PDB Short entry for 1Q3B HEADER HYDROLASE 29-JUL-03 1Q3B TITLE CRYSTAL STRUCTURE OF THE DNA REPAIR ENZYME ENDONUCLEASE-VIII (NEI) TITLE 2 FROM E. COLI: THE R252A MUTANT AT 2.05 RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE VIII; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: NEI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET13A KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.GOLAN,D.O.ZHARKOV,H.FEINBERG,A.S.FERNANDES,E.I.ZAIKA,J.H.KYCIA, AUTHOR 2 A.P.GROLLMAN,G.SHOHAM REVDAT 6 16-AUG-23 1Q3B 1 REMARK REVDAT 5 27-OCT-21 1Q3B 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 1Q3B 1 VERSN REVDAT 3 24-FEB-09 1Q3B 1 VERSN REVDAT 2 20-SEP-05 1Q3B 1 JRNL REVDAT 1 03-AUG-04 1Q3B 0 JRNL AUTH G.GOLAN,D.O.ZHARKOV,H.FEINBERG,A.S.FERNANDES,E.I.ZAIKA, JRNL AUTH 2 J.H.KYCIA,A.P.GROLLMAN,G.SHOHAM JRNL TITL STRUCTURE OF THE UNCOMPLEXED DNA REPAIR ENZYME ENDONUCLEASE JRNL TITL 2 VIII INDICATES SIGNIFICANT INTERDOMAIN FLEXIBILITY. JRNL REF NUCLEIC ACIDS RES. V. 33 5006 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 16145054 JRNL DOI 10.1093/NAR/GKI796 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.21 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) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 25024 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) : 0.228 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2095 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3770 REMARK 3 BIN R VALUE (WORKING SET) : 0.3710 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 317 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2068 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -13.87000 REMARK 3 B22 (A**2) : 22.45000 REMARK 3 B33 (A**2) : -8.58000 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.42 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.42 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.370 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.190 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.030 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 59.31 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : GOL.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : GOL.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Q3B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000019862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.102 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25032 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.430 REMARK 200 R MERGE (I) : 0.06000 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) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.42100 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: AMORE REMARK 200 STARTING MODEL: THE PROTEIN CHAIN FROM PDB CODE 1K3W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG 400, 0.1M TRIS-HCL PH 8.4, REMARK 280 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K 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 28.86100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.02550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 84.65550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.86100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.02550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 84.65550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.86100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.02550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 84.65550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.86100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.02550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 84.65550 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 SER A 250 REMARK 465 SER A 251 REMARK 465 ALA A 252 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 2 CG CD OE1 OE2 REMARK 470 ILE A 6 CG1 CG2 CD1 REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 LEU A 249 CG CD1 CD2 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 530 O HOH A 530 3555 1.94 REMARK 500 O HOH A 518 O HOH A 518 3555 2.05 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 GLU A 2 3.73 -164.47 REMARK 500 GLU A 5 -57.59 -29.96 REMARK 500 ASP A 61 -4.02 80.60 REMARK 500 GLN A 69 -126.78 53.24 REMARK 500 SER A 104 -33.66 62.99 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 A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 184 NE2 REMARK 620 2 HIS A 262 O 116.6 REMARK 620 3 HIS A 262 OXT 97.1 49.1 REMARK 620 4 HIS A 262 NE2 118.4 99.6 70.4 REMARK 620 5 HOH A 530 O 96.0 107.3 156.4 119.