94.9 140.9 REMARK 620 5 DC E 306 OP2 98.6 141.3 93.0 100.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 251 OD2 REMARK 620 2 ASP A 254 OD1 122.9 REMARK 620 3 HOH A 401 O 111.6 101.1 REMARK 620 4 ASP B 89 OD2 105.3 112.7 101.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 145 OE2 REMARK 620 2 ASP B 179 OD1 93.1 REMARK 620 3 HIS B 216 ND1 97.1 127.8 REMARK 620 4 GLU B 261 OE1 166.9 90.0 91.0 REMARK 620 5 HOH B 471 O 84.5 134.5 97.4 84.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 182 NE2 REMARK 620 2 ASP B 229 OD1 94.5 REMARK 620 3 ASP B 229 OD2 90.3 55.5 REMARK 620 4 HIS B 231 NE2 121.0 99.7 143.2 REMARK 620 5 DC M 306 OP2 105.0 143.5 93.3 96.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NQJ RELATED DB: PDB REMARK 900 RELATED ID: 2NQ9 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHAINS E AND H, AND CHAINS M AND O ARE FORM THE SAME DNA STRAND REMARK 999 WHICH IS CLEAVED BETWEEN THE BASE 306 AND THE BASE 307. DBREF 4K1G A 1 285 UNP P0A6C1 END4_ECOLI 1 285 DBREF 4K1G B 1 285 UNP P0A6C1 END4_ECOLI 1 285 DBREF 4K1G E 301 306 PDB 4K1G 4K1G 301 306 DBREF 4K1G M 301 306 PDB 4K1G 4K1G 301 306 DBREF 4K1G H 307 315 PDB 4K1G 4K1G 307 315 DBREF 4K1G O 307 315 PDB 4K1G 4K1G 307 315 DBREF 4K1G F 331 345 PDB 4K1G 4K1G 331 345 DBREF 4K1G N 331 345 PDB 4K1G 4K1G 331 345 SEQADV 4K1G ALA A 69 UNP P0A6C1 HIS 69 ENGINEERED MUTATION SEQADV 4K1G ALA B 69 UNP P0A6C1 HIS 69 ENGINEERED MUTATION SEQRES 1 A 285 MET LYS TYR ILE GLY ALA HIS VAL SER ALA ALA GLY GLY SEQRES 2 A 285 LEU ALA ASN ALA ALA ILE ARG ALA ALA GLU ILE ASP ALA SEQRES 3 A 285 THR ALA PHE ALA LEU PHE THR LYS ASN GLN ARG GLN TRP SEQRES 4 A 285 ARG ALA ALA PRO LEU THR THR GLN THR ILE ASP GLU PHE SEQRES 5 A 285 LYS ALA ALA CYS GLU LYS TYR HIS TYR THR SER ALA GLN SEQRES 6 A 285 ILE LEU PRO ALA ASP SER TYR LEU ILE ASN LEU GLY HIS SEQRES 7 A 285 PRO VAL THR GLU ALA LEU GLU LYS SER ARG ASP ALA PHE SEQRES 8 A 285 ILE ASP GLU MET GLN ARG CYS GLU GLN LEU GLY LEU SER SEQRES 9 A 285 LEU LEU ASN PHE HIS PRO GLY SER HIS LEU MET GLN ILE SEQRES 10 A 285 SER GLU GLU ASP CYS LEU ALA ARG ILE ALA GLU SER ILE SEQRES 11 A 285 ASN ILE ALA LEU ASP LYS THR GLN GLY VAL THR ALA VAL SEQRES 12 A 285 ILE GLU ASN THR ALA GLY GLN GLY SER ASN LEU GLY PHE SEQRES 13 A 285 LYS PHE GLU HIS LEU ALA ALA ILE ILE ASP GLY VAL GLU SEQRES 14 A 285 ASP LYS SER ARG VAL GLY VAL CYS ILE ASP THR CYS HIS SEQRES 15 A 285 ALA PHE ALA ALA GLY TYR ASP LEU ARG THR PRO ALA GLU SEQRES 16 A 285 CYS GLU LYS THR PHE ALA ASP PHE ALA ARG THR VAL GLY SEQRES 17 A 285 PHE LYS TYR LEU ARG GLY MET HIS LEU ASN ASP ALA LYS SEQRES 18 A 285 SER THR PHE GLY SER ARG VAL ASP ARG HIS HIS SER LEU SEQRES 19 A 285 GLY GLU GLY ASN ILE GLY HIS ASP ALA PHE ARG TRP ILE SEQRES 20 A 285 MET GLN ASP ASP ARG PHE ASP GLY ILE PRO LEU ILE LEU SEQRES 21 A 285 GLU THR ILE ASN PRO ASP ILE TRP ALA GLU GLU ILE ALA SEQRES 22 A 285 TRP LEU LYS ALA GLN GLN