HEADER HYDROLASE 07-DEC-98 2DFP TITLE X-RAY STRUCTURE OF AGED DI-ISOPROPYL-PHOSPHORO-FLUORIDATE (DFP) BOUND TITLE 2 TO ACETYLCHOLINESTERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ACETYLCHOLINESTERASE); COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.7; COMPND 5 OTHER_DETAILS: THE PROTEIN, ACETYLCHOLINESTERASE, WAS TREATED WITH COMPND 6 THE ORGANOPHOSPHATE, DFP, PRIOR TO CRYSTALLIZATION. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TORPEDO CALIFORNICA; SