HEADER HYDROLASE/DNA 04-NOV-14 4WUZ TITLE CRYSTAL STRUCTURE OF LAMBDA EXONUCLEASE IN COMPLEX WITH DNA AND CA2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXONUCLEASE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 3.1.11.3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*TP*T*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3'); COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3'); COMPND 12 CHAIN: E; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 3 ORGANISM_TAXID: 10710; SOURCE 4 GENE: EXO, RED-ALPHA, REDX; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (AI); SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS EXONUCLEASE, TYPE II RESTRICTION ENDONUCLEASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHANG,C.E.BELL REVDAT 7 27-DEC-23 4WUZ 1 LINK REVDAT 6 27-NOV-19 4WUZ 1 REMARK REVDAT 5 13-SEP-17 4WUZ 1 SOURCE KEYWDS JRNL REMARK REVDAT 4 10-DEC-14 4WUZ 1 JRNL REVDAT 3 03-DEC-14 4WUZ 1 JRNL REVDAT 2 26-NOV-14 4WUZ 1 JRNL REVDAT 1 19-NOV-14 4WUZ 0 JRNL AUTH J.ZHANG,X.PAN,C.E.BELL JRNL TITL CRYSTAL STRUCTURE OF LAMBDA EXONUCLEASE IN COMPLEX WITH DNA JRNL TITL 2 AND CA(2+). JRNL REF BIOCHEMISTRY V. 53 7415 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 25370446 JRNL DOI 10.1021/BI501155Q REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 33237 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) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.319 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1754 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) : 2.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2448 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.4470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5366 REMARK 3 NUCLEIC ACID ATOMS : 533 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 236 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.21000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.31000 REMARK 3 B12 (A**2) : -0.10000 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): 0.479 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.332 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.245 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.441 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.857 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6106 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8381 ; 1.751 ; 2.058 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 674 ; 6.641 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 259 ;35.018 ;23.707 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 912 ;17.612 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;17.827 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 891 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4510 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 3367 ; 0.893 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5400 ; 1.673 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2739 ; 2.444 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2981 ; 3.784 ; 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 : NULL 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4WUZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33237 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 69.