HEADER RECOMBINATION/DNA 19-JUL-21 7RHY TITLE CRE RECOMBINASE MUTANT (D33A/A36V/R192A) IN COMPLEX WITH LOXA DNA TITLE 2 HAIRPIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECOMBINASE CRE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (49-MER); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE P1; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE P1; SOURCE 4 ORGANISM_TAXID: 10678; SOURCE 5 GENE: CRE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE P1; SOURCE 11 ORGANISM_TAXID: 10678 KEYWDS CRE, RECOMBINASE, MONOMER, HAIRPIN, RECOMBINATION-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR K.STACHOWSKI,M.P.FOSTER REVDAT 2 03-AUG-22 7RHY 1 JRNL REVDAT 1 19-JAN-22 7RHY 0 JRNL AUTH K.STACHOWSKI,A.S.NORRIS,D.POTTER,V.H.WYSOCKI,M.P.FOSTER JRNL TITL MECHANISMS OF CRE RECOMBINASE SYNAPTIC COMPLEX ASSEMBLY AND JRNL TITL 2 ACTIVATION ILLUMINATED BY CRYO-EM. JRNL REF NUCLEIC ACIDS RES. V. 50 1753 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35104890 JRNL DOI 10.1093/NAR/GKAC032 REMARK 2 REMARK 2 RESOLUTION. 3.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, EPU, CRYOSPARC, ISOLDE, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2HOI REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 248.400 REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.910 REMARK 3 NUMBER OF PARTICLES : 146715 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7RHY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000257367. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : COMPLEX OF CRE RECOMBINASE REMARK 245 MUTANT D33A/A36V/R192A AND LOXA REMARK 245 DNA HAIRPIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 7.50 REMARK 245 SAMPLE SUPPORT DETAILS : PELCO EASIGLOW AT 20 MA REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 6235 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 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 THR A 19 REMARK 465 ARG A 199 REMARK 465 THR A 200 REMARK 465 LYS A 201 REMARK 465 THR A 202 REMARK 465 LEU A 203 REMARK 465 VAL A 204 REMARK 465 SER A 205 REMARK 465 THR A 206 REMARK 465 ALA A 207 REMARK 465 SER A 330 REMARK 465 GLU A 331 REMARK 465 THR A 332 REMARK 465 GLY A 333 REMARK 465 ALA A 334 REMARK 465 MET A 335 REMARK 465 VAL A 336 REMARK 465 ARG A 337 REMARK 465 LEU A 338 REMARK 465 LEU A 339 REMARK 465 GLU A 340 REMARK 465 ASP A 341 REMARK 465 GLY A 342 REMARK 465 ASP A 343 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 H ARG A 181 OD2 ASP A 184 1.59 REMARK 500 O SER A 20 H ARG A 24 1.60 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 DC B 21 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC B 26 O4' - C1' - N1 ANGL. DEV. = 2.2 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 319 1.07 -66.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-24471 RELATED DB: EMDB REMARK 900 CRE RECOMBINASE MUTANT (D33A/A36V/R192A) IN COMPLEX WITH LOXA DNA REMARK 900 HAIRPIN DBREF 7RHY A 1 343 UNP P06956 RECR_BPP1 1 343 DBREF 7RHY B -1 47 PDB 7RHY 7RHY -1 47 SEQADV 7RHY ALA A 33 UNP P06956 ASP 33 ENGINEERED MUTATION SEQADV 7RHY VAL A 36 UNP P06956 ALA 36 ENGINEERED MUTATION SEQADV 7RHY ALA A 192 UNP P06956 ARG 192 ENGINEERED MUTATION SEQRES 1 A 343 MET SER ASN LEU LEU THR VAL HIS GLN ASN LEU PRO ALA SEQRES 2 A 343 LEU PRO VAL ASP ALA THR SER ASP GLU VAL ARG LYS ASN SEQRES 3 A 343 LEU MET ASP MET PHE ARG ALA ARG GLN VAL PHE SER GLU SEQRES 4 A 343 HIS THR TRP LYS MET LEU LEU SER VAL CYS ARG SER TRP SEQRES 5 A 343 ALA ALA TRP CYS LYS LEU ASN ASN ARG LYS TRP PHE PRO SEQRES 6 A 343 ALA GLU PRO GLU ASP VAL ARG ASP TYR LEU LEU TYR LEU SEQRES 7 A 343 GLN ALA ARG GLY LEU ALA VAL LYS THR ILE GLN GLN HIS SEQRES 8 A 343 LEU GLY GLN LEU ASN MET LEU HIS ARG ARG SER GLY LEU SEQRES 9 A 343 PRO ARG PRO SER ASP SER ASN ALA VAL SER LEU VAL MET SEQRES 10 A 343 ARG ARG ILE ARG LYS GLU ASN VAL ASP ALA GLY GLU ARG SEQRES 11 A 343 ALA LYS GLN ALA LEU ALA PHE GLU ARG THR ASP PHE ASP SEQRES 12 A 343 GLN VAL ARG SER LEU MET GLU ASN SER ASP ARG CYS GLN SEQRES 13 A 343 ASP ILE ARG ASN LEU ALA PHE LEU GLY ILE ALA TYR ASN SEQRES 14 A 343 THR LEU LEU ARG ILE ALA GLU ILE ALA ARG ILE ARG VAL SEQRES 15 A 343 LYS ASP ILE SER ARG THR ASP GLY GLY ALA MET LEU ILE SEQRES 16 A 343 HIS ILE GLY ARG THR LYS THR LEU VAL SER THR ALA GLY SEQRES 17 A 343 VAL GLU LYS ALA LEU SER LEU GLY VAL THR LYS LEU VAL SEQRES 18 A 343 GLU ARG TRP ILE SER VAL SER GLY VAL ALA ASP ASP PRO SEQRES 19 A 343 ASN ASN TYR LEU PHE CYS ARG VAL ARG LYS ASN GLY VAL SEQRES 20 A 343 ALA ALA PRO SER ALA THR SER GLN LEU SER THR ARG ALA SEQRES 21 A 343 LEU GLU GLY ILE PHE GLU ALA THR HIS ARG LEU ILE TYR SEQRES 22 A 343 GLY ALA LYS ASP ASP SER GLY GLN ARG TYR LEU ALA TRP SEQRES 23 A 343 SER GLY HIS SER ALA ARG VAL GLY ALA ALA ARG ASP MET SEQRES 24 A 343 ALA ARG ALA GLY VAL SER ILE PRO GLU ILE MET GLN ALA SEQRES 25 A 343 GLY GLY TRP THR ASN VAL ASN ILE VAL MET ASN TYR ILE SEQRES 26 A 343 ARG ASN LEU ASP SER GLU THR GLY ALA MET VAL ARG LEU SEQRES 27 A 343 LEU GLU ASP GLY ASP SEQRES 1 B 49 DG DC DA DT DA DA DC DT DT DC DG DT DA SEQRES 2 B 49 DT DA DG DC DA DT DA DT DG DC DG DA DA SEQRES 3 B 49 DG DC DA DT DA DT DG DC DT DA DT DA DC SEQRES 4 B 49 DG DA DA DG DT DT DA DT DG DC HELIX 1 AA1 SER A 20 ARG A 34 1 15 HELIX 2 AA2 SER A 38 ASN A 59 1 22 HELIX 3 AA3 GLU A 67 ARG A 81 1 15 HELIX 4 AA4 ALA A 84 GLY A 103 1 20 HELIX 5 AA5 ARG A 106 ASP A 109 5 4 HELIX 6 AA6 SER A 110 ALA A 127 1 18 HELIX 7 AA7 GLU A 138 GLU A 150 1 13 HELIX 8 AA8 ARG A 154 THR A 170 1 17 HELIX 9 AA9 ARG A 173 ALA A 178 1 6 HELIX 10 AB1 ARG A 179 ILE A 180 5 2 HELIX 11 AB2 ARG A 181 LYS A 183 5 3 HELIX 12 AB3 GLY A 216 GLY A 229 1 14 HELIX 13 AB4 VAL A 230 ASP A 233 5 4 HELIX 14 AB5 SER A 257 TYR A 273 1 17 HELIX 15 AB6 SER A 287 ALA A 302 1 16 HELIX 16 AB7 SER A 305 GLY A 314 1 10 HELIX 17 AB8 ASN A 319 ILE A 325 1 7 SHEET 1 AA1 3 ILE A 185 ARG A 187 0 SHEET 2 AA1 3 MET A 193 ILE A 197 -1 O LEU A 194 N SER A 186 SHEET 3 AA1 3 VAL A 209 LEU A 213 -1 O LYS A 211 N ILE A 195 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000