HEADER RECOMBINATION/DNA 28-JUN-03 1PVP TITLE BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF TITLE 2 SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, ALSHG BOUND TO THE TITLE 3 ENGINEERED RECOGNITION SITE LOXM7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 34-MER; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: TOP STRAND OF LOXM7 ENGINEERED DNA SUBSTRATE COMPND 6 (LOXP(C7/G28,T8/A27,A9/T26); COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 34-MER; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: BOTTOM STRAND OF LOXM7 ENGINEERED DNA SUBSTRATE COMPND 12 (LOXP(C7/G28,T8/A27,A9/T26); COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: RECOMBINASE CRE; COMPND 15 CHAIN: A, B; COMPND 16 ENGINEERED: YES; COMPND 17 MUTATION: YES; COMPND 18 OTHER_DETAILS: CRE SITE-SPECIFIC RECOMBINASE MUTANT (I174A, T258L, COMPND 19 R259S, E262H, E266G) SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA VIRUS P1; SOURCE 4 ORGANISM_TAXID: 10678; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: ESCHERICHIA VIRUS P1; SOURCE 8 ORGANISM_TAXID: 10678; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE P1; SOURCE 11 ORGANISM_COMMON: BACTERIOPHAGE P1; SOURCE 12 ORGANISM_TAXID: 10678; SOURCE 13 GENE: CRE; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET28B(+) KEYWDS CRE, RECOMBINASE, DNA, CRE-LOXP RECOMBINATION, RECOMBINATION-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.P.BALDWIN,S.S.MARTIN,J.ABEL,K.A.GELATO,H.KIM,P.G.SCHULTZ, AUTHOR 2 S.W.SANTORO REVDAT 7 16-AUG-23 1PVP 1 REMARK REVDAT 6 07-APR-21 1PVP 1 COMPND SOURCE REMARK DBREF REVDAT 6 2 1 SEQADV HET HETNAM FORMUL REVDAT 5 01-FEB-12 1PVP 1 VERSN REVDAT 4 13-JUL-11 1PVP 1 SHEET REVDAT 3 24-FEB-09 1PVP 1 VERSN REVDAT 2 20-APR-04 1PVP 1 HELIX REVDAT 1 17-FEB-04 1PVP 0 JRNL AUTH E.P.BALDWIN,S.S.MARTIN,J.ABEL,K.A.GELATO,H.KIM,P.G.SCHULTZ, JRNL AUTH 2 S.W.SANTORO JRNL TITL A SPECIFICITY SWITCH IN SELECTED CRE RECOMBINASE VARIANTS IS JRNL TITL 2 MEDIATED BY MACROMOLECULAR PLASTICITY AND WATER. JRNL REF CHEM.BIOL. V. 10 1085 2003 JRNL REFN ISSN 1074-5521 JRNL PMID 14652076 JRNL DOI 10.1016/J.CHEMBIOL.2003.10.015 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.W.SANTORO,P.G.SCHULTZ REMARK 1 TITL DIRECTED EVOLUTION OF THE SITE SPECIFICITY OF CRE REMARK 1 TITL 2 RECOMBINASE. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 99 4185 2002 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.022039799 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.S.MARTIN,V.C.CHU,E.BALDWIN REMARK 1 TITL MODULATION OF THE ACTIVE COMPLEX ASSEMBLY AND TURNOVER RATE REMARK 1 TITL 2 BY PROTEIN-DNA INTERACTIONS IN CRE-LOXP RECOMBINATION. REMARK 1 REF BIOCHEMISTRY V. 42 6814 2003 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI0272306 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.S.MARTIN,E.PULIDO,V.C.CHU,T.S.LECHNER,E.P.BALDWIN