2NQJ - Header Asymmetric Unit

HEADER HYDROLASE 31-OCT-06 2NQJ

TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV (ENDO TITLE 2 IV) E261Q MUTANT BOUND TO DAMAGED DNA

COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*CP*CP*(3DR) COMPND 3 P*CP*GP*AP*CP*GP*AP*CP*G)-3'; COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'- COMPND 8 D(*CP*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)-3'; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ENDONUCLEASE 4; COMPND 13 CHAIN: A, B; COMPND 14 SYNONYM: ENDONUCLEASE IV, ENDODEOXYRIBONUCLEASE IV; COMPND 15 EC: 3.1.21.2; COMPND 16 ENGINEERED: YES; COMPND 17 MUTATION: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562; SOURCE 8 STRAIN: NFO- STRAIN BW565DE3; SOURCE 9 GENE: NFO; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PET24

KEYWDS TIM_BARREL, TRINUCLEAR ZINC SITE, HYDROLASE

EXPDTA X-RAY DIFFRACTION

AUTHOR E.D.GARCIN-HOSFIELD,D.J.HOSFIELD,J.A.TAINER

REVDAT 4 24-FEB-09 2NQJ 1 VERSN REVDAT 3 20-MAY-08 2NQJ 1 JRNL REVDAT 2 22-APR-08 2NQJ 1 JRNL REVDAT 1 06-NOV-07 2NQJ 0

JRNL AUTH E.D.GARCIN,D.J.HOSFIELD,S.A.DESAI,B.J.HAAS, JRNL AUTH 2 M.BJORAS,R.P.CUNNINGHAM,J.A.TAINER JRNL TITL DNA APURINIC-APYRIMIDINIC SITE BINDING AND JRNL TITL 2 EXCISION BY ENDONUCLEASE IV. JRNL REF NAT.STRUCT.MOL.BIOL. V. 15 515 2008 JRNL REFN ISSN 1545-9993 JRNL PMID 18408731 JRNL DOI 10.1038/NSMB.1414

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 24906 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1252 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 4346 REMARK 3 NUCLEIC ACID ATOMS : 601 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 325 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -19.74400 REMARK 3 B22 (A**2) : 13.22100 REMARK 3 B33 (A**2) : 6.52300 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 50.96 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 : PARAM19X.ZN REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 2NQJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-06. REMARK 100 THE RCSB ID CODE IS RCSB040180.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24943 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: EPMR REMARK 200 STARTING MODEL: 1QTW REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% MPEG-2000, 0.1M HEPES PH 7, REMARK 280 0.4M SODIUM ACETATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.80000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.80000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.10000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL

REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 300 ALTHOUGH CHAIN B COULD BE MOVED BY A SYMMETRY OPERATION, REMARK 300 THE COMPLEX FORMED BY CHAIN B WITH CHAIN C AND D IS NOT REMARK 300 BIOLOGICALLY RELEVANT.

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: C, D, A 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 THR A 280 REMARK 465 GLU A 281 REMARK 465 LYS A 282 REMARK 465 ALA A 283 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 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 HIS A 60 40.07 72.27 REMARK 500 ARG A 191 0.09 -59.10 REMARK 500 LEU B 114 16.58 56.50 REMARK 500 REMARK 500 REMARK: NULL

REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 355 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH D 350 DISTANCE = 9.24 ANGSTROMS REMARK 525 HOH D 352 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 369 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH C 334 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH A 408 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 433 DISTANCE = 11.82 ANGSTROMS REMARK 525 HOH A 435 DISTANCE = 7.93 ANGSTROMS REMARK 525 HOH A 445 DISTANCE = 7.14 ANGSTROMS REMARK 525 HOH B 528 DISTANCE = 5.13 ANGSTROMS

REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 351 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 3DR C 307 OP1 REMARK 620 2 HIS A 69 NE2 102.9 REMARK 620 3 HIS A 109 NE2 84.2 87.2 REMARK 620 4 GLU A 145 OE2 148.4 107.7 89.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 352 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 145 OE1 REMARK 620 2 ASP A 179 OD1 100.9 REMARK 620 3 HIS A 216 ND1 83.8 108.9 REMARK 620 4 GLN A 261 OE1 164.4 94.4 88.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 353 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 182 NE2 REMARK 620 2 ASP A 229 OD2 84.5 REMARK 620 3 HIS A 231 NE2 113.6 88.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 182 NE2 REMARK 620 2 ASP B 229 OD2 92.1 REMARK 620 3 HIS B 231 NE2 124.1 88.4 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 ZN A 351 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 352 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 353 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 403

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NQ9 RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF ESCHERICHIA COLI REMARK 900 ENDONUCLEASE IV (ENDO IV) Y72A MUTANT BOUND TO DAMAGED DNA REMARK 900 RELATED ID: 2NQH RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF ESCHERICHIA COLI REMARK 900 ENDONUCLEASE IV (ENDO IV) E261Q MUTANT

DBREF 2NQJ A 1 285 UNP P0A6C1 END4_ECOLI 1 285 DBREF 2NQJ B 1 285 UNP P0A6C1 END4_ECOLI 1 285 DBREF 2NQJ C 301 315 PDB 2NQJ 2NQJ 301 315 DBREF 2NQJ D 331 345 PDB 2NQJ 2NQJ 331 345

SEQADV 2NQJ GLN A 261 UNP P0A6C1 GLU 261 ENGINEERED SEQADV 2NQJ GLN B 261 UNP P0A6C1 GLU 261 ENGINEERED

SEQRES 1 C 15 DG DC DG DT DC DC 3DR DC DG DA DC DG DA SEQRES 2 C 15 DC DG SEQRES 1 D 15 DC DG DT DC DG DT DC DG DG DG DG DA DC SEQRES 2 D 15 DG DC 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 HIS 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 GLN 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 HIS 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 GLN 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

HET 3DR C 307 11 HET ZN A 351 1 HET ZN A 352 1 HET ZN A 353 1 HET ZN B 403 1

HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM ZN ZINC ION

HETSYN 3DR ABASIC DIDEOXYRIBOSE

FORMUL 1 3DR C5 H11 O6 P FORMUL 5 ZN 4(ZN 2+) FORMUL 9 HOH *325(H2 O)

HELIX 1 1 GLY A 13 ILE A 24 1 12 HELIX 2 2 THR A 45 HIS A 60 1 16 HELIX 3 3 THR A 62 ALA A 64 5 3 HELIX 4 4 VAL A 80 GLY A 102 1 23 HELIX 5 5 SER A 118 LYS A 136 1 19 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 GLY A 187 1 8 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 GLY A 240 GLN A 249 1 10 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 278 1 12 HELIX 15 15 GLY B 13 ILE B 24 1 12 HELIX 16 16 THR B 45 TYR B 59 1 15 HELIX 17 17 THR B 62 ALA B 64 5 3 HELIX 18 18 VAL B 80 GLY B 102 1 23 HELIX 19 19 SER B 118 LYS B 136 1 19 HELIX 20 20 LYS B 157 GLY B 167 1 11 HELIX 21 21 ASP B 170 SER B 172 5 3 HELIX 22 22 THR B 180 GLY B 187 1 8 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 GLY B 240 ASP B 250 1 11 HELIX 26 26 ASP B 251 ASP B 254 5 4 HELIX 27 27 ASN B 264 ASP B 266 5 3 HELIX 28 28 ILE B 267 GLN B 278 1 12

