HEADER HYDROLASE 06-JAN-05 2BGW TITLE XPF FROM AEROPYRUM PERNIX, COMPLEX WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: XPF ENDONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.7.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*GP*AP*TP*CP*AP*CP*AP*GP*AP*TP *GP*CP*TP*GP*A)-3'; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP *TP*GP*AP*TP*C)-3'; COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 56636; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: ROSETTA/PLYSS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-14B-3C; SOURCE 9 OTHER_DETAILS: A PERNIX GENOME SEQUENCING PROJECT GENE APE1436, SOURCE 10 ACCESSION CODE C72622; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE, STRUCTURE SPECIFIC ENDONUCLEASE, NUCLEOTIDE EXCISION KEYWDS 2 REPAIR EXPDTA X-RAY DIFFRACTION AUTHOR M.NEWMAN,J.MURRAY-RUST,J.LALLY,J.RUDOLF,A.FADDEN,P.P.KNOWLES, AUTHOR 2 M.F.WHITE,N.Q.MCDONALD REVDAT 6 13-DEC-23 2BGW 1 LINK REVDAT 5 08-MAY-19 2BGW 1 REMARK REVDAT 4 14-MAR-18 2BGW 1 SOURCE AUTHOR JRNL REVDAT 3 24-FEB-09 2BGW 1 VERSN REVDAT 2 15-JUN-05 2BGW 1 JRNL REVDAT 1 23-FEB-05 2BGW 0 JRNL AUTH M.NEWMAN,J.MURRAY-RUST,J.LALLY,J.RUDOLF,A.FADDEN, JRNL AUTH 2 P.P.KNOWLES,M.F.WHITE,N.Q.MCDONALD JRNL TITL STRUCTURE OF AN XPF ENDONUCLEASE WITH AND WITHOUT DNA JRNL TITL 2 SUGGESTS A MODEL FOR SUBSTRATE RECOGNITION. JRNL REF EMBO J. V. 24 895 2005 JRNL REFN ISSN 0261-4189 JRNL PMID 15719018 JRNL DOI 10.1038/SJ.EMBOJ.7600581 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 22599 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1223 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1514 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.3740 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3224 REMARK 3 NUCLEIC ACID ATOMS : 609 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.85000 REMARK 3 B22 (A**2) : 0.85000 REMARK 3 B33 (A**2) : -1.28000 REMARK 3 B12 (A**2) : 0.43000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.472 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.313 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.235 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3989 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5528 ; 1.959 ; 2.187 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 416 ; 7.155 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;32.722 ;22.015 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 558 ;21.573 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;21.720 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 625 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2772 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1837 ; 0.245 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2635 ; 0.326 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 142 ; 0.177 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 61 ; 0.289 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.223 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2131 ; 0.712 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3357 ; 1.193 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2270 ; 1.798 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2171 ; 2.976 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 18 A 147 6 REMARK 3 1 B 18 B 147 6 REMARK 3 2 A 168 A 228 6 REMARK 3 2 B 168 B 228 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 1445 ; 7.54 ; 5.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 1445 ; 3.78 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BGW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1290022281. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21619 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 46.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1J25 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 0.2M AMMONIUM REMARK 280 SULFATE, 20% PEG MME 2K, HANGING DROP, ROOM TEMPERATURE, VAPOR REMARK 280 DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.87400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.43700 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.43700 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 56.87400 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 S SO4 A1231 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 B 11 REMARK 465 LEU B 12 REMARK 465 GLU B 13 REMARK 465 ASP B 14 REMARK 465 PRO B 15 REMARK 465 GLY B 16 REMARK 465 GLY B 17 REMARK 465 ARG B 149 REMARK 465 GLU B 150 REMARK 465 GLY B 151 REMARK 465 GLY B 152 REMARK 465 GLN B 153 REMARK 465 ARG B 154 REMARK 465 ILE B 155 REMARK 465 VAL B 156 REMARK 465 ILE B 157 REMARK 465 HIS B 158 REMARK 465 LYS B 159 REMARK 465 LYS B 229 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 ARG A 20 NE CZ NH1 NH2 REMARK 470 ARG A 29 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 80 CD OE1 OE2 REMARK 470 ARG A 103 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 ARG A 183 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 190 CD OE1 OE2 REMARK 470 ARG A 197 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 203 CG CD CE NZ REMARK 470 LYS A 208 CG CD CE NZ REMARK 470 GLU A 210 CG CD OE1 OE2 REMARK 470 GLU A 214 CG CD OE1 OE2 REMARK 470 LYS A 215 CG CD CE NZ REMARK 470 ARG A 216 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 218 CG CD OE1 OE2 REMARK 470 LYS A 222 CG CD CE NZ REMARK 470 LYS A 229 CG CD CE NZ REMARK 470 ARG B 20 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 37 CG CD OE1 OE2 REMARK 470 LYS B 46 CG CD CE NZ REMARK 470 LYS B 71 CD CE NZ REMARK 470 GLU B 87 CG CD OE1 OE2 REMARK 470 GLU B 90 CD OE1 OE2 REMARK 470 ARG B 103 CZ NH1 NH2 REMARK 470 ARG B 104 CZ NH1 NH2 REMARK 470 LYS B 160 CB CG CD CE NZ REMARK 470 ARG B 162 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG B 183 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 203 CE NZ REMARK 470 GLU B 214 CD OE1 OE2 REMARK 470 LYS B 215 CG CD CE NZ REMARK 470 GLU B 218 OE1 OE2 REMARK 470 LYS B 222 CG CD CE NZ 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 S SO4 A 1231 O1 SO4 A 1231 4556 1.44 REMARK 500 S SO4 A 1231 O2 SO4 A 1231 4556 1.47 REMARK 500 O1 SO4 A 1231 O1 SO4 A 1231 4556 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 2 O3' DA C 2 C3' -0.063 REMARK 500 DT D 1 O3' DT D 1 C3' -0.043 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 VAL A 23 CB - CA - C ANGL. DEV. = -14.3 DEGREES REMARK 500 DG C 1 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA C 2 O5' - C5' - C4' ANGL. DEV. = -8.7 DEGREES REMARK 500 DA C 2 O4' - C4' - C3' ANGL. DEV. = -5.6 DEGREES REMARK 500 DA C 2 C1' - O4' - C4' ANGL. DEV. = -8.3 DEGREES REMARK 500 DA C 2 N9 - C1' - C2' ANGL. DEV. = 12.3 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT C 3 O5' - C5' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DT C 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC C 4 O5' - C5' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DC C 4 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC C 6 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES REMARK 500 DA C 7 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA C 9 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DT C 10 N1 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 DG C 11 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG C 11 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES REMARK 500 DG C 11 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 DT C 13 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 DT C 13 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DA C 15 