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 195 OD1 REMARK 620 2 ASP A 195 OD2 49.1 REMARK 620 3 HIS A 199 NE2 115.2 85.7 REMARK 620 4 HIS A 220 NE2 111.1 93.0 115.6 REMARK 620 5 HOH A 468 O 98.1 147.2 112.2 102.5 REMARK 620 N 1 2 3 4 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 CYS A 237 SG REMARK 620 2 CYS A 240 SG 113.9 REMARK 620 3 CYS A 257 SG 107.9 93.2 REMARK 620 4 CYS A 260 SG 105.9 118.2 117.3 REMARK 620 N 1 2 3 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 MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 351 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q39 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DNA REPAIR ENZYME ENDONUCLEASE-VIII (NEI) REMARK 900 FROM E. COLI: THE WT ENZYME AT 2.8 RESOLUTION. REMARK 900 RELATED ID: 1Q3C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DNA REPAIR ENZYME ENDONUCLEASE-VIII (NEI) REMARK 900 FROM E. COLI: THE E2A MUTANT AT 2.3 RESOLUTION. REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCING AND CRYSTALLOGRAPHY CONFIRM THE REMARK 999 SEQUENCE AS THR A 34 AND ARG A 112. DBREF 1Q3B A 1 262 UNP P50465 END8_ECOLI 1 262 SEQADV 1Q3B THR A 34 UNP P50465 PRO 34 SEE REMARK 999 SEQADV 1Q3B ARG A 112 UNP P50465 THR 112 SEE REMARK 999 SEQADV 1Q3B ALA A 252 UNP P50465 ARG 252 ENGINEERED MUTATION SEQRES 1 A 262 PRO GLU GLY PRO GLU ILE ARG ARG ALA ALA ASP ASN LEU SEQRES 2 A 262 GLU ALA ALA ILE LYS GLY LYS PRO LEU THR ASP VAL TRP SEQRES 3 A 262 PHE ALA PHE PRO GLN LEU LYS THR TYR GLN SER GLN LEU SEQRES 4 A 262 ILE GLY GLN HIS VAL THR HIS VAL GLU THR ARG GLY LYS SEQRES 5 A 262 ALA LEU LEU THR HIS PHE SER ASN ASP LEU THR LEU TYR SEQRES 6 A 262 SER HIS ASN GLN LEU TYR GLY VAL TRP ARG VAL VAL ASP SEQRES 7 A 262 THR GLY GLU GLU PRO GLN THR THR ARG VAL LEU ARG VAL SEQRES 8 A 262 LYS LEU GLN THR ALA ASP LYS THR ILE LEU LEU TYR SER SEQRES 9 A 262 ALA SER ASP ILE GLU MET LEU ARG PRO GLU GLN LEU THR SEQRES 10 A 262 THR HIS PRO PHE LEU GLN ARG VAL GLY PRO ASP VAL LEU SEQRES 11 A 262 ASP PRO ASN LEU THR PRO GLU VAL VAL LYS GLU ARG LEU SEQRES 12 A 262 LEU SER PRO ARG PHE ARG ASN ARG GLN PHE ALA GLY LEU SEQRES 13 A 262 LEU LEU ASP GLN ALA PHE LEU ALA GLY LEU GLY ASN TYR SEQRES 14 A 262 LEU ARG VAL GLU ILE LEU TRP GLN VAL GLY LEU THR GLY SEQRES 15 A 262 ASN HIS LYS ALA LYS ASP LEU ASN ALA ALA GLN LEU ASP SEQRES 16 A 262 ALA LEU ALA HIS ALA LEU LEU GLU ILE PRO ARG PHE SER SEQRES 17 A 262 TYR ALA THR ARG GLY GLN VAL ASP GLU ASN LYS HIS HIS SEQRES 18 A 262 GLY ALA LEU PHE ARG PHE LYS VAL PHE HIS ARG ASP GLY SEQRES 19 A 262 GLU PRO CYS GLU ARG CYS GLY SER ILE ILE GLU LYS THR SEQRES 20 A 262 THR LEU SER SER ALA PRO PHE TYR TRP CYS PRO GLY CYS SEQRES 21 A 262 GLN HIS HET ZN A 301 1 HET MG A 302 1 HET MG A 303 1 HET GOL A 351 6 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 MG 2(MG 2+) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *133(H2 O) HELIX 1 1 GLY A 3 LYS A 18 1 16 HELIX 2 2 PHE A 29 THR A 34 5 6 HELIX 3 3 TYR A 35 ILE A 40 1 6 HELIX 4 4 ARG A 112 THR A 117 1 6 HELIX 5 5 HIS A 119 VAL A 125 1 7 HELIX 6 6 THR A 135 SER A 145 1 11 HELIX 7 7 GLN A 152 LEU A 157 1 6 HELIX 8 8 GLY A 167 VAL A 178 1 12 HELIX 9 9 LYS A 185 LEU A 189 5 5 HELIX 10 10 ASN A 190 ARG A 212 1 23 HELIX 11 11 ASP A 216 HIS A 220 5 5 SHEET 1 A 4 ASP A 24 PHE A 27 0 SHEET 2 A 4 LEU A 89 GLN A 94 -1 O GLN A 94 N ASP A 24 SHEET 3 A 4 LYS A 98 TYR A 103 -1 O LEU A 102 N VAL A 91 SHEET 4 A 4 VAL A 73 ASP A 78 -1 N VAL A 77 O THR A 99 SHEET 1 B 4 VAL A 44 ARG A 50 0 SHEET 2 B 4 ALA A 53 PHE A 58 -1 O LEU A 55 N GLU A 48 SHEET 3 B 4 THR A 63 HIS A 67 -1 O LEU A 64 N THR A 56 SHEET 4 B 4 ASP A 107 LEU A 111 -1 O LEU A 111 N THR A 63 SHEET 1 C 2 GLU A 245 LYS A 246 0 SHEET 2 C 2 TYR A 255 TRP A 256 -1 O TRP A 256 N GLU A 245 LINK NE2 HIS A 184 MG MG A 302 1555 1555 2.39 LINK OD1 ASP A 195 MG MG A 303 2555 1555 1.84 LINK OD2 ASP A 195 MG MG A 303 2555 1555 2.91 LINK NE2 HIS A 199 MG MG A 303 2555 1555 1.92 LINK NE2 HIS A 220 MG MG A 303 1555 1555 2.02 LINK SG CYS A 237 ZN ZN A 301 1555 1555 2.33 LINK SG CYS A 240 ZN ZN A 301 1555 1555 2.38 LINK SG CYS A 257 ZN ZN A 301 1555 1555 2.28 LINK SG CYS A 260 ZN ZN A 301 1555 1555 2.28 LINK O HIS A 262 MG MG A 302 1555 1555 1.91 LINK OXT HIS A 262 MG MG A 302 1555 1555 2.92 LINK NE2 HIS A 262 MG MG A 302 3555 1555 2.28 LINK MG MG A 302 O HOH A 530 1555 1555 2.27 LINK MG MG A 303 O HOH A 468 1555 1555 2.32 SITE 1 AC1 4 CYS A 237 CYS A 240 CYS A 257 CYS A 260 SITE 1 AC2 3 HIS A 184 HIS A 262 HOH A 530 SITE 1 AC3 4 ASP A 195 HIS A 199 HIS A 220 HOH A 468 SITE 1 AC4 3 ASN A 12 VAL A 76 HOH A 526 CRYST1 57.722 80.051 169.311 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017324 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005906 0.00000