REMARK 1 TITL THE ORDER OF STRAND EXCHANGES IN CRE-LOXP RECOMBINATION AND REMARK 1 TITL 2 ITS BASIS SUGGESTED BY THE CRYSTAL STRUCTURE OF A CRE-LOXP REMARK 1 TITL 3 HOLLIDAY JUNCTION COMPLEX. REMARK 1 REF J.MOL.BIOL. V. 319 107 2002 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1016/S0022-2836(02)00246-2 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 40013 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1916 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 44309 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5053 REMARK 3 NUCLEIC ACID ATOMS : 1348 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 47.000 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.006 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.200 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : ISOTROPIC REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PVP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019610. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46927 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 81.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7000 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) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.36500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: TNT REMARK 200 STARTING MODEL: PDB ENTRY 1KBU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, CALCIUM CHLORIDE, 2,4 REMARK 280 -METHYLPENTANEDIOL, PH 5.75, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 90.34500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 90.34500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 53.89000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.73500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 53.89000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.73500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 90.34500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 53.89000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 60.73500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 90.34500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 53.89000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 60.73500 REMARK 290 SMTRY3 8 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 300 REMARK: THE SECOND PART OF THE TETRAMERIC BIOLOGICAL ASSEMBLY IS REMARK 300 GENERATED BY THE TWO FOLD AXIS: X, -Y+1, -Z+1. 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, B 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 121.47000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 180.69000 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 DT C 17 REMARK 465 MET A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 SER A 2 REMARK 465 ASN A 3 REMARK 465 LEU A 4 REMARK 465 LEU A 5 REMARK 465 THR A 6 REMARK 465 VAL A 7 REMARK 465 HIS A 8 REMARK 465 GLN A 9 REMARK 465 ASN A 10 REMARK 465 LEU A 11 REMARK 465 PRO A 12 REMARK 465 ALA A 13 REMARK 465 LEU A 14 REMARK 465 PRO A 15 REMARK 465 VAL A 16 REMARK 465 ASP A 17 REMARK 465 ALA A 18 REMARK 465 GLY A 342 REMARK 465 ASP A 343 REMARK 465 MET B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 HIS B 1 REMARK 465 SER B 2 REMARK 465 ASN B 3 REMARK 465 LEU B 4 REMARK 465 LEU B 5 REMARK 465 THR B 6 REMARK 465 VAL B 7 REMARK 465 HIS B 8 REMARK 465 GLN B 9 REMARK 465 ASN B 10 REMARK 465 LEU B 11 REMARK 465 PRO B 12 REMARK 465 ALA B 13 REMARK 465 LEU B 14 REMARK 465 PRO B 15 REMARK 465 VAL B 16 REMARK 465 ASP B 17 REMARK 465 ALA B 18 REMARK 465 ASN B 327 REMARK 465 LEU B 328 REMARK 465 ASP B 329 REMARK 465 SER B 330 REMARK 465 GLU B 331 REMARK 465 GLY B 342 REMARK 465 ASP B 343 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 DA C 18 P OP1 OP2 O5' C5' C4' O4' REMARK 470 DA C 18 C3' C2' C1' N9 C8 N7 C5 REMARK 470 DA C 18 C6 N6 N1 C2 N3 C4 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY A 191 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 189 CG OD1 OD2 REMARK 480 VAL A 209 CG1 CG2 REMARK 480 ASN A 236 C O CB REMARK 480 LYS A 276 CB CG CD CE NZ REMARK 480 ARG A 282 CA CB CG CD REMARK 480 GLY A 303 CA REMARK 480 PRO A 307 CB CG CD REMARK 480 GLN A 311 CB CG CD OE1 NE2 REMARK 480 ASN A 317 CB CG OD1 ND2 REMARK 480 ARG B 24 CD NE CZ NH1 NH2 REMARK 480 MET B 28 CB CG SD CE REMARK 480 ARG B 130 CB CG REMARK 480 ILE B 320 CB CG1 CG2 CD1 REMARK 480 ASN B 323 CB CG OD1 ND2 REMARK 480 ILE B 325 CB CG1 CG2 CD1 REMARK 480 ARG B 326 N REMARK 480 ARG B 337 CB CG CD 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 N7 DA D 1 O HOH D 63 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 DT D 10 O3' DT D 10 C3' -0.041 REMARK 500 DT D 10 C5 DT D 10 C7 0.049 REMARK 500 DC D 15 O3' DA D 16 P 0.230 REMARK 500 DC D 19 O3' DA D 20 P -0.343 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 DA C 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC C 7 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 DT C 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 12 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT C 12 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DT C 26 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT C 34 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA D 3 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DA D 3 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DA D 4 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DA D 4 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 DT D 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT D 10 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA D 16 O3' - P - O5' ANGL. DEV. = 37.2 DEGREES REMARK 500 DA D 16 O3' - P - OP2 