THR GLU LYS ALA VAL ALA SEQRES 1 B 285 MET LYS TYR ILE GLY ALA HIS VAL SER ALA ALA GLY GLY SEQRES 2 B 285 LEU ALA ASN ALA ALA ILE ARG ALA ALA GLU ILE ASP ALA SEQRES 3 B 285 THR ALA PHE ALA LEU PHE THR LYS ASN GLN ARG GLN TRP SEQRES 4 B 285 ARG ALA ALA PRO LEU THR THR GLN THR ILE ASP GLU PHE SEQRES 5 B 285 LYS ALA ALA CYS GLU LYS TYR HIS TYR THR SER ALA GLN SEQRES 6 B 285 ILE LEU PRO ALA ASP SER TYR LEU ILE ASN LEU GLY HIS SEQRES 7 B 285 PRO VAL THR GLU ALA LEU GLU LYS SER ARG ASP ALA PHE SEQRES 8 B 285 ILE ASP GLU MET GLN ARG CYS GLU GLN LEU GLY LEU SER SEQRES 9 B 285 LEU LEU ASN PHE HIS PRO GLY SER HIS LEU MET GLN ILE SEQRES 10 B 285 SER GLU GLU ASP CYS LEU ALA ARG ILE ALA GLU SER ILE SEQRES 11 B 285 ASN ILE ALA LEU ASP LYS THR GLN GLY VAL THR ALA VAL SEQRES 12 B 285 ILE GLU ASN THR ALA GLY GLN GLY SER ASN LEU GLY PHE SEQRES 13 B 285 LYS PHE GLU HIS LEU ALA ALA ILE ILE ASP GLY VAL GLU SEQRES 14 B 285 ASP LYS SER ARG VAL GLY VAL CYS ILE ASP THR CYS HIS SEQRES 15 B 285 ALA PHE ALA ALA GLY TYR ASP LEU ARG THR PRO ALA GLU SEQRES 16 B 285 CYS GLU LYS THR PHE ALA ASP PHE ALA ARG THR VAL GLY SEQRES 17 B 285 PHE LYS TYR LEU ARG GLY MET HIS LEU ASN ASP ALA LYS SEQRES 18 B 285 SER THR PHE GLY SER ARG VAL ASP ARG HIS HIS SER LEU SEQRES 19 B 285 GLY GLU GLY ASN ILE GLY HIS ASP ALA PHE ARG TRP ILE SEQRES 20 B 285 MET GLN ASP ASP ARG PHE ASP GLY ILE PRO LEU ILE LEU SEQRES 21 B 285 GLU THR ILE ASN PRO ASP ILE TRP ALA GLU GLU ILE ALA SEQRES 22 B 285 TRP LEU LYS ALA GLN GLN THR GLU LYS ALA VAL ALA SEQRES 1 E 6 DG DC DG DT DC DC SEQRES 1 F 15 DC DG DT DC DG DT DC DG DT DG DG DA DC SEQRES 2 F 15 DG DC SEQRES 1 H 9 DA DC DG DA DC DG DA DC DG SEQRES 1 M 6 DG DC DG DT DC DC SEQRES 1 N 15 DC DG DT DC DG DT DC DG DT DG DG DA DC SEQRES 2 N 15 DG DC SEQRES 1 O 9 DA DC DG DA DC DG DA DC DG HET ZN A 301 1 HET ZN A 302 1 HET ZN A 303 1 HET PEG A 304 7 HET ZN B 301 1 HET ZN B 302 1 HET PEG B 303 7 HETNAM ZN ZINC ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 9 ZN 5(ZN 2+) FORMUL 12 PEG 2(C4 H10 O3) FORMUL 16 HOH *610(H2 O) HELIX 1 1 LEU A 14 ILE A 24 1 11 HELIX 2 2 THR A 45 TYR A 59 1 15 HELIX 3 3 THR A 62 ILE A 66 5 5 HELIX 4 4 VAL A 80 LEU A 101 1 22 HELIX 5 5 SER A 118 THR A 137 1 20 HELIX 6 6 LYS A 157 GLY A 167 1 11 HELIX 7 7 ASP A 170 SER A 172 5 3 HELIX 8 8 THR A 180 ALA A 186 1 7 HELIX 9 9 THR A 192 VAL A 207 1 16 HELIX 10 10 GLY A 208 LYS A 210 5 3 HELIX 11 11 HIS A 241 GLN A 249 1 9 HELIX 12 12 ASP A 250 ASP A 254 5 5 HELIX 13 13 ASN A 264 ASP A 266 5 3 HELIX 14 14 ILE A 267 GLN A 279 1 13 HELIX 15 15 LEU B 14 ILE B 24 1 11 HELIX 16 16 THR B 45 TYR B 59 1 15 HELIX 17 17 THR B 62 ILE B 66 5 5 HELIX 18 18 VAL B 80 LEU B 101 1 22 HELIX 19 19 SER B 118 LYS B 136 1 19 HELIX 20 20 LYS B 157 VAL B 168 1 12 HELIX 21 21 ASP B 170 SER B 172 5 3 HELIX 22 22 THR B 180 ALA B 186 1 7 HELIX 23 23 THR B 192 VAL B 207 1 16 HELIX 24 24 GLY B 208 LYS B 210 5 3 