HEADER DNA BINDING PROTEIN 10-MAR-26 11QF TITLE I-PNOMI WITH SOLUBILIZING MUTATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: I-PNOMI; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (26-MER); COMPND 7 CHAIN: C, E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (26-MER); COMPND 11 CHAIN: D, F; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHAEOSPHAERIA NODORUM; SOURCE 3 ORGANISM_TAXID: 13684; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS HOMING ENDONUCLEASE, ENZYME, DNA, MUTATION, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.DOYLE,B.STODDARD REVDAT 1 25-MAR-26 11QF 0 JRNL AUTH B.STODDARD JRNL TITL I-PNOMI WITH SOLUBILIZING MUTATIONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 78699 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.560 REMARK 3 FREE R VALUE TEST SET COUNT : 2012 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 46.6800 - 4.5100 0.98 5530 148 0.1640 0.2128 REMARK 3 2 4.5100 - 3.5800 0.99 5587 149 0.1538 0.1825 REMARK 3 3 3.5800 - 3.1200 0.97 5450 131 0.1686 0.2097 REMARK 3 4 3.1200 - 2.8400 0.99 5540 148 0.1956 0.2613 REMARK 3 5 2.8400 - 2.6400 0.98 5521 139 0.1991 0.2259 REMARK 3 6 2.6400 - 2.4800 0.99 5457 159 0.2009 0.2469 REMARK 3 7 2.4800 - 2.3600 0.99 5557 134 0.1995 0.2315 REMARK 3 8 2.3600 - 2.2500 0.99 5541 143 0.2012 0.2764 REMARK 3 9 2.2500 - 2.1700 0.98 5507 156 0.2051 0.2946 REMARK 3 10 2.1700 - 2.0900 0.99 5496 138 0.2081 0.2474 REMARK 3 11 2.0900 - 2.0300 0.99 5429 150 0.2089 0.2862 REMARK 3 12 2.0300 - 1.9700 0.99 5545 136 0.2245 0.2644 REMARK 3 13 1.9700 - 1.9200 0.99 5493 133 0.2499 0.2909 REMARK 3 14 1.9200 - 1.8700 0.91 5034 148 0.2842 0.3141 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 7129 REMARK 3 ANGLE : 1.138 10116 REMARK 3 CHIRALITY : 0.065 1163 REMARK 3 PLANARITY : 0.009 917 REMARK 3 DIHEDRAL : 22.918 2839 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 11QF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1000305877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-24 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL 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 : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78761 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 46.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.75200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% W/V PEG 3000 0.2 M AMMONIUM REMARK 280 CITRATE TRIBASIC 50 MM TRIS PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 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+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -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 36.02290 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 84.11700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.40045 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.02290 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 84.11700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 38.40045 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 621 LIES ON A SPECIAL POSITION. 