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DT D 1 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC D 2 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 DC D 5 O5' - C5' - C4' ANGL. DEV. = -5.7 DEGREES REMARK 500 DC D 5 C1' - O4' - C4' ANGL. DEV. = -8.4 DEGREES REMARK 500 DC D 5 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DC D 5 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT D 9 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT D 9 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DG D 10 O4' - C1' - N9 ANGL. DEV. = -8.1 DEGREES REMARK 500 DG D 12 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG D 12 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES REMARK 500 DA D 13 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DT D 14 O4' - C1' - N1 ANGL. DEV. = 3.4 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 GLU A 28 -36.11 -28.08 REMARK 500 SER A 30 149.86 -33.98 REMARK 500 ARG A 104 -3.12 -43.49 REMARK 500 ARG A 106 154.43 -48.49 REMARK 500 ARG A 108 8.63 -68.84 REMARK 500 THR A 148 -162.71 -65.92 REMARK 500 ARG A 149 116.72 82.18 REMARK 500 GLN A 153 108.21 -51.06 REMARK 500 ARG A 191 -71.52 -54.80 REMARK 500 LYS A 203 -54.57 -24.52 REMARK 500 SER B 38 33.43 -78.88 REMARK 500 ARG B 104 -17.33 -44.38 REMARK 500 SER B 147 54.93 -100.59 REMARK 500 ARG B 162 -36.45 150.00 REMARK 500 LEU B 163 130.19 -9.11 REMARK 500 SER B 164 67.01 -43.80 REMARK 500 ARG B 167 -37.70 -38.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 150 GLY A 151 -142.23 REMARK 500 LYS B 160 PRO B 161 32.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SO4 A 1231 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 A1230 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 52 OD1 REMARK 620 2 ASP A 52 OD2 45.1 REMARK 620 3 GLU A 62 OE2 95.0 90.1 REMARK 620 4 ARG A 63 O 120.7 75.6 86.2 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 MG A1230 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1231 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1232 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1233 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1229 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1230 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D1016 DBREF 2BGW A 11 17 PDB 2BGW 2BGW 11 17 DBREF 2BGW A 18 229 UNP Q9YC15 Q9YC15 18 229 DBREF 2BGW B 11 17 PDB 2BGW 2BGW 11 17 DBREF 2BGW B 18 229 UNP Q9YC15 Q9YC15 18 229 DBREF 2BGW C 1 15 PDB 2BGW 2BGW 1 15 DBREF 2BGW D 1 15 PDB 2BGW 2BGW 1 15 SEQRES 1 A 219 MET LEU GLU ASP PRO GLY GLY ARG PRO ARG VAL TYR VAL SEQRES 2 A 219 ASP VAL ARG GLU GLU ARG SER PRO VAL PRO SER ILE LEU SEQRES 3 A 219 GLU SER LEU GLY VAL GLN VAL ILE PRO LYS GLN LEU PRO SEQRES 4 A 219 MET GLY ASP TYR LEU VAL SER ASP SER ILE ILE VAL GLU SEQRES 5 A 219 ARG LYS THR SER SER ASP PHE ALA LYS SER LEU PHE ASP SEQRES 6 A 219 GLY ARG LEU PHE GLU GLN ALA SER ARG LEU ALA GLU HIS SEQRES 7 A 219 TYR GLU THR VAL PHE ILE ILE VAL GLU GLY PRO PRO VAL SEQRES 8 A 219 PRO ARG ARG TYR ARG GLY ARG GLU ARG SER LEU TYR ALA SEQRES 9 A 219 ALA MET ALA ALA LEU GLN LEU ASP TYR GLY ILE ARG LEU SEQRES 10 A 219 MET ASN THR MET ASP PRO LYS GLY THR ALA LEU VAL ILE SEQRES 11 A 219 GLU SER LEU ALA ARG LEU SER THR ARG GLU GLY GLY GLN SEQRES 12 A 219 ARG ILE VAL ILE HIS LYS LYS PRO ARG LEU SER ASP VAL SEQRES 13 A 219 ARG GLU TRP GLN LEU TYR ILE LEU GLN SER PHE PRO GLY SEQRES 14 A 219 ILE GLY ARG ARG THR ALA GLU ARG ILE LEU GLU ARG PHE SEQRES 15 A 219 GLY SER LEU GLU ARG PHE PHE THR ALA SER LYS ALA GLU SEQRES 16 A 219 ILE SER LYS VAL GLU GLY ILE GLY GLU LYS ARG ALA GLU SEQRES 17 A 219 GLU ILE LYS LYS ILE LEU MET THR PRO TYR LYS SEQRES 1 B 219 MET LEU GLU ASP PRO GLY GLY ARG PRO ARG VAL TYR VAL SEQRES 2 B 219 ASP VAL ARG GLU GLU ARG SER PRO VAL PRO SER ILE LEU SEQRES 3 B 219 GLU SER LEU