PDB Short entry for 1A77 HEADER 5'-3' EXO/ENDO NUCLEASE 20-MAR-98 1A77 TITLE FLAP ENDONUCLEASE-1 FROM METHANOCOCCUS JANNASCHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAP ENDONUCLEASE-1 PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190 KEYWDS 5'-3' EXO/ENDO NUCLEASE, DNA REPLICATION, RTH, RAD27, DNA REPAIR, 5'- KEYWDS 2 3' EXO-ENDO NUCLEASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.Y.HWANG,K.BAEK,H.KIM,Y.CHO REVDAT 3 07-FEB-24 1A77 1 REMARK LINK REVDAT 2 24-FEB-09 1A77 1 VERSN REVDAT 1 03-AUG-99 1A77 0 JRNL AUTH K.Y.HWANG,K.BAEK,H.Y.KIM,Y.CHO JRNL TITL THE CRYSTAL STRUCTURE OF FLAP ENDONUCLEASE-1 FROM JRNL TITL 2 METHANOCOCCUS JANNASCHII. JRNL REF NAT.STRUCT.BIOL. V. 5 707 1998 JRNL REFN ISSN 1072-8368 JRNL PMID 9699635 JRNL DOI 10.1038/1406 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.4 REMARK 3 NUMBER OF REFLECTIONS : 17985 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 SET) : 0.218 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1783 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2220 REMARK 3 BIN R VALUE (WORKING SET) : 0.1990 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 242 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2546 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 142 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.020 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.760 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.270 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.500 ; 2.500 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PARAM11.WAT REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1A77 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_1000170478. 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) : M 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 3.851 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.24000 REMARK 290 SMTRY3 2 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 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 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 LYS A 317 REMARK 465 GLN A 318 REMARK 465 LYS A 319 REMARK 465 THR A 320 REMARK 465 LEU A 321 REMARK 465 ASP A 322 REMARK 465 ALA A 323 REMARK 465 TRP A 324 REMARK 465 PHE A 325 REMARK 465 LYS A 326 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 OE1 GLU A 152 O HOH A 435 1.83 REMARK 500 CG1 VAL A 124 O HOH A 461 2.14 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 LYS A 87 104.61 -41.03 REMARK 500 LYS A 89 -77.60 3.32 REMARK 500 ARG A 91 54.63 -155.20 REMARK 500 ARG A 94 -125.72 -98.40 REMARK 500 MET A 97 -146.70 -175.32 REMARK 500 GLU A 102 97.67 -34.36 REMARK 500 LYS A 104 107.78 54.88 REMARK 500 ALA A 108 33.26 -146.90 REMARK 500 LYS A 110 163.10 -45.10 REMARK 500 ALA A 117 25.10 -77.84 REMARK 500 ALA A 118 11.41 -153.58 REMARK 500 TYR A 120 -31.57 -147.97 REMARK 500 LYS A 122 -48.24 -173.23 REMARK 500 SER A 125 -167.14 55.08 REMARK 500 SER A 151 -117.79 -138.41 REMARK 500 ASN A 226 65.17 -157.27 REMARK 500 LYS A 231 118.34 -22.11 REMARK 500 REMARK 500 REMARK: NULL 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 A 340 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 154 OE1 REMARK 620 2 HOH A 353 O 134.4 REMARK 620 3 HOH A 399 O 122.1 101.4 REMARK 620 4 HOH A 435 O 102.9 95.6 81.5 REMARK 620 5 HOH A 438 O 102.6 59.8 92.1 153.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 341 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 224 OD2 REMARK 620 2 HOH A 366 O 175.6 REMARK 620 3 HOH A 418 O 67.9 107.