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 MET A 0 REMARK 465 TYR A 1 REMARK 465 ARG A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 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 LYS A 27 CD CE NZ REMARK 470 LYS A 29 CG CD CE NZ REMARK 470 LYS A 30 NZ REMARK 470 LYS A 47 CD CE NZ REMARK 470 LYS A 48 CE NZ REMARK 470 GLN A 58 CD OE1 NE2 REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 ASP A 73 CG OD1 OD2 REMARK 470 LYS A 83 CG CD CE NZ REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LYS A 110 CD CE NZ REMARK 470 LYS A 118 CE NZ REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 LYS A 128 NZ REMARK 470 GLU A 155 CD OE1 OE2 REMARK 470 VAL A 158 CG1 CG2 REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 GLU A 217 CG CD OE1 OE2 REMARK 470 LYS A 223 CG CD CE NZ REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 LYS A 241 CG CD CE NZ REMARK 470 LYS A 269 CE NZ REMARK 470 LYS A 290 CE NZ REMARK 470 LYS B 27 CG CD CE NZ REMARK 470 LYS B 29 CG CD CE NZ REMARK 470 LYS B 30 CE NZ REMARK 470 ARG B 31 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 32 CG CD CE NZ REMARK 470 GLN B 58 CG CD OE1 NE2 REMARK 470 LYS B 83 CG CD CE NZ REMARK 470 LYS B 94 CG CD CE NZ REMARK 470 LYS B 110 CD CE NZ REMARK 470 GLU B 124 CG CD OE1 OE2 REMARK 470 GLU B 127 CG CD OE1 OE2 REMARK 470 LYS B 128 CG CD CE NZ REMARK 470 GLU B 155 CG CD OE1 OE2 REMARK 470 SER B 187 OG REMARK 470 ASN B 189 CG OD1 ND2 REMARK 470 SER B 190 OG REMARK 470 LYS B 191 CG CD CE NZ REMARK 470 LEU B 192 CG CD1 CD2 REMARK 470 TYR B 194 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 223 CD CE NZ REMARK 470 LYS B 230 CD CE NZ REMARK 470 LYS B 241 CG CD CE NZ REMARK 470 GLU B 283 CG CD OE1 OE2 REMARK 470 ILE B 285 CG1 CG2 CD1 REMARK 470 ASN B 286 CG OD1 ND2 REMARK 470 LYS B 290 CG CD CE NZ REMARK 470 ASN B 300 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 18 O HOH A 501 2.00 REMARK 500 O HOH B 628 O HOH B 634 2.02 REMARK 500 O HOH E 109 O HOH F 127 2.02 REMARK 500 O HOH A 622 O HOH C 153 2.06 REMARK 500 O HOH D 118 O HOH D 136 2.10 REMARK 500 O HOH C 116 O HOH C 129 2.11 REMARK 500 O HOH C 145 O HOH C 146 2.12 REMARK 500 O HOH D 137 O HOH D 142 2.13 REMARK 500 OE2 GLU B 18 O HOH B 501 2.14 REMARK 500 OP1 DA E 4 O HOH E 101 2.14 REMARK 500 O HOH B 549 O HOH F 141 2.14 REMARK 500 O HOH E 116 O HOH E 140 2.15 REMARK 500 O HOH B 601 O HOH B 633 2.16 REMARK 500 O HOH B 604 O HOH E 140 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 635 O HOH A 648 2555 2.03 REMARK 500 REMARK 