ANGL. DEV. = -15.5 DEGREES REMARK 500 DT D 26 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT D 32 C3' - C2' - C1' ANGL. DEV. = -6.7 DEGREES REMARK 500 DT D 32 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 ARG A 173 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 THR A 202 N - CA - C ANGL. DEV. = 21.0 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 ASP A 33 53.06 -109.92 REMARK 500 ASN A 60 71.17 46.25 REMARK 500 ASP A 109 20.31 -69.57 REMARK 500 ASP A 126 38.15 -99.36 REMARK 500 ALA A 127 3.56 -150.26 REMARK 500 ASP A 184 7.40 -61.32 REMARK 500 SER A 186 -157.49 -101.88 REMARK 500 THR A 188 -157.86 -94.49 REMARK 500 ASP A 189 103.05 -37.38 REMARK 500 ILE A 197 -150.95 -115.16 REMARK 500 THR A 202 -160.75 5.37 REMARK 500 LEU A 203 -109.72 77.45 REMARK 500 SER A 205 -142.54 -143.32 REMARK 500 VAL A 209 -20.78 -156.18 REMARK 500 GLU A 210 123.99 56.88 REMARK 500 SER A 228 -33.94 -37.62 REMARK 500 ALA A 231 -19.21 -48.78 REMARK 500 PRO A 234 -8.54 -32.67 REMARK 500 SER A 251 138.37 -173.60 REMARK 500 ALA A 275 134.77 4.90 REMARK 500 LYS A 276 152.22 -36.28 REMARK 500 ASP A 277 -163.78 -108.44 REMARK 500 ASP A 278 59.16 -13.15 REMARK 500 SER A 279 133.20 -6.03 REMARK 500 GLN A 281 177.98 89.00 REMARK 500 ARG A 282 98.49 76.43 REMARK 500 SER A 305 138.34 158.23 REMARK 500 ILE A 309 -70.96 -79.74 REMARK 500 ASN A 317 78.69 -119.06 REMARK 500 VAL A 318 -35.30 -10.13 REMARK 500 ASN A 319 -17.43 -46.77 REMARK 500 ASP B 33 51.69 -109.76 REMARK 500 GLN B 35 -8.68 -57.67 REMARK 500 GLU B 129 124.54 9.76 REMARK 500 ALA B 248 -173.38 -67.09 REMARK 500 ALA B 249 70.11 -161.83 REMARK 500 ASP B 277 164.88 -29.64 REMARK 500 TYR B 283 30.19 73.95 REMARK 500 ASN B 317 -140.74 -97.67 REMARK 500 VAL B 318 35.34 -159.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KBU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CRE-LOXP HOLLIDAY JUNCTION COMPLEX REMARK 900 RELATED ID: 1MA7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CRE-LOXP(A8/T27) HOLLIDAY JUNCTION COMPLEX REMARK 900 RELATED ID: 1CRX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A COVALENT CRE-SUICIDE SUBSTRATE DNA COMPLEX REMARK 900 RELATED ID: 4CRX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN UNCLEAVED COMPLEX OF CRE BOUND TO LOXS, A REMARK 900 SYMMETRIZED LOX SEQUENCE REMARK 900 RELATED ID: 1NZB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CRE-LOXP PRECLEAVAGE COMPLEX REMARK 900 RELATED ID: 1OUQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CRE-LOXP COVALENT COMPLEX REMARK 900 RELATED ID: 3CRX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CRE COMPLEXED WITH AN IMMOBILIZED DNA HOLLIDAY REMARK 900 JUNCTION REMARK 900 RELATED ID: 1F44 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A TRIMERIC CRE-LOX SYNAPSE REMARK 900 RELATED ID: 1PVQ RELATED DB: PDB REMARK 900 BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF REMARK 900 SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, LNSGG BOUND TO REMARK 900 THE ENGINEERED RECOGNITION SITE LOXM7 REMARK 900 RELATED ID: 1PVR RELATED DB: PDB REMARK 900 BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF REMARK 900 SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, LNSGG BOUND TO REMARK 900 THE LOXP (WILDTYPE) RECOGNITION SITE DBREF 1PVP C 1 34 GB M10145 M10145.1 24 57 DBREF 1PVP D 1 34 GB M10494 M10494.1 14 47 DBREF 1PVP A 2 343 UNP P06956 RECR_BPP1 2 343 DBREF 1PVP B 2 343 UNP P06956 RECR_BPP1 2 343 SEQADV 1PVP DC C 7 GB M10145 DT 30 ENGINEERED MUTATION SEQADV 1PVP DT C 8 GB M10145 DC 31 ENGINEERED MUTATION SEQADV 1PVP DA C 9 GB M10145 DG 32 ENGINEERED MUTATION SEQADV 1PVP DT C 26 GB M10145 DC 49 ENGINEERED MUTATION SEQADV 1PVP DA C 27 GB M10145 DG 50 ENGINEERED MUTATION SEQADV 1PVP DG C 28 GB M10145 DA 51 ENGINEERED MUTATION SEQADV 1PVP DC D 7 GB M10494 DT 20 ENGINEERED MUTATION SEQADV 1PVP DT D 8 GB M10494 DC 21 ENGINEERED MUTATION SEQADV 1PVP DA D 9 GB M10494 DG 22 ENGINEERED MUTATION SEQADV 1PVP DT D 26 GB M10494 DC 39 ENGINEERED MUTATION SEQADV 1PVP DA D 27 GB M10494 DG 40 ENGINEERED MUTATION SEQADV 1PVP DG D 28 GB M10494 DA 41 ENGINEERED MUTATION SEQADV 1PVP MET A -5 UNP P06956 INITIATING METHIONINE SEQADV 1PVP HIS A -4 UNP P06956 EXPRESSION TAG SEQADV 1PVP HIS A -3 UNP P06956 EXPRESSION TAG SEQADV 1PVP HIS A -2 UNP P06956 EXPRESSION TAG SEQADV 1PVP HIS A -1 UNP P06956 EXPRESSION TAG SEQADV 1PVP HIS A 0 UNP P06956 EXPRESSION TAG SEQADV 1PVP HIS A 1 UNP P06956 EXPRESSION TAG SEQADV 1PVP ALA A 174 UNP P06956 ILE 174 ENGINEERED MUTATION SEQADV 1PVP LEU A 258 UNP P06956 THR 258 ENGINEERED MUTATION SEQADV 1PVP SER A 259 UNP P06956 ARG 259 ENGINEERED MUTATION SEQADV 1PVP HIS A 262 UNP P06956 GLU 262 ENGINEERED MUTATION SEQADV 1PVP GLY A 266 UNP P06956 GLU 266 ENGINEERED MUTATION SEQADV 1PVP MET B -5 UNP P06956 INITIATING METHIONINE SEQADV 1PVP HIS B -4 UNP P06956 EXPRESSION TAG SEQADV 1PVP HIS B -3 UNP P06956 EXPRESSION TAG SEQADV 1PVP HIS B -2 UNP P06956 EXPRESSION TAG SEQADV 1PVP HIS B -1 UNP P06956 EXPRESSION TAG SEQADV 1PVP HIS B 0 UNP P06956 EXPRESSION TAG SEQADV 1PVP HIS B 1 UNP P06956 EXPRESSION TAG SEQADV 1PVP ALA B 174 UNP P06956 ILE 174 ENGINEERED MUTATION SEQADV 1PVP LEU B 258 UNP P06956 THR 258 ENGINEERED MUTATION SEQADV 1PVP SER B 259 UNP P06956 ARG 259 ENGINEERED MUTATION SEQADV 1PVP HIS B 262 UNP P06956 GLU 262 ENGINEERED MUTATION SEQADV 1PVP GLY B 266 UNP P06956 GLU 266 ENGINEERED MUTATION SEQRES 1 C 34 DA DT DA DA DC DT DC DT DA DT DA DT DA SEQRES 2 C 34 DA DT DG DT DA DT DG DC DT DA DT DA DT SEQRES 3 C 34 DA DG DA DG DT DT DA DT SEQRES 1 D 34 DA DT DA DA DC DT DC DT DA DT DA DT DA SEQRES 2 D 34 DG DC DA DT DA DC DA DT DT DA DT DA DT SEQRES 3 D 34 DA DG DA DG DT DT DA DT