GLY VAL GLN VAL ILE PRO LYS GLN LEU PRO SEQRES 4 B 219 MET GLY ASP TYR LEU VAL SER ASP SER ILE ILE VAL GLU SEQRES 5 B 219 ARG LYS THR SER SER ASP PHE ALA LYS SER LEU PHE ASP SEQRES 6 B 219 GLY ARG LEU PHE GLU GLN ALA SER ARG LEU ALA GLU HIS SEQRES 7 B 219 TYR GLU THR VAL PHE ILE ILE VAL GLU GLY PRO PRO VAL SEQRES 8 B 219 PRO ARG ARG TYR ARG GLY ARG GLU ARG SER LEU TYR ALA SEQRES 9 B 219 ALA MET ALA ALA LEU GLN LEU ASP TYR GLY ILE ARG LEU SEQRES 10 B 219 MET ASN THR MET ASP PRO LYS GLY THR ALA LEU VAL ILE SEQRES 11 B 219 GLU SER LEU ALA ARG LEU SER THR ARG GLU GLY GLY GLN SEQRES 12 B 219 ARG ILE VAL ILE HIS LYS LYS PRO ARG LEU SER ASP VAL SEQRES 13 B 219 ARG GLU TRP GLN LEU TYR ILE LEU GLN SER PHE PRO GLY SEQRES 14 B 219 ILE GLY ARG ARG THR ALA GLU ARG ILE LEU GLU ARG PHE SEQRES 15 B 219 GLY SER LEU GLU ARG PHE PHE THR ALA SER LYS ALA GLU SEQRES 16 B 219 ILE SER LYS VAL GLU GLY ILE GLY GLU LYS ARG ALA GLU SEQRES 17 B 219 GLU ILE LYS LYS ILE LEU MET THR PRO TYR LYS SEQRES 1 C 15 DG DA DT DC DA DC DA DG DA DT DG DC DT SEQRES 2 C 15 DG DA SEQRES 1 D 15 DT DC DA DG DC DA DT DC DT DG DT DG DA SEQRES 2 D 15 DT DC HET MG A1230 1 HET SO4 A1231 3 HET SO4 A1232 5 HET SO4 A1233 5 HET SO4 B1229 5 HET SO4 B1230 5 HET SO4 D1016 5 HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 5 MG MG 2+ FORMUL 6 SO4 6(O4 S 2-) FORMUL 12 HOH *7(H2 O) HELIX 1 1 PRO A 31 LEU A 39 1 9 HELIX 2 2 SER A 66 GLY A 76 1 11 HELIX 3 3 GLY A 76 TYR A 89 1 14 HELIX 4 4 PRO A 102 ARG A 106 5 5 HELIX 5 5 ARG A 108 TYR A 123 1 16 HELIX 6 6 ASP A 132 THR A 148 1 17 HELIX 7 7 SER A 164 SER A 176 1 13 HELIX 8 8 GLY A 181 GLY A 193 1 13 HELIX 9 9 SER A 194 PHE A 199 1 6 HELIX 10 10 SER A 202 VAL A 209 1 8 HELIX 11 11 GLY A 213 THR A 226 1 14 HELIX 12 12 ARG B 26 GLU B 28 5 3 HELIX 13 13 PRO B 31 SER B 38 1 8 HELIX 14 14 SER B 66 GLY B 76 1 11 HELIX 15 15 GLY B 76 TYR B 89 1 14 HELIX 16 16 PRO B 102 ARG B 106 5 5 HELIX 17 17 ARG B 108 GLY B 124 1 17 HELIX 18 18 ASP B 132 SER B 147 1 16 HELIX 19 19 ASP B 165 SER B 176 1 12 HELIX 20 20 GLY B 181 GLY B 193 1 13 HELIX 21 21 SER B 194 PHE B 199 1 6 HELIX 22 22 SER B 202 SER B 207 1 6 HELIX 23 23 GLY B 213 THR B 226 1 14 SHEET 1 AA 6 GLN A 42 LYS A 46 0 SHEET 2 AA 6 ARG A 20 ASP A 24 1 O VAL A 21 N ILE A 44 SHEET 3 AA 6 TYR A 53 SER A 56 -1 O LEU A 54 N TYR A 22 SHEET 4 AA 6 ILE A 59 THR A 65 -1 O ILE A 59 N VAL A 55 SHEET 5 AA 6 THR A 91 GLU A 97 1 O THR A 91 N ILE A 60 SHEET 6 AA 6 ARG A 126 THR A 130 1 O ARG A 126 N ILE A 94 SHEET 1 BA 6 GLN B 42 LYS B 46 0 SHEET 2 BA 6 ARG B 20 ASP B 24 1 O VAL B 21 N ILE B 44 SHEET 3 BA 6 TYR B 53 LEU B 54 -1 O LEU B 54 N TYR B 22 SHEET 4 BA 6 ILE B 59 THR B 65 -1 N VAL B 61 O TYR B 53 SHEET 5 BA 6 THR B 91 GLU B 97 1 O THR B 91 N ILE B 60 SHEET 6 BA 6 ARG B 126 THR B 130 1 O ARG B 126 N ILE B 94 LINK OD1 ASP A 52 MG MG A1230 1555 1555 3.11 LINK OD2 ASP A 52 MG MG A1230 1555 1555 2.44 LINK OE2 GLU A 62 MG MG A1230 1555 1555 2.28 LINK O ARG A 63 MG MG A1230 1555 1555 2.64 SITE 1 AC1 3 ASP A 52 GLU A 62 ARG A 63 SITE 1 AC2 2 ARG A 145 ARG A 149 SITE 1 AC3 2 SER A 30 ARG A 63 SITE 1 AC4 4 MET A 50 GLY A 51 GLN A 81 ARG A 84 SITE 1 AC5 3 MET B 50 GLY B 51 ARG B 84 SITE 1 AC6 4 GLN A 47 PHE B 177 PRO B 178 GLY B 179 SITE 1 AC7 3 ARG A 126 ARG B 126 DT D 1 CRYST1 141.312 141.312 85.311 90.00 90.00 120.00 P 32 2 1 12 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 0.007077 0.004086 0.000000 0.00000 SCALE2 0.000000 0.008171 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011722 0.00000 MTRIX1 1 -0.468940 -0.879440 0.081780 117.65600 1 MTRIX2 1 -0.877140 0.452840 -0.159890 76.58600 1 MTRIX3 1 0.103580 -0.146710 -0.983740 52.28900 1 MTRIX1 2 0.829320 -0.459050 -0.318590 34.84459 1 MTRIX2 2 -0.463010 -0.883730 0.068100 122.48342 1 MTRIX3 2 -0.312810 0.091030 -0.945440 22.31824 1