500 REMARK: NULL 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 C 4 O3' DA C 4 C3' -0.041 REMARK 500 DC D 6 O3' DC D 6 C3' -0.041 REMARK 500 DG D 18 O3' DG D 18 C3' -0.039 REMARK 500 DT F 16 O3' DT F 16 C3' -0.051 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 C 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT C 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC C 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT C 10 O5' - P - OP2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DT C 10 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA C 20 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG C 22 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG D 10 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA D 14 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG D 16 OP1 - P - OP2 ANGL. DEV. = -13.3 DEGREES REMARK 500 DG D 19 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT D 21 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG E 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT E 7 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC E 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA E 20 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC F 6 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG F 11 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG F 17 OP1 - P - OP2 ANGL. DEV. = -11.2 DEGREES REMARK 500 DG F 20 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DG F 20 O4' - C1' - N9 ANGL. DEV. = 2.8 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 ASN A 137 -117.45 44.57 REMARK 500 ILE A 246 -62.37 -121.19 REMARK 500 ASN A 296 -117.10 57.13 REMARK 500 ASP B 80 -35.98 -139.73 REMARK 500 LYS B 118 7.79 58.03 REMARK 500 ASN B 137 -113.82 46.36 REMARK 500 ILE B 246 -55.64 -124.52 REMARK 500 ASN B 296 -122.21 59.13 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 B 639 DISTANCE = 7.83 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 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 17 O REMARK 620 2 GLU A 178 OE1 115.7 REMARK 620 3 GLU A 178 OE2 74.5 46.7 REMARK 620 4 HOH A 522 O 91.0 76.4 98.1 REMARK 620 5 HOH A 605 O 82.6 147.6 156.6 76.9 REMARK 620 6 DC C 16 OP2 84.4 111.0 86.4 172.5 96.6 REMARK 620 7 DT D 15 OP1 161.8 82.4 123.1 90.9 80.1 91.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 18 OE2 REMARK 620 2 ALA A 177 O 92.6 REMARK 620 3 HOH A 601 O 83.4 87.1 REMARK 620 4 HOH A 613 O 158.9 88.4 75.6 REMARK 620 5 DA C 15 OP1 94.5 171.0 99.1 86.9 REMARK 620 6 DG D 16 OP2 105.6 79.0 163.6 95.3 93.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 17 O REMARK 620 2 GLU B 178 OE1 113.7 REMARK 620 3 GLU B 178 OE2 75.5 43.4 REMARK 620 4 HOH B 542 O 93.1 78.5 100.3 REMARK 620 5 HOH B 556 O 77.1 150.8 151.6 73.7 REMARK 620 6 DC E 16 OP2 84.4 105.8 82.6 175.6 102.1 REMARK 620 7 DT F 16 OP1 164.9 81.3 117.9 91.3 90.3 90.