HEADER DNA BINDING PROTEIN 14-MAR-25 9QGX TITLE SCIA(H42A) ENDONUCLEASE FROM ESCHERICHIA PHAGE T5 IN COMPLEX WITH 10 TITLE 2 BP DNA (GCGC SEQUENCE 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKING ENDONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.21.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: N-TERMINAL 3 AMINO ACIDS ARE LEFT OVER FROM THE COMPND 8 TOBACCO ETCH VIRUS CLEAVAGE SITE.; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*C*CP*AP*GP*GP*CP*GP*CP*AP*G)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*C*TP*GP*CP*GP*CP*CP*TP*GP*G)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE T5; SOURCE 3 ORGANISM_TAXID: 2695836; SOURCE 4 GENE: ORF142, T5.153, T5P149; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE T5; SOURCE 10 ORGANISM_TAXID: 2695836; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE T5; SOURCE 13 ORGANISM_TAXID: 2695836; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HNH ENDONUCLEASE, HIS-ME ENDONUCLEASE, BACTERIOPHAGE T5, NICKED KEYWDS 2 GENOME, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.RICHARDSON,S.A.MACNEILL REVDAT 1 25-MAR-26 9QGX 0 JRNL AUTH J.M.RICHARDSON,S.A.MACNEILL JRNL TITL STRUCTURE AND FUNCTION OF THE NICKING ENDONUCLEASE FROM JRNL TITL 2 ESCHERICHIA PHAGE T5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 7827 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.330 REMARK 3 FREE R VALUE TEST SET COUNT : 417 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 32.9000 - 3.3800 1.00 2523 149 0.1801 0.2374 REMARK 3 2 3.3800 - 2.6900 0.99 2464 153 0.2566 0.2960 REMARK 3 3 2.4300 - 2.3500 0.97 2423 115 0.3216 0.3569 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.826 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.56 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 : 0.003 1477 REMARK 3 ANGLE : 0.484 2067 REMARK 3 CHIRALITY : 0.037 225 REMARK 3 PLANARITY : 0.003 196 REMARK 3 DIHEDRAL : 24.365 583 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 9QGX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292146380. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95373 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7927 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.347 REMARK 200 RESOLUTION RANGE LOW (A) : 36.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.20600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 2.05300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE PH 7.0 REMARK 280 AND 20% (W/V) PEG 3350 (PEGION SCREEN CONDITION G2, HAMPTON REMARK 280 RESEARCH), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K 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 36.06100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 GLN A -2 REMARK 465 GLY A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 THR A 3 REMARK 465 ASN A 4 REMARK 465 THR A 5 REMARK 465 LYS A 6 REMARK 465 TYR A 7 REMARK 465 GLU A 129 REMARK 465 LYS A 130 REMARK 465 THR A 131 REMARK 465 GLN A 132 REMARK 465 VAL A 133 REMARK 465 LYS A 134 REMARK 465 THR A 135 REMARK 465 GLU A 136 REMARK 465 THR A 137 REMARK 465 LYS A 138 REMARK 465 SER A 139 REMARK 465 GLY A 140 REMARK 465 PHE A 141 REMARK 465 ALA A 142 REMARK 465 ARG A 143 REMARK 465 PHE A 144 REMARK 465 LEU A 145 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 ILE A 31 -61.60 -97.60 REMARK 500 ILE A 124 -43.62 -130.03 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 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 29 SG REMARK 620 2 CYS A 32 SG 109.4 REMARK 620 3 CYS A 90 SG 112.1 111.9 REMARK 620 4 HIS A 93 ND1 119.3 108.0 95.