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 341 DBREF 1A77 A 1 326 UNP Q58839 FEN_METJA 1 326 SEQRES 1 A 326 MET GLY VAL GLN PHE GLY ASP PHE ILE PRO LYS ASN ILE SEQRES 2 A 326 ILE SER PHE GLU ASP LEU LYS GLY LYS LYS VAL ALA ILE SEQRES 3 A 326 ASP GLY MET ASN ALA LEU TYR GLN PHE LEU THR SER ILE SEQRES 4 A 326 ARG LEU ARG ASP GLY SER PRO LEU ARG ASN ARG LYS GLY SEQRES 5 A 326 GLU ILE THR SER ALA TYR ASN GLY VAL PHE TYR LYS THR SEQRES 6 A 326 ILE HIS LEU LEU GLU ASN ASP ILE THR PRO ILE TRP VAL SEQRES 7 A 326 PHE ASP GLY GLU PRO PRO LYS LEU LYS GLU LYS THR ARG SEQRES 8 A 326 LYS VAL ARG ARG GLU MET LYS GLU LYS ALA GLU LEU LYS SEQRES 9 A 326 MET LYS GLU ALA ILE LYS LYS GLU ASP PHE GLU GLU ALA SEQRES 10 A 326 ALA LYS TYR ALA LYS ARG VAL SER TYR LEU THR PRO LYS SEQRES 11 A 326 MET VAL GLU ASN CYS LYS TYR LEU LEU SER LEU MET GLY SEQRES 12 A 326 ILE PRO TYR VAL GLU ALA PRO SER GLU GLY GLU ALA GLN SEQRES 13 A 326 ALA SER TYR MET ALA LYS LYS GLY ASP VAL TRP ALA VAL SEQRES 14 A 326 VAL SER GLN ASP TYR ASP ALA LEU LEU TYR GLY ALA PRO SEQRES 15 A 326 ARG VAL VAL ARG ASN LEU THR THR THR LYS GLU MET PRO SEQRES 16 A 326 GLU LEU ILE GLU LEU ASN GLU VAL LEU GLU ASP LEU ARG SEQRES 17 A 326 ILE SER LEU ASP ASP LEU ILE ASP ILE ALA ILE PHE MET SEQRES 18 A 326 GLY THR ASP TYR ASN PRO GLY GLY VAL LYS GLY ILE GLY SEQRES 19 A 326 PHE LYS ARG ALA TYR GLU LEU VAL ARG SER GLY VAL ALA SEQRES 20 A 326 LYS ASP VAL LEU LYS LYS GLU VAL GLU TYR TYR ASP GLU SEQRES 21 A 326 ILE LYS ARG ILE PHE LYS GLU PRO LYS VAL THR ASP ASN SEQRES 22 A 326 TYR SER LEU SER LEU LYS LEU PRO ASP LYS GLU GLY ILE SEQRES 23 A 326 ILE LYS PHE LEU VAL ASP GLU ASN ASP PHE ASN TYR ASP SEQRES 24 A 326 ARG VAL LYS LYS HIS VAL ASP LYS LEU TYR ASN LEU ILE SEQRES 25 A 326 ALA ASN LYS THR LYS GLN LYS THR LEU ASP ALA TRP PHE SEQRES 26 A 326 LYS HET MG A 340 1 HET MG A 341 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 2(MG 2+) FORMUL 4 HOH *142(H2 O) HELIX 1 1 GLY A 6 PHE A 8 5 3 HELIX 2 2 GLU A 17 LEU A 19 5 3 HELIX 3 3 GLY A 28 SER A 38 1 11 HELIX 4 4 SER A 56 ASN A 71 1 16 HELIX 5 5 LYS A 111 PHE A 114 1 4 HELIX 6 6 PRO A 129 MET A 142 1 14 HELIX 7 7 GLY A 153 LYS A 163 1 11 HELIX 8 8 ASP A 175 TYR A 179 5 5 HELIX 9 9 LEU A 200 LEU A 207 1 8 HELIX 10 10 LEU A 211 MET A 221 1 11 HELIX 11 11 PHE A 235 ARG A 243 1 9 HELIX 12 12 ALA A 247 GLU A 254 1 8 HELIX 13 13 TYR A 258 LYS A 266 1 9 HELIX 14 14 LYS A 283 LEU A 290 1 8 HELIX 15 15 TYR A 298 ASN A 314 1 17 SHEET 1 A 4 ALA A 168 VAL A 170 0 SHEET 2 A 4 LYS A 23 ASP A 27 1 N ALA A 25 O ALA A 168 SHEET 3 A 4 THR A 74 PHE A 79 1 N THR A 74 O VAL A 24 SHEET 4 A 4 TYR A 146 GLU A 148 1 N VAL A 147 O TRP A 77 SHEET 1 B 2 ARG A 183 ARG A 186 0 SHEET 2 B 2 GLU A 196 GLU A 199 -1 N ILE A 198 O VAL A 184 LINK OE1 GLU A 154 MG MG A 340 1555 1555 2.02 LINK OD2 ASP A 224 MG MG A 341 1555 1555 2.79 LINK MG MG A 340 O HOH A 353 1555 1555 2.75 LINK MG MG A 340 O HOH A 399 1555 1555 1.85 LINK MG MG A 340 O HOH A 435 1555 1555 2.01 LINK MG MG A 340 O HOH A 438 1555 1555 1.92 LINK MG MG A 341 O HOH A 366 1555 1555 2.23 LINK MG MG A 341 O HOH A 418 1555 1555 2.86 SITE 1 AC1 6 GLU A 152 GLU A 154 HOH A 353 HOH A 399 SITE 2 AC1 6 HOH A 435 HOH A 438 SITE 1 AC2 5 GLU A 154 ASP A 175 ASP A 224 HOH A 366 SITE 2 AC2 5 HOH A 418 CRYST1 58.830 42.480 62.560 90.00 92.24 90.00 P 1 21 1 2 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 0.016998 0.000000 0.000665 0.00000 SCALE2 0.000000 0.023540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015997 0.00000