HELIX 25 25 HIS B 241 GLN B 249 1 9 HELIX 26 26 ASP B 250 ASP B 254 5 5 HELIX 27 27 ASN B 264 ASP B 266 5 3 HELIX 28 28 ILE B 267 GLN B 279 1 13 SHEET 1 A 7 ALA A 28 ALA A 30 0 SHEET 2 A 7 TYR A 3 HIS A 7 1 N ALA A 6 O ALA A 30 SHEET 3 A 7 PRO A 257 LEU A 260 1 O LEU A 258 N GLY A 5 SHEET 4 A 7 LEU A 212 LEU A 217 1 N MET A 215 O ILE A 259 SHEET 5 A 7 VAL A 174 ASP A 179 1 N VAL A 176 O ARG A 213 SHEET 6 A 7 THR A 141 GLU A 145 1 N ILE A 144 O GLY A 175 SHEET 7 A 7 LEU A 105 PHE A 108 1 N PHE A 108 O GLU A 145 SHEET 1 B 2 ASP A 219 ALA A 220 0 SHEET 2 B 2 HIS A 231 HIS A 232 -1 O HIS A 232 N ASP A 219 SHEET 1 C 7 ALA B 28 ALA B 30 0 SHEET 2 C 7 TYR B 3 HIS B 7 1 N ALA B 6 O ALA B 30 SHEET 3 C 7 PRO B 257 LEU B 260 1 O LEU B 258 N GLY B 5 SHEET 4 C 7 LEU B 212 LEU B 217 1 N MET B 215 O ILE B 259 SHEET 5 C 7 VAL B 174 ASP B 179 1 N VAL B 176 O ARG B 213 SHEET 6 C 7 THR B 141 GLU B 145 1 N ILE B 144 O GLY B 175 SHEET 7 C 7 LEU B 105 PHE B 108 1 N LEU B 106 O VAL B 143 SHEET 1 D 2 ASP B 219 ALA B 220 0 SHEET 2 D 2 HIS B 231 HIS B 232 -1 O HIS B 232 N ASP B 219 LINK OE2 GLU A 145 ZN ZN A 301 1555 1555 2.06 LINK OD1 ASP A 179 ZN ZN A 301 1555 1555 2.05 LINK NE2 HIS A 182 ZN ZN A 302 1555 1555 2.02 LINK ND1 HIS A 216 ZN ZN A 301 1555 1555 2.15 LINK OD1 ASP A 229 ZN ZN A 302 1555 1555 2.08 LINK OD2 ASP A 229 ZN ZN A 302 1555 1555 2.52 LINK NE2 HIS A 231 ZN ZN A 302 1555 1555 1.99 LINK OD2 ASP A 251 ZN ZN A 303 1555 1555 1.96 LINK OD1 ASP A 254 ZN ZN A 303 1555 1555 1.90 LINK OE1 GLU A 261 ZN ZN A 301 1555 1555 2.12 LINK ZN ZN A 301 O HOH A 508 1555 1555 1.95 LINK ZN ZN A 302 OP2 DC E 306 1555 1555 1.91 LINK ZN ZN A 303 O HOH A 401 1555 1555 2.26 LINK ZN ZN A 303 OD2 ASP B 89 1555 1555 2.20 LINK OE2 GLU B 145 ZN ZN B 301 1555 1555 2.09 LINK OD1 ASP B 179 ZN ZN B 301 1555 1555 1.95 LINK NE2 HIS B 182 ZN ZN B 302 1555 1555 1.96 LINK ND1 HIS B 216 ZN ZN B 301 1555 1555 1.97 LINK OD1 ASP B 229 ZN ZN B 302 1555 1555 1.93 LINK OD2 ASP B 229 ZN ZN B 302 1555 1555 2.56 LINK NE2 HIS B 231 ZN ZN B 302 1555 1555 2.09 LINK OE1 GLU B 261 ZN ZN B 301 1555 1555 2.28 LINK ZN ZN B 301 O HOH B 471 1555 1555 1.98 LINK ZN ZN B 302 OP2 DC M 306 1555 1555 1.89 SITE 1 AC1 5 GLU A 145 ASP A 179 HIS A 216 GLU A 261 SITE 2 AC1 5 HOH A 508 SITE 1 AC2 5 HIS A 182 ASP A 229 HIS A 231 DC E 305 SITE 2 AC2 5 DC E 306 SITE 1 AC3 4 ASP A 251 ASP A 254 HOH A 401 ASP B 89 SITE 1 AC4 6 ALA A 204 ARG A 205 THR A 206 VAL A 207 SITE 2 AC4 6 LYS A 210 GLN B 138 SITE 1 AC5 5 GLU B 145 ASP B 179 HIS B 216 GLU B 261 SITE 2 AC5 5 HOH B 471 SITE 1 AC6 4 HIS B 182 ASP B 229 HIS B 231 DC M 306 SITE 1 AC7 4 ALA B 204 ARG B 205 VAL B 207 LYS B 210 CRYST1 117.950 136.660 112.460 90.00 90.00 90.00 C 2 2 21 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 0.008478 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007317 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008892 0.00000