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 18 OE1 REMARK 620 2 ALA B 177 O 90.1 REMARK 620 3 HOH B 590 O 83.5 87.6 REMARK 620 4 HOH B 611 O 159.9 88.1 76.5 REMARK 620 5 DA E 15 OP1 92.5 176.2 95.3 90.3 REMARK 620 6 DG F 17 OP2 105.0 79.5 164.5 94.3 97.2 REMARK 620 N 1 2 3 4 5 DBREF 11QF A 0 301 PDB 11QF 11QF 0 301 DBREF 11QF B 0 301 PDB 11QF 11QF 0 301 DBREF 11QF C 1 26 PDB 11QF 11QF 1 26 DBREF 11QF D 0 25 PDB 11QF 11QF 0 25 DBREF 11QF E 1 26 PDB 11QF 11QF 1 26 DBREF 11QF F 1 26 PDB 11QF 11QF 1 26 SEQRES 1 A 302 MET TYR ARG SER THR ILE VAL ASN PRO TRP VAL TRP SER SEQRES 2 A 302 GLY LEU ILE ASP GLY GLU GLY SER PHE SER ILE ILE ILE SEQRES 3 A 302 SER LYS SER LYS LYS ARG LYS LEU GLY TRP ARG VAL GLU SEQRES 4 A 302 LEU LYS PHE GLN LEU GLY LEU HIS LYS LYS ASP LEU ASN SEQRES 5 A 302 LEU LEU GLU LEU LEU GLN GLN HIS LEU GLY GLY ILE GLY SEQRES 6 A 302 SER ILE HIS LEU ALA LYS ASN ARG ASP MET VAL ASN TYR SEQRES 7 A 302 SER ILE ASP SER ILE LYS ASP LEU ASN ASN LEU ILE ASP SEQRES 8 A 302 TYR LEU ASP LYS TYR PRO LEU LEU THR GLN LYS ALA ALA SEQRES 9 A 302 ASP PHE LEU LEU LEU LYS LYS ALA VAL GLU LEU VAL ASN SEQRES 10 A 302 ASN LYS ALA HIS LEU THR LEU GLU GLY LEU GLU LYS ILE SEQRES 11 A 302 VAL ASN ILE LYS ALA SER MET ASN LEU GLY LEU SER ASP SEQRES 12 A 302 MET LEU ILE SER GLU PHE PRO GLY TYR VAL PRO VAL GLU SEQRES 13 A 302 ARG PRO VAL ILE ASN ASN ASP ASN VAL ILE LEU ASN PRO SEQRES 14 A 302 TYR TRP ILE SER GLY PHE VAL SER ALA GLU GLY ASN PHE SEQRES 15 A 302 ASP VAL ARG VAL PRO SER THR ASN SER LYS LEU GLY TYR SEQRES 16 A 302 ARG VAL GLN LEU ARG PHE ARG ILE SER GLN HIS SER ARG SEQRES 17 A 302 ASP LEU ILE LEU MET GLN LYS ILE VAL GLU TYR LEU GLY SEQRES 18 A 302 CYS GLY LYS ILE TYR LYS TYR ALA GLY LYS SER SER ILE SEQRES 19 A 302 SER LEU THR ILE VAL ASP PHE LYS ASP ILE THR ASN ILE SEQRES 20 A 302 LEU VAL PRO PHE PHE ASP GLU TYR PRO ILE ILE GLY ILE SEQRES 21 A 302 LYS LEU HIS ASP TYR LEU ASP TRP CYS LYS ILE HIS SER SEQRES 22 A 302 LEU MET LEU ASN LYS SER HIS LEU THR VAL GLU GLY ILE SEQRES 23 A 302 ASN SER ILE ARG LYS ILE LYS SER GLY MET ASN THR GLY SEQRES 24 A 302 ARG ASN PHE SEQRES 1 B 302 MET TYR ARG SER THR ILE VAL ASN PRO TRP VAL TRP SER SEQRES 2 B 302 GLY LEU ILE ASP GLY GLU GLY SER PHE SER ILE ILE ILE SEQRES 3 B 302 SER LYS SER LYS LYS ARG LYS LEU GLY TRP ARG VAL GLU SEQRES 4 B 302 LEU LYS PHE GLN LEU GLY LEU HIS LYS LYS ASP LEU ASN SEQRES 5 B 302 LEU LEU GLU LEU LEU GLN GLN HIS LEU GLY GLY ILE GLY SEQRES 6 B 302 SER ILE HIS LEU ALA LYS ASN ARG ASP MET VAL ASN TYR SEQRES 7 B 302 SER ILE ASP SER ILE LYS ASP LEU ASN ASN LEU ILE ASP SEQRES 8 B 302 TYR LEU ASP LYS TYR PRO LEU LEU THR GLN LYS ALA ALA SEQRES 9 B 302 ASP PHE LEU LEU LEU LYS LYS ALA VAL GLU LEU VAL ASN SEQRES 