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 41 ND1 REMARK 620 2 HIS A 94 NE2 112.5 REMARK 620 3 HIS A 98 NE2 94.0 106.2 REMARK 620 4 IMD A 201 N1 137.2 79.0 123.4 REMARK 620 5 IMD A 201 N3 105.6 132.0 99.0 53.1 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9QGV RELATED DB: PDB REMARK 900 CONTAINS SAME PROTEIN IN COMPLEX WITH DSDNA CONTAINING DIFFERENT REMARK 900 SEQUENCE DBREF 9QGX A 1 145 UNP Q6QGD4 ENDON_BPT5 1 145 DBREF 9QGX B 1 10 PDB 9QGX 9QGX 1 10 DBREF 9QGX C -10 -1 PDB 9QGX 9QGX -10 -1 SEQADV 9QGX GLN A -2 UNP Q6QGD4 EXPRESSION TAG SEQADV 9QGX GLY A -1 UNP Q6QGD4 EXPRESSION TAG SEQADV 9QGX ALA A 0 UNP Q6QGD4 EXPRESSION TAG SEQADV 9QGX ALA A 42 UNP Q6QGD4 HIS 42 ENGINEERED MUTATION SEQRES 1 A 148 GLN GLY ALA MET ALA THR ASN THR LYS TYR LYS ARG ASP SEQRES 2 A 148 ALA ILE SER ILE MET ARG ASP GLY ILE LYS SER ARG TYR SEQRES 3 A 148 SER LYS ASP GLY CYS CYS ALA ILE CYS GLY SER SER GLU SEQRES 4 A 148 ASP LEU GLU LEU HIS ALA TYR HIS THR ILE SER GLN LEU SEQRES 5 A 148 ILE LYS LYS PHE ALA LYS GLU LEU GLN LEU ASP PHE THR SEQRES 6 A 148 ASP GLU ASN ILE VAL LEU SER ASN ARG GLU ALA PHE TYR SEQRES 7 A 148 LYS LYS TYR GLU HIS GLU LEU VAL ARG ASP VAL VAL THR SEQRES 8 A 148 LEU CYS GLN HIS HIS HIS GLN LEU LEU HIS LYS VAL TYR SEQRES 9 A 148 THR LYS GLU PRO PRO LEU PHE SER ALA ASN LYS GLN LYS SEQRES 10 A 148 ALA TRP VAL GLN LYS GLN LYS ASP LYS ILE GLN ASN PRO SEQRES 11 A 148 GLN GLU LYS THR GLN VAL LYS THR GLU THR LYS SER GLY SEQRES 12 A 148 PHE ALA ARG PHE LEU SEQRES 1 B 10 DC DC DA DG DG DC DG DC DA DG SEQRES 1 C 10 DC DT DG DC DG DC DC DT DG DG HET IMD A 201 10 HET ACT A 202 7 HET ZN A 203 1 HET ZN A 204 1 HETNAM IMD IMIDAZOLE HETNAM ACT ACETATE ION HETNAM ZN ZINC ION FORMUL 4 IMD C3 H5 N2 1+ FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 ZN 2(ZN 2+) FORMUL 8 HOH *27(H2 O) HELIX 1 AA1 ASP A 10 GLY A 18 1 9 HELIX 2 AA2 ILE A 19 TYR A 23 5 5 HELIX 3 AA3 THR A 45 LEU A 57 1 13 HELIX 4 AA4 ASP A 63 ASN A 70 1 8 HELIX 5 AA5 ASN A 70 ARG A 84 1 15 HELIX 6 AA6 GLN A 91 TYR A 101 1 11 HELIX 7 AA7 PRO A 106 PHE A 108 5 3 HELIX 8 AA8 SER A 109 ASN A 126 1 18 SHEET 1 AA1 2 LEU A 38 ALA A 42 0 SHEET 2 AA1 2 VAL A 86 CYS A 90 -1 O LEU A 89 N GLU A 39 LINK SG CYS A 29 ZN ZN A 203 1555 1555 2.32 LINK SG CYS A 32 ZN ZN A 203 1555 1555 2.32 LINK ND1 HIS A 41 ZN ZN A 204 1555 1555 2.29 LINK SG CYS A 90 ZN ZN A 203 1555 1555 2.32 LINK ND1 HIS A 93 ZN ZN A 203 1555 1555 2.08 LINK NE2 HIS A 94 ZN ZN A 204 1555 1555 2.31 LINK NE2 HIS A 98 ZN ZN A 204 1555 1555 2.28 LINK N1 IMD A 201 ZN ZN A 204 1555 1555 2.54 LINK N3 IMD A 201 ZN ZN A 204 1555 1555 2.37 CRYST1 33.125 72.122 40.334 90.00 96.63 90.00 P 1 21 1 2 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 0.030189 0.000000 0.003507 0.00000 SCALE2 0.000000 0.013865 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024960 0.00000 CONECT 342 2645 CONECT 381 2645 CONECT 501 2646 CONECT 1334 2645 CONECT 1379 2645 CONECT 1399 2646 CONECT 1471 2646 CONECT 2628 2629 2632 2633 2646 CONECT 2629 2628 2630 2634 CONECT 2630 2629 2631 2635 2646 CONECT 2631 2630 2632 2636 CONECT 2632 2628 2631 2637 CONECT 2633 2628 CONECT 2634 2629 CONECT 2635 2630 CONECT 2636 2631 CONECT 2637 2632 CONECT 2638 2639 2640 2641 CONECT 2639 2638 CONECT 2640 2638 CONECT 2641 2638 2642 2643 2644 CONECT 2642 2641 CONECT 2643 2641 CONECT 2644 2641 CONECT 2645 342 381 1334 1379 CONECT 2646 501 1399 1471 2628 CONECT 2646 2630 MASTER 263 0 4 8 2 0 0 6 1439 3 27 14 END