SEQRES 1 A 349 MET HIS HIS HIS HIS HIS HIS SER ASN LEU LEU THR VAL SEQRES 2 A 349 HIS GLN ASN LEU PRO ALA LEU PRO VAL ASP ALA THR SER SEQRES 3 A 349 ASP GLU VAL ARG LYS ASN LEU MET ASP MET PHE ARG ASP SEQRES 4 A 349 ARG GLN ALA PHE SER GLU HIS THR TRP LYS MET LEU LEU SEQRES 5 A 349 SER VAL CYS ARG SER TRP ALA ALA TRP CYS LYS LEU ASN SEQRES 6 A 349 ASN ARG LYS TRP PHE PRO ALA GLU PRO GLU ASP VAL ARG SEQRES 7 A 349 ASP TYR LEU LEU TYR LEU GLN ALA ARG GLY LEU ALA VAL SEQRES 8 A 349 LYS THR ILE GLN GLN HIS LEU GLY GLN LEU ASN MET LEU SEQRES 9 A 349 HIS ARG ARG SER GLY LEU PRO ARG PRO SER ASP SER ASN SEQRES 10 A 349 ALA VAL SER LEU VAL MET ARG ARG ILE ARG LYS GLU ASN SEQRES 11 A 349 VAL ASP ALA GLY GLU ARG ALA LYS GLN ALA LEU ALA PHE SEQRES 12 A 349 GLU ARG THR ASP PHE ASP GLN VAL ARG SER LEU MET GLU SEQRES 13 A 349 ASN SER ASP ARG CYS GLN ASP ILE ARG ASN LEU ALA PHE SEQRES 14 A 349 LEU GLY ILE ALA TYR ASN THR LEU LEU ARG ALA ALA GLU SEQRES 15 A 349 ILE ALA ARG ILE ARG VAL LYS ASP ILE SER ARG THR ASP SEQRES 16 A 349 GLY GLY ARG MET LEU ILE HIS ILE GLY ARG THR LYS THR SEQRES 17 A 349 LEU VAL SER THR ALA GLY VAL GLU LYS ALA LEU SER LEU SEQRES 18 A 349 GLY VAL THR LYS LEU VAL GLU ARG TRP ILE SER VAL SER SEQRES 19 A 349 GLY VAL ALA ASP ASP PRO ASN ASN TYR LEU PHE CYS ARG SEQRES 20 A 349 VAL ARG LYS ASN GLY VAL ALA ALA PRO SER ALA THR SER SEQRES 21 A 349 GLN LEU SER LEU SER ALA LEU HIS GLY ILE PHE GLY ALA SEQRES 22 A 349 THR HIS ARG LEU ILE TYR GLY ALA LYS ASP ASP SER GLY SEQRES 23 A 349 GLN ARG TYR LEU ALA TRP SER GLY HIS SER ALA ARG VAL SEQRES 24 A 349 GLY ALA ALA ARG ASP MET ALA ARG ALA GLY VAL SER ILE SEQRES 25 A 349 PRO GLU ILE MET GLN ALA GLY GLY TRP THR ASN VAL ASN SEQRES 26 A 349 ILE VAL MET ASN TYR ILE ARG ASN LEU ASP SER GLU THR SEQRES 27 A 349 GLY ALA MET VAL ARG LEU LEU GLU ASP GLY ASP SEQRES 1 B 349 MET HIS HIS HIS HIS HIS HIS SER ASN LEU LEU THR VAL SEQRES 2 B 349 HIS GLN ASN LEU PRO ALA LEU PRO VAL ASP ALA THR SER SEQRES 3 B 349 ASP GLU VAL ARG LYS ASN LEU MET ASP MET PHE ARG ASP SEQRES 4 B 349 ARG GLN ALA PHE SER GLU HIS THR TRP LYS MET LEU LEU SEQRES 5 B 349 SER VAL CYS ARG SER TRP ALA ALA TRP CYS LYS LEU ASN SEQRES 6 B 349 ASN ARG LYS TRP PHE PRO ALA GLU PRO GLU ASP VAL ARG SEQRES 7 B 349 ASP TYR LEU LEU TYR LEU GLN ALA ARG GLY LEU ALA VAL SEQRES 8 B 349 LYS THR ILE GLN GLN HIS LEU GLY GLN LEU ASN MET LEU SEQRES 9 B 349 HIS ARG ARG SER GLY LEU PRO ARG PRO SER ASP SER ASN SEQRES 10 B 349 ALA VAL SER LEU VAL MET ARG ARG ILE ARG LYS GLU ASN SEQRES 11 B 349 VAL ASP ALA GLY GLU ARG ALA LYS GLN ALA LEU ALA PHE SEQRES 12 B 349 GLU ARG THR ASP PHE ASP GLN VAL ARG SER LEU MET GLU SEQRES 13 B 349 ASN SER ASP ARG CYS GLN ASP ILE ARG ASN LEU ALA PHE SEQRES 14 B 349 LEU GLY ILE ALA TYR ASN THR LEU LEU ARG ALA ALA GLU SEQRES 15 B 349 ILE ALA ARG ILE ARG VAL LYS ASP ILE SER ARG THR ASP