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.18700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.60 REMARK 200 R MERGE FOR SHELL (I) : 0.64400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23.4% PEG 3350, 0.3M SODIUM ACETATE, REMARK 280 0.1 M TRIS, PH 9.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 161.06400 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 80.53200 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 120.79800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.26600 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 201.33000 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -111.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 GLY C -2 REMARK 465 SER C -1 REMARK 465 HIS C 0 REMARK 465 MET C 1 REMARK 465 DT D -1 REMARK 465 DT D 0 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 15 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 72 CG CD OE1 OE2 REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 ARG A 226 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 15 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 19 CG CD OE1 NE2 REMARK 470 ARG B 45 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LYS B 180 CG CD CE NZ REMARK 470 LYS B 194 CG CD CE NZ REMARK 470 ARG B 226 CG CD NE CZ NH1 NH2 REMARK 470 ASP C 4 CG OD1 OD2 REMARK 470 GLN C 8 CG CD OE1 NE2 REMARK 470 ARG C 15 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 18 CG CD OE1 OE2 REMARK 470 GLN C 19 CG CD OE1 NE2 REMARK 470 GLU C 110 CG CD OE1 OE2 REMARK 470 LYS C 180 CG CD CE NZ REMARK 470 ARG C 226 CG CD NE CZ NH1 NH2 REMARK 470 DT D 1 P OP1 OP2 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 NH1 ARG B 28 OP2 DA E 1 1.71 REMARK 500 OG SER A 35 O2 PO4 A 302 2.09 REMARK 500 NH1 ARG C 28 O4 PO4 C 301 2.15 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 E 1 P DA E 1 OP3 -0.127 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 ARG A 143 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 PRO C 3 C - N - CA ANGL. DEV. = 10.8 DEGREES REMARK 500 DT D 1 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG D 3 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC D 7 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG D 9 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG D 9 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT D 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT D 10 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 DA D 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG D 12 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG D 12 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 DA E 1 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA E 1 C3' - O3' - P ANGL. DEV. = 12.2 DEGREES REMARK 500 DG E 2 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT E 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT E 4 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC E 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT E 7 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG E 8 C1' - O4' - C4' ANGL. DEV. = -8.3 DEGREES REMARK 500 DG E 8 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 DT E 9 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC E 12 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA E 14 O5' - C5' - C4' ANGL. DEV. = -5.8 DEGREES REMARK 500 DA E 14 O4' - C1' - C2' ANGL. DEV. = 3.0 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 THR A 2 -168.73 -165.24 REMARK 500 ASP A 21 -167.94 -78.65 REMARK 500 PHE A 147 -68.36 -14.35 REMARK 500 ILE A 150 115.92 -17.16 REMARK 500 ARG A 166 -12.98 71.49 REMARK 500 ALA B 16 35.53 -84.96 REMARK 500 ARG B 166 12.08 88.52 REMARK 500 PRO C 3 -38.30 1.33 REMARK 500 ASP C 21 -155.48 -78.71 REMARK 500 ASN C 74 53.53 38.83 REMARK 500 ILE C 105 135.91 -11.56 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 C 475 DISTANCE = 6.03 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 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 119 OD1 REMARK 620 2 ASP A 119 OD2 45.4 REMARK 620 3 GLU A 129 OE2 124.5 80.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 119 OD1 REMARK 620 2 ASP B 119 OD2 43.8 REMARK 620 3 GLU B 129 OE2 110.3 88.3 REMARK 620 4 LEU B 130 O 111.0 71.2 83.1 REMARK 620 5 DG E 2 OP1 139.7 162.0 74.0 109.3 REMARK 620 6 HOH E 103 O 73.5 116.8 110.6 163.6 67.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 119 OD1 REMARK 620 2 ASP C 119 OD2 46.5 REMARK 620 3 GLU C 129 OE2 118.4 79.6 REMARK 620 4 HOH C 463 O 73.5 88.4 78.7 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 CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA C 302 DBREF 4WUZ A 1 226 UNP P03697 EXO_LAMBD 1 226 DBREF 4WUZ B 1 226 UNP P03697 EXO_LAMBD 1 226 DBREF 4WUZ C 1 226 UNP P03697 EXO_LAMBD 1 226 DBREF 4WUZ D -1 12 PDB 4WUZ 4WUZ -1 12 DBREF 4WUZ E 1 14 PDB 4WUZ 4WUZ 1 14 SEQADV 4WUZ GLY A -2 UNP P03697 EXPRESSION TAG SEQADV 4WUZ SER A -1 UNP P03697 EXPRESSION TAG SEQADV 4WUZ HIS A 0 UNP P03697 EXPRESSION TAG SEQADV 4WUZ GLY B -2 UNP P03697 EXPRESSION TAG SEQADV 4WUZ SER B -1 UNP P03697 EXPRESSION TAG SEQADV 4WUZ HIS B 0 UNP P03697 EXPRESSION TAG SEQADV 4WUZ GLY C -2 UNP P03697 EXPRESSION TAG SEQADV 4WUZ SER C -1 UNP P03697 EXPRESSION TAG SEQADV 4WUZ HIS C 0 UNP P03697 EXPRESSION TAG SEQRES 1 A 229 GLY SER HIS MET THR PRO ASP ILE ILE LEU GLN ARG THR SEQRES 2 A 229 GLY ILE ASP VAL ARG ALA VAL GLU GLN GLY ASP ASP ALA SEQRES 3 A 229 TRP HIS LYS LEU ARG LEU GLY VAL ILE THR ALA SER GLU SEQRES 4 A 229 VAL HIS ASN VAL ILE ALA LYS PRO ARG SER GLY LYS LYS SEQRES 5 A 229 TRP PRO ASP MET LYS MET SER TYR PHE HIS THR LEU LEU SEQRES 6 A 229 ALA GLU VAL CYS THR GLY VAL ALA PRO GLU VAL ASN ALA SEQRES 7 A 229 LYS ALA LEU ALA TRP GLY LYS GLN TYR GLU ASN ASP ALA SEQRES 8 A 229 ARG THR LEU PHE GLU PHE THR SER GLY VAL ASN VAL THR SEQRES 9 A 229 GLU SER PRO ILE ILE TYR ARG ASP GLU SER MET ARG THR SEQRES 10 A 229 ALA CYS SER PRO ASP GLY LEU CYS SER ASP GLY ASN GLY SEQRES 11 A 229 LEU GLU LEU LYS CYS PRO PHE THR SER ARG ASP PHE MET SEQRES 12 A 229 LYS PHE ARG LEU GLY GLY PHE GLU ALA ILE LYS SER ALA SEQRES 13 A 229 TYR MET ALA GLN VAL GLN TYR SER MET TRP VAL THR ARG SEQRES 14 A 229 LYS ASN ALA TRP TYR PHE ALA ASN TYR ASP PRO ARG MET SEQRES 15 A 229 LYS ARG GLU GLY LEU HIS TYR VAL VAL ILE GLU ARG ASP SEQRES 16 A 229 GLU LYS TYR MET ALA SER PHE ASP GLU ILE VAL PRO GLU SEQRES 17 A 229 PHE ILE GLU LYS MET ASP GLU ALA LEU ALA GLU ILE GLY SEQRES 18 A 229 PHE VAL PHE GLY GLU GLN TRP ARG SEQRES 1 B 229 GLY SER HIS MET THR PRO ASP ILE ILE LEU GLN ARG THR SEQRES 2 B 229 GLY ILE ASP VAL ARG ALA VAL GLU GLN GLY ASP ASP ALA SEQRES 3 B 229 TRP HIS LYS LEU ARG LEU GLY VAL ILE THR ALA SER GLU SEQRES 4 B 229 VAL HIS ASN VAL ILE ALA LYS PRO ARG SER GLY LYS LYS SEQRES 5 B 229 TRP PRO ASP MET LYS MET SER TYR PHE HIS THR LEU LEU SEQRES 6 B 229 ALA GLU VAL CYS THR GLY VAL ALA PRO GLU VAL ASN ALA SEQRES 7 B 229 LYS ALA LEU ALA TRP GLY LYS GLN TYR GLU ASN ASP ALA SEQRES 8 B 229 ARG THR LEU PHE GLU PHE THR SER GLY VAL ASN VAL THR SEQRES 9 B 229 GLU SER PRO ILE ILE TYR ARG ASP GLU SER MET ARG THR SEQRES 10 B 229 ALA CYS SER PRO ASP GLY LEU CYS SER ASP GLY ASN GLY SEQRES 11 B 229 LEU GLU LEU LYS CYS PRO PHE THR SER ARG ASP PHE MET SEQRES 12 B 229 LYS PHE ARG LEU GLY GLY PHE GLU ALA ILE LYS SER ALA SEQRES 13 B 229 TYR MET ALA GLN VAL GLN TYR SER MET TRP VAL THR ARG SEQRES 14 B 229 LYS ASN ALA TRP TYR PHE ALA ASN TYR ASP PRO ARG MET SEQRES 15 B 229 LYS ARG GLU GLY LEU HIS TYR VAL VAL ILE GLU ARG ASP SEQRES 16 B 229 GLU LYS TYR MET ALA SER PHE ASP GLU ILE VAL PRO GLU SEQRES 17 B 229 PHE ILE GLU LYS MET ASP GLU ALA LEU ALA GLU ILE GLY SEQRES 18 B 229 PHE VAL PHE GLY GLU GLN TRP ARG SEQRES 1 C 229 GLY SER HIS MET THR PRO ASP ILE ILE LEU GLN ARG THR SEQRES 2 C 229 GLY ILE ASP VAL ARG ALA VAL GLU GLN GLY ASP ASP ALA SEQRES 3 C 229 TRP HIS LYS LEU ARG LEU GLY VAL ILE THR ALA SER GLU SEQRES 4 C 229 VAL HIS ASN VAL ILE ALA LYS PRO ARG SER GLY LYS LYS SEQRES 5 C 229 TRP PRO ASP MET LYS MET SER TYR PHE HIS THR LEU LEU SEQRES 6 C 229 ALA GLU VAL CYS THR GLY VAL ALA PRO GLU VAL ASN ALA SEQRES 7 C 229 LYS ALA LEU ALA TRP GLY LYS GLN TYR GLU ASN ASP ALA SEQRES 8 C 229 ARG THR LEU PHE GLU PHE THR SER GLY VAL ASN VAL THR SEQRES 9 C 229 GLU SER PRO ILE ILE TYR ARG ASP GLU SER MET ARG THR SEQRES 10 C 229 ALA CYS SER PRO ASP GLY LEU CYS SER ASP GLY ASN GLY SEQRES 11 C 229 LEU GLU LEU LYS CYS PRO PHE THR SER ARG ASP PHE MET SEQRES 12 C 229 LYS PHE ARG LEU GLY GLY PHE GLU ALA ILE LYS SER ALA SEQRES 13 C 229 TYR MET ALA GLN VAL GLN TYR SER MET TRP VAL THR ARG SEQRES 14 C 229 LYS ASN ALA TRP TYR PHE ALA ASN TYR ASP PRO ARG MET SEQRES 15 C 229 LYS ARG GLU GLY LEU HIS TYR VAL VAL ILE GLU ARG ASP SEQRES 16 C 229 GLU LYS TYR MET ALA SER PHE ASP GLU ILE VAL PRO GLU SEQRES 17 C 229 PHE ILE GLU LYS MET ASP GLU ALA LEU ALA GLU ILE GLY SEQRES 18 C 229 PHE VAL PHE GLY GLU GLN TRP ARG SEQRES 1 D 14 DT DT DT DC DG DG DT DA DC DA DG DT DA SEQRES 2 D 14 DG SEQRES 1 E 14 DA DG DC DT DA DC DT DG DT DA DC DC DG SEQRES 2 E 14 DA HET CA A 301 1 HET PO4 A 302 5 HET CA B 301 1 HET PO4 C 301 5 HET CA C 302 1 HETNAM CA CALCIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 6 CA 3(CA 2+) FORMUL 7 PO4 2(O4 P 3-) FORMUL 11 HOH *236(H2 O) HELIX 1 AA1 THR A 2 GLY A 11 1 10 HELIX 2 AA2 ASP A 13 VAL A 17 5 5 HELIX 3 AA3 ASP A 21 LEU A 27 1 7 HELIX 4 AA4 GLU A 36 ALA A 42 1 7 HELIX 5 AA5 PRO A 51 GLY A 68 1 18 HELIX 6 AA6 ASN A 74 GLY A 97 1 24 HELIX 7 AA7 THR A 135 GLY A 146 1 12 HELIX 8 AA8 PHE A 147 ALA A 149 5 3 HELIX 9 AA9 LYS A 151 ARG A 166 1 16 HELIX 10 AB1 ASP A 192 GLY A 218 1 27 HELIX 11 AB2 GLY A 222 ARG A 