HEADER SITE-SPECIFIC RECOMBINASE 31-AUG-93 1GDR TITLE MODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PACKING TITLE 2 OF GAMMA DELTA RESOLVASE SUBUNITS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA DELTA-RESOLVASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS SITE-SPECIFIC RECOMBINASE EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR P.A.RICE,T.A.STEITZ REVDAT 3 07-FEB-24 1GDR 1 SHEET REVDAT 2 24-FEB-09 1GDR 1 VERSN REVDAT 1 30-APR-94 1GDR 0 JRNL AUTH P.A.RICE,T.A.STEITZ JRNL TITL MODEL FOR A DNA-MEDIATED SYNAPTIC COMPLEX SUGGESTED BY JRNL TITL 2 CRYSTAL PACKING OF GAMMA DELTA RESOLVASE SUBUNITS. JRNL REF EMBO J. V. 13 1514 1994 JRNL REFN ISSN 0261-4189 JRNL PMID 8156989 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.R.SANDERSON,P.S.FREEMONT,P.A.RICE,A.GOLDMAN,G.F.HATFULL, REMARK 1 AUTH 2 N.D.F.GRINDLEY REMARK 1 TITL THE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE SITE REMARK 1 TITL 2 SPECIFIC RECOMBINATION ENZYME GD RESOLVASE AT 2.7 RESOLUTION REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 63 1323 1990 REMARK 1 REFN ISSN 0092-8674 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.S.ABDEL-MEGUID,H.M.K.MURTHY,T.A.STEITZ REMARK 1 TITL PRELIMINARY X-RAY DIFFRACTION STUDIES OF THE PUTATIVE REMARK 1 TITL 2 CATALYTIC DOMAIN OF GD RESOLVASE FROM ESCHERICHIA COLI REMARK 1 REF J.BIOL.CHEM. V. 261 15934 1986 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.S.ABDEL-MUGUID,N.D.F.GRINDLEY,N.S.TEMPLETON,T.A.STEITZ REMARK 1 TITL CLEAVAGE OF THE SITE-SPECIFIC RECOMBINATION PROTEIN GD REMARK 1 TITL 2 RESOLVASE: THE SMALLER OF TWO FRAGMENTS BINDS DNA REMARK 1 TITL 3 SPECIFICALLY REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 81 2001 1984 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 4 REMARK 1 AUTH P.C.WEBER,D.L.OLLIS,W.R.BEBRIN,S.S.ABDEL-MEGUID,T.A.STEITZ REMARK 1 TITL CRYSTALLIZATION OF RESOLVASE, A REPRESSOR THAT ALSO REMARK 1 TITL 2 CATALYZES SITE-SPECIFIC DNA RECOMBINATION REMARK 1 REF J.MOL.BIOL. V. 157 689 1982 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.310 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 105 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 3.550 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GDR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173537. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 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 56.70000 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 113.40000 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 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 56.70000 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 113.40000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.70000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 113.40000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 56.70000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 113.40000 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 MATRIX GIVEN BELOW WILL APPROXIMATELY SUPERIMPOSE REMARK 300 MONOMER-B FROM THE C2221 CRYSTAL STRUCTURE ONTO THE REMARK 300 THE STRUCTURE PRESENTED IN THIS ENTRY. REMARK 300 REMARK 300 0.77672 0.02093 -0.62949 (X - 25.22352) + -9.96070 REMARK 300 0.62967 -0.00232 0.77686 (X - 53.97461) + 43.29039 REMARK 300 0.01480 -0.99978 -0.01498 (X - 47.00185) + 12.88526 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 400 REMARK 400 COMPOUND REMARK 400 THESE CRYSTALS DO NOT DIFFRACT AS WELL AS THE C2221 REMARK 400 CRYSTAL FORM (PDB ENTRY 2RSL) AND ARE MAINLY OF INTEREST REMARK 400 IN REGARDS TO CRYSTAL PACKING. THE AUTHORS HAVE PROPOSED REMARK 400 A MODEL OF THE SYNAPTIC COMPLEX BASED ON THE PACKING OF REMARK 400 PROTOMERS IN THIS UNIT CELL. 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 SER A 12 REMARK 465 GLN A 13 REMARK 465 GLN A 14 REMARK 465 ALA A 38 REMARK 465 SER A 39 REMARK 465 GLY A 40 REMARK 465 SER A 41 REMARK 465 SER A 42 REMARK 465 SER A 43 REMARK 465 ASP A 44 REMARK 465 GLN A 116 REMARK 465 ALA A 117 REMARK 465 GLU A 118 REMARK 465 ARG A 119 REMARK 465 GLN A 120 REMARK 465 ARG A 121 REMARK 465 ILE A 122 REMARK 465 LEU A 123 REMARK 465 GLU A 124 REMARK 465 ARG A 125 REMARK 465 THR A 126 REMARK 465 ASN A 127 REMARK 465 GLU A 128 REMARK 465 GLY A 129 REMARK 465 ARG A 130 REMARK 465 GLN A 131 REMARK 465 GLU A 132 REMARK 465 ALA A 133 REMARK 465 MET A 134 REMARK 465 ALA A 135 REMARK 465 LYS A 136 REMARK 465 GLY A 137 REMARK 465 VAL A 138 REMARK 465 VAL A 139 REMARK 465 PHE A 140 DBREF 1GDR A 1 140 UNP P03012 TNR1_ECOLI 1 140 SEQRES 1 A 140 MET ARG LEU PHE GLY TYR ALA ARG VAL SER THR SER GLN SEQRES 2 A 140 GLN SER LEU ASP ILE GLN VAL ARG ALA LEU LYS ASP ALA SEQRES 3 A 140 GLY VAL LYS ALA ASN ARG ILE PHE THR ASP LYS ALA SER SEQRES 4 A 140 GLY SER SER SER ASP ARG LYS GLY LEU ASP LEU LEU ARG SEQRES 5 A 140 MET LYS VAL GLU GLU GLY ASP VAL ILE LEU VAL LYS LYS SEQRES 6 A 140 LEU ASP ARG LEU GLY ARG ASP THR ALA ASP MET ILE GLN SEQRES 7 A 140 LEU ILE LYS GLU PHE ASP ALA GLN GLY VAL SER ILE ARG SEQRES 8 A 140 PHE ILE ASP ASP GLY ILE SER THR ASP GLY GLU MET GLY SEQRES 9 A 140 LYS MET VAL VAL THR ILE LEU SER ALA VAL ALA GLN ALA SEQRES 10 A 140 GLU ARG GLN ARG ILE LEU GLU ARG THR ASN GLU GLY ARG SEQRES 11 A 140 GLN GLU ALA MET ALA LYS GLY VAL VAL PHE HELIX 1 B GLY A 47 VAL A 55 1 9 HELIX 2 C LYS A 65 LEU A 69 1 5 HELIX 3 D ASP A 72 GLY A 87 1 16 HELIX 4 E GLY A 101 ALA A 115 1 15 SHEET 1 S1 4 MET A 1 SER A 10 0 SHEET 2 S1 4 GLY A 58 LYS A 64 1 SHEET 3 S1 4 GLY A 87 ILE A 93 1 SHEET 4 S1 4 GLY A 96 ASP A 100 -1 CRYST1 60.200 60.200 170.100 90.00 90.00 120.00 P 64 2 2 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 0.016611 0.009591 0.000000 0.00000 SCALE2 0.000000 0.019181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005879 0.00000