SEQRES 16 B 349 GLY GLY ARG MET LEU ILE HIS ILE GLY ARG THR LYS THR SEQRES 17 B 349 LEU VAL SER THR ALA GLY VAL GLU LYS ALA LEU SER LEU SEQRES 18 B 349 GLY VAL THR LYS LEU VAL GLU ARG TRP ILE SER VAL SER SEQRES 19 B 349 GLY VAL ALA ASP ASP PRO ASN ASN TYR LEU PHE CYS ARG SEQRES 20 B 349 VAL ARG LYS ASN GLY VAL ALA ALA PRO SER ALA THR SER SEQRES 21 B 349 GLN LEU SER LEU SER ALA LEU HIS GLY ILE PHE GLY ALA SEQRES 22 B 349 THR HIS ARG LEU ILE TYR GLY ALA LYS ASP ASP SER GLY SEQRES 23 B 349 GLN ARG TYR LEU ALA TRP SER GLY HIS SER ALA ARG VAL SEQRES 24 B 349 GLY ALA ALA ARG ASP MET ALA ARG ALA GLY VAL SER ILE SEQRES 25 B 349 PRO GLU ILE MET GLN ALA GLY GLY TRP THR ASN VAL ASN SEQRES 26 B 349 ILE VAL MET ASN TYR ILE ARG ASN LEU ASP SER GLU THR SEQRES 27 B 349 GLY ALA MET VAL ARG LEU LEU GLU ASP GLY ASP FORMUL 5 HOH *256(H2 O) HELIX 1 1 THR A 19 ASP A 33 1 15 HELIX 2 2 ARG A 34 PHE A 37 5 4 HELIX 3 3 SER A 38 ASN A 59 1 22 HELIX 4 4 GLU A 67 ARG A 81 1 15 HELIX 5 5 ALA A 84 ARG A 101 1 18 HELIX 6 6 ARG A 106 ASP A 109 5 4 HELIX 7 7 SER A 110 ASP A 126 1 17 HELIX 8 8 GLU A 138 GLU A 150 1 13 HELIX 9 9 ARG A 154 LEU A 171 1 18 HELIX 10 10 ARG A 173 ILE A 180 1 8 HELIX 11 11 SER A 214 GLY A 229 1 16 HELIX 12 12 VAL A 230 ASP A 233 5 4 HELIX 13 13 SER A 257 GLY A 274 1 18 HELIX 14 14 HIS A 289 ALA A 302 1 14 HELIX 15 15 SER A 305 GLY A 313 1 9 HELIX 16 16 VAL A 318 ARG A 326 1 9 HELIX 17 17 GLY A 333 GLU A 340 1 8 HELIX 18 18 THR B 19 ASP B 33 1 15 HELIX 19 19 ARG B 34 PHE B 37 5 4 HELIX 20 20 SER B 38 ASN B 59 1 22 HELIX 21 21 GLU B 67 ARG B 81 1 15 HELIX 22 22 ALA B 84 ARG B 101 1 18 HELIX 23 23 ARG B 106 ASP B 109 5 4 HELIX 24 24 SER B 110 VAL B 125 1 16 HELIX 25 25 GLU B 138 GLU B 150 1 13 HELIX 26 26 ARG B 154 LEU B 171 1 18 HELIX 27 27 ARG B 173 ALA B 178 1 6 HELIX 28 28 ARG B 181 LYS B 183 5 3 HELIX 29 29 SER B 214 GLY B 229 1 16 HELIX 30 30 VAL B 230 ASP B 233 5 4 HELIX 31 31 SER B 257 GLY B 274 1 18 HELIX 32 32 HIS B 289 ALA B 302 1 14 HELIX 33 33 SER B 305 GLY B 313 1 9 HELIX 34 34 ASN B 319 TYR B 324 1 6 HELIX 35 35 GLY B 333 GLU B 340 1 8 SHEET 1 A 2 LEU A 194 ILE A 195 0 SHEET 2 A 2 LYS A 211 ALA A 212 -1 O LYS A 211 N ILE A 195 SHEET 1 B 2 ARG A 241 VAL A 242 0 SHEET 2 B 2 ALA A 248 ALA A 249 -1 O ALA A 249 N ARG A 241 SHEET 1 C 3 ILE B 185 ARG B 187 0 SHEET 2 C 3 MET B 193 THR B 200 -1 O LEU B 194 N SER B 186 SHEET 3 C 3 LEU B 203 ALA B 212 -1 O VAL B 209 N ILE B 197 SHEET 1 D 2 ARG B 241 VAL B 242 0 SHEET 2 D 2 ALA B 248 ALA B 249 -1 O ALA B 249 N ARG B 241 CISPEP 1 PHE A 64 PRO A 65 0 -3.29 CISPEP 2 PHE B 64 PRO B 65 0 -2.18 CRYST1 107.780 121.470 180.690 90.00 90.00 90.00 C 2 2 21 16 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 0.009278 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008232 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005534 0.00000