SHEET 1 A 9 TYR A 3 HIS A 7 0 SHEET 2 A 9 ALA A 28 PHE A 32 1 O ALA A 30 N ALA A 6 SHEET 3 A 9 ILE A 66 HIS A 69 1 O HIS A 69 N LEU A 31 SHEET 4 A 9 LEU A 105 PHE A 108 1 O ASN A 107 N PRO A 68 SHEET 5 A 9 THR A 141 GLU A 145 1 O VAL A 143 N LEU A 106 SHEET 6 A 9 VAL A 174 ASP A 179 1 O GLY A 175 N ALA A 142 SHEET 7 A 9 LEU A 212 LEU A 217 1 O ARG A 213 N VAL A 176 SHEET 8 A 9 PRO A 257 LEU A 260 1 O ILE A 259 N MET A 215 SHEET 9 A 9 TYR A 3 HIS A 7 1 N TYR A 3 O LEU A 258 SHEET 1 B 2 GLY A 111 SER A 112 0 SHEET 2 B 2 ASN A 153 LEU A 154 -1 O LEU A 154 N GLY A 111 SHEET 1 C 2 ASP A 219 ALA A 220 0 SHEET 2 C 2 HIS A 231 HIS A 232 -1 O HIS A 232 N ASP A 219 SHEET 1 D 9 TYR B 3 HIS B 7 0 SHEET 2 D 9 ALA B 28 PHE B 32 1 N ALA B 30 O ALA B 6 SHEET 3 D 9 ILE B 66 HIS B 69 1 O HIS B 69 N LEU B 31 SHEET 4 D 9 LEU B 105 PHE B 108 1 O ASN B 107 N PRO B 68 SHEET 5 D 9 THR B 141 GLU B 145 1 O VAL B 143 N LEU B 106 SHEET 6 D 9 VAL B 174 ASP B 179 1 O GLY B 175 N ILE B 144 SHEET 7 D 9 LEU B 212 LEU B 217 1 O ARG B 213 N VAL B 176 SHEET 8 D 9 PRO B 257 LEU B 260 1 O ILE B 259 N MET B 215 SHEET 9 D 9 TYR B 3 HIS B 7 1 N HIS B 7 O LEU B 260 SHEET 1 E 2 ASP B 219 ALA B 220 0 SHEET 2 E 2 HIS B 231 HIS B 232 -1 O HIS B 232 N ASP B 219

LINK OP1 3DR C 307 ZN ZN A 351 1555 1555 2.36 LINK NE2 HIS A 69 ZN ZN A 351 1555 1555 2.19 LINK NE2 HIS A 109 ZN ZN A 351 1555 1555 2.17 LINK OE1 GLU A 145 ZN ZN A 352 1555 1555 2.36 LINK OE2 GLU A 145 ZN ZN A 351 1555 1555 2.11 LINK OD1 ASP A 179 ZN ZN A 352 1555 1555 2.36 LINK NE2 HIS A 182 ZN ZN A 353 1555 1555 2.22 LINK ND1 HIS A 216 ZN ZN A 352 1555 1555 2.33 LINK OD2 ASP A 229 ZN ZN A 353 1555 1555 2.34 LINK NE2 HIS A 231 ZN ZN A 353 1555 1555 2.03 LINK OE1 GLN A 261 ZN ZN A 352 1555 1555 2.30 LINK NE2 HIS B 182 ZN ZN B 403 1555 1555 2.09 LINK OD2 ASP B 229 ZN ZN B 403 1555 1555 2.30 LINK NE2 HIS B 231 ZN ZN B 403 1555 1555 2.03 LINK O3' DC C 306 P 3DR C 307 1555 1555 1.64 LINK O3' 3DR C 307 P DC C 308 1555 1555 1.61

SITE 1 AC1 5 HIS A 69 HIS A 109 GLU A 145 ZN A 352 SITE 2 AC1 5 3DR C 307 SITE 1 AC2 7 GLU A 145 ASP A 179 HIS A 182 HIS A 216 SITE 2 AC2 7 GLN A 261 ZN A 351 3DR C 307 SITE 1 AC3 5 HIS A 182 ASP A 229 HIS A 231 DC C 306 SITE 2 AC3 5 3DR C 307 SITE 1 AC4 4 HIS B 182 ASP B 229 HIS B 231 DG C 315

CRYST1 55.600 86.200 148.300 90.00 90.00 90.00 P 21 21 21 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 0.017986 0.000000 0.000000 0.00000

SCALE2 0.000000 0.011601 0.000000 0.00000

SCALE3 0.000000 0.000000 0.006743 0.00000