10 B 302 ASN LYS ALA HIS LEU THR LEU GLU GLY LEU GLU LYS ILE SEQRES 11 B 302 VAL ASN ILE LYS ALA SER MET ASN LEU GLY LEU SER ASP SEQRES 12 B 302 MET LEU ILE SER GLU PHE PRO GLY TYR VAL PRO VAL GLU SEQRES 13 B 302 ARG PRO VAL ILE ASN ASN ASP ASN VAL ILE LEU ASN PRO SEQRES 14 B 302 TYR TRP ILE SER GLY PHE VAL SER ALA GLU GLY ASN PHE SEQRES 15 B 302 ASP VAL ARG VAL PRO SER THR ASN SER LYS LEU GLY TYR SEQRES 16 B 302 ARG VAL GLN LEU ARG PHE ARG ILE SER GLN HIS SER ARG SEQRES 17 B 302 ASP LEU ILE LEU MET GLN LYS ILE VAL GLU TYR LEU GLY SEQRES 18 B 302 CYS GLY LYS ILE TYR LYS TYR ALA GLY LYS SER SER ILE SEQRES 19 B 302 SER LEU THR ILE VAL ASP PHE LYS ASP ILE THR ASN ILE SEQRES 20 B 302 LEU VAL PRO PHE PHE ASP GLU TYR PRO ILE ILE GLY ILE SEQRES 21 B 302 LYS LEU HIS ASP TYR LEU ASP TRP CYS LYS ILE HIS SER SEQRES 22 B 302 LEU MET LEU ASN LYS SER HIS LEU THR VAL GLU GLY ILE SEQRES 23 B 302 ASN SER ILE ARG LYS ILE LYS SER GLY MET ASN THR GLY SEQRES 24 B 302 ARG ASN PHE SEQRES 1 C 26 DG DG DA DA DG DA DT DC DC DT DC DA DT SEQRES 2 C 26 DA DA DC DC DA DA DA DG DG DT DT DG DG SEQRES 1 D 26 DC DC DC DA DA DC DC DT DT DT DG DG DT SEQRES 2 D 26 DT DA DT DG DA DG DG DA DT DC DT DT DC SEQRES 1 E 26 DG DG DA DA DG DA DT DC DC DT DC DA DT SEQRES 2 E 26 DA DA DC DC DA DA DA DG DG DT DT DG DG SEQRES 1 F 26 DC DC DC DA DA DC DC DT DT DT DG DG DT SEQRES 2 F 26 DT DA DT DG DA DG DG DA DT DC DT DT DC HET CA A 401 1 HET CA A 402 1 HET CA B 401 1 HET CA B 402 1 HETNAM CA CALCIUM ION FORMUL 7 CA 4(CA 2+) FORMUL 11 HOH *493(H2 O) HELIX 1 AA1 ASN A 7 GLY A 19 1 13 HELIX 2 AA2 ASP A 49 LEU A 60 1 12 HELIX 3 AA3 SER A 81 TYR A 95 1 15 HELIX 4 AA4 GLN A 100 ASN A 117 1 18 HELIX 5 AA5 LYS A 118 LEU A 121 5 4 HELIX 6 AA6 THR A 122 ALA A 134 1 13 HELIX 7 AA7 SER A 141 PHE A 148 1 8 HELIX 8 AA8 ASN A 167 GLU A 178 1 12 HELIX 9 AA9 ASP A 208 GLY A 220 1 13 HELIX 10 AB1 ASP A 239 ILE A 246 1 8 HELIX 11 AB2 ILE A 246 TYR A 254 1 9 HELIX 12 AB3 ILE A 259 ASN A 276 1 18 HELIX 13 AB4 LYS A 277 LEU A 280 5 4 HELIX 14 AB5 THR A 281 GLY A 294 1 14 HELIX 15 AB6 MET A 295 ARG A 299 5 5 HELIX 16 AB7 ASN B 7 GLU B 18 1 12 HELIX 17 AB8 ASP B 49 LEU B 60 1 12 HELIX 18 AB9 SER B 81 TYR B 95 1 15 HELIX 19 AC1 GLN B 100 ASN B 117 1 18 HELIX 20 AC2 LYS B 118 LEU B 121 5 4 HELIX 21 AC3 THR B 122 ALA B 134 1 13 HELIX 22 AC4 SER B 141 PHE B 148 1 8 HELIX 23 AC5 ASN B 167 GLU B 178 1 12 HELIX 24 AC6 ASP B 208 GLY B 220 1 13 HELIX 25 AC7 ASP B 239 ILE B 246 1 8 HELIX 26 AC8 ILE B 246 TYR B 254 1 9 HELIX 27 AC9 ILE B 259 ASN B 276 1 18 HELIX 28 AD1 LYS B 277 LEU B 280 5 4 HELIX 29 AD2 THR B 281 GLY B 294 1 14 HELIX 30 AD3 MET B 295 ARG B 299 5 5 SHEET 1 AA1 4 SER A 20 LYS A 27 0 SHEET 2 AA1 4 TRP A 35 HIS A 46 -1 O ARG A 36 N SER A 26 SHEET 3 AA1 4 MET A 74 ILE A 79 -1 O VAL A 75 N LEU A 45 SHEET 4 