226 5 5 HELIX 12 AB3 THR B 2 GLY B 11 1 10 HELIX 13 AB4 ASP B 21 LEU B 29 1 9 HELIX 14 AB5 VAL B 37 ALA B 42 1 6 HELIX 15 AB6 PRO B 51 GLY B 68 1 18 HELIX 16 AB7 ALA B 75 GLY B 97 1 23 HELIX 17 AB8 THR B 135 GLY B 146 1 12 HELIX 18 AB9 PHE B 147 ILE B 150 5 4 HELIX 19 AC1 LYS B 151 ARG B 166 1 16 HELIX 20 AC2 ASP B 192 GLY B 218 1 27 HELIX 21 AC3 PRO C 3 GLY C 11 1 9 HELIX 22 AC4 ASP C 13 VAL C 17 5 5 HELIX 23 AC5 ASP C 21 LEU C 29 1 9 HELIX 24 AC6 SER C 35 VAL C 40 5 6 HELIX 25 AC7 PRO C 51 GLY C 68 1 18 HELIX 26 AC8 ASN C 74 GLY C 97 1 24 HELIX 27 AC9 THR C 135 GLY C 146 1 12 HELIX 28 AD1 PHE C 147 ILE C 150 5 4 HELIX 29 AD2 LYS C 151 ARG C 166 1 16 HELIX 30 AD3 ASP C 192 ILE C 217 1 26 SHEET 1 AA1 3 ILE A 32 THR A 33 0 SHEET 2 AA1 3 THR A 114 CYS A 116 1 O ALA A 115 N ILE A 32 SHEET 3 AA1 3 ILE A 106 TYR A 107 -1 N ILE A 106 O CYS A 116 SHEET 1 AA2 5 VAL A 100 THR A 101 0 SHEET 2 AA2 5 GLY A 120 CYS A 122 -1 O LEU A 121 N THR A 101 SHEET 3 AA2 5 GLY A 127 LYS A 131 -1 O LEU A 128 N GLY A 120 SHEET 4 AA2 5 ALA A 169 TYR A 175 1 O TYR A 171 N GLY A 127 SHEET 5 AA2 5 LEU A 184 GLU A 190 -1 O ILE A 189 N TRP A 170 SHEET 1 AA3 3 ILE B 32 THR B 33 0 SHEET 2 AA3 3 THR B 114 CYS B 116 1 O ALA B 115 N ILE B 32 SHEET 3 AA3 3 ILE B 106 TYR B 107 -1 N ILE B 106 O CYS B 116 SHEET 1 AA4 5 VAL B 100 THR B 101 0 SHEET 2 AA4 5 GLY B 120 CYS B 122 -1 O LEU B 121 N THR B 101 SHEET 3 AA4 5 GLY B 127 LYS B 131 -1 O LEU B 128 N GLY B 120 SHEET 4 AA4 5 ALA B 169 TYR B 175 1 O TYR B 171 N GLY B 127 SHEET 5 AA4 5 LEU B 184 GLU B 190 -1 O HIS B 185 N ASN B 174 SHEET 1 AA5 3 ILE C 32 THR C 33 0 SHEET 2 AA5 3 THR C 114 CYS C 116 1 O ALA C 115 N ILE C 32 SHEET 3 AA5 3 ILE C 106 TYR C 107 -1 N ILE C 106 O CYS C 116 SHEET 1 AA6 5 VAL C 100 THR C 101 0 SHEET 2 AA6 5 GLY C 120 CYS C 122 -1 O LEU C 121 N THR C 101 SHEET 3 AA6 5 GLY C 127 LYS C 131 -1 O LEU C 128 N GLY C 120 SHEET 4 AA6 5 ALA C 169 TYR C 175 1 O ALA C 173 N GLU C 129 SHEET 5 AA6 5 LEU C 184 GLU C 190 -1 O ILE C 189 N TRP C 170 LINK OD1 ASP A 119 CA CA A 301 1555 1555 2.93 LINK OD2 ASP A 119 CA CA A 301 1555 1555 2.69 LINK OE2 GLU A 129 CA CA A 301 1555 1555 2.72 LINK OD1 ASP B 119 CA CA B 301 1555 1555 3.12 LINK OD2 ASP B 119 CA CA B 301 1555 1555 2.23 LINK OE2 GLU B 129 CA CA B 301 1555 1555 2.44 LINK O LEU B 130 CA CA B 301 1555 1555 2.62 LINK CA CA B 301 OP1 DG E 2 1555 1555 3.11 LINK CA CA B 301 O HOH E 103 1555 1555 2.11 LINK OD1 ASP C 119 CA CA C 302 1555 1555 2.83 LINK OD2 ASP C 119 CA CA C 302 1555 1555 2.74 LINK OE2 GLU C 129 CA CA C 302 1555 1555 2.39 LINK CA CA C 302 O HOH C 463 1555 1555 2.74 CISPEP 1 GLN A 19 GLY A 20 0 -4.88 SITE 1 AC1 2 ASP A 119 GLU A 129 SITE 1 AC2 8 ARG A 28 THR A 33 ALA A 34 SER A 35 SITE 2 AC2 8 ALA A 115 CYS A 116 SER A 117 HOH A 440 SITE 1 AC3 5 ASP B 119 GLU B 129 LEU B 130 DG E 2 SITE 2 AC3 5 HOH E 103 SITE 1 AC4 8 ARG C 28 THR C 33 ALA C 34 SER C 35 SITE 2 AC4 8 ALA C 115 CYS C 116 SER C 117 GLN C 157 SITE 1 AC5 3 ASP C 119 GLU C 129 HOH C 463 CRYST1 80.038 80.038 241.596 90.00 90.00 120.00 P 65 18 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 0.012494 0.007213 0.000000 0.00000 SCALE2 0.000000 0.014427 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004139 0.00000