AA1 4 SER A 65 LEU A 68 -1 N SER A 65 O SER A 78 SHEET 1 AA2 4 GLY A 179 ARG A 184 0 SHEET 2 AA2 4 GLN A 197 HIS A 205 -1 O GLN A 197 N ARG A 184 SHEET 3 AA2 4 SER A 232 ILE A 237 -1 O ILE A 233 N GLN A 204 SHEET 4 AA2 4 LYS A 223 LYS A 226 -1 N LYS A 223 O THR A 236 SHEET 1 AA3 4 GLY B 19 LYS B 27 0 SHEET 2 AA3 4 TRP B 35 HIS B 46 -1 O ARG B 36 N SER B 26 SHEET 3 AA3 4 MET B 74 ILE B 79 -1 O VAL B 75 N LEU B 45 SHEET 4 AA3 4 SER B 65 LEU B 68 -1 N SER B 65 O SER B 78 SHEET 1 AA4 4 GLY B 179 ARG B 184 0 SHEET 2 AA4 4 GLN B 197 HIS B 205 -1 O ARG B 199 N ASP B 182 SHEET 3 AA4 4 SER B 232 ILE B 237 -1 O LEU B 235 N ILE B 202 SHEET 4 AA4 4 LYS B 223 LYS B 226 -1 N LYS B 223 O THR B 236 LINK O GLY A 17 CA CA A 402 1555 1555 2.25 LINK OE2 GLU A 18 CA CA A 401 1555 1555 2.32 LINK O ALA A 177 CA CA A 401 1555 1555 2.42 LINK OE1 GLU A 178 CA CA A 402 1555 1555 2.50 LINK OE2 GLU A 178 CA CA A 402 1555 1555 2.94 LINK CA CA A 401 O HOH A 601 1555 1555 2.22 LINK CA CA A 401 O HOH A 613 1555 1555 2.47 LINK CA CA A 401 OP1 DA C 15 1555 1555 2.35 LINK CA CA A 401 OP2 DG D 16 1555 1555 2.06 LINK CA CA A 402 O HOH A 522 1555 1555 2.50 LINK CA CA A 402 O HOH A 605 1555 1555 2.63 LINK CA CA A 402 OP2 DC C 16 1555 1555 2.24 LINK CA CA A 402 OP1 DT D 15 1555 1555 2.27 LINK O GLY B 17 CA CA B 402 1555 1555 2.21 LINK OE1 GLU B 18 CA CA B 401 1555 1555 2.33 LINK O ALA B 177 CA CA B 401 1555 1555 2.37 LINK OE1 GLU B 178 CA CA B 402 1555 1555 2.60 LINK OE2 GLU B 178 CA CA B 402 1555 1555 3.14 LINK CA CA B 401 O HOH B 590 1555 1555 2.21 LINK CA CA B 401 O HOH B 611 1555 1555 2.57 LINK CA CA B 401 OP1 DA E 15 1555 1555 2.30 LINK CA CA B 401 OP2 DG F 17 1555 1555 2.20 LINK CA CA B 402 O HOH B 542 1555 1555 2.29 LINK CA CA B 402 O HOH B 556 1555 1555 2.57 LINK CA CA B 402 OP2 DC E 16 1555 1555 2.31 LINK CA CA B 402 OP1 DT F 16 1555 1555 2.20 CRYST1 76.945 168.234 76.957 90.00 93.65 90.00 I 1 2 1 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 0.012996 0.000000 0.000830 0.00000 SCALE2 0.000000 0.005944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013021 0.00000 CONECT 103 6784 CONECT 112 6783 CONECT 1329 6783 CONECT 1338 6784 CONECT 1339 6784 CONECT 2470 6786 CONECT 2478 6785 CONECT 3691 6785 CONECT 3700 6786 CONECT 3701 6786 CONECT 4942 6783 CONECT 4964 6784 CONECT 5492 6784 CONECT 5513 6783 CONECT 6004 6785 CONECT 6026 6786 CONECT 6557 6786 CONECT 6578 6785 CONECT 6783 112 1329 4942 5513 CONECT 6783 6887 6899 CONECT 6784 103 1338 1339 4964 CONECT 6784 5492 6808 6891 CONECT 6785 2478 3691 6004 6578 CONECT 6785 7029 7050 CONECT 6786 2470 3700 3701 6026 CONECT 6786 6557 6981 6995 CONECT 6808 6784 CONECT 6887 6783 CONECT 6891 6784 CONECT 6899 6783 CONECT 6981 6786 CONECT 6995 6786 CONECT 7029 6785 CONECT 7050 6785 MASTER 486 0 4 30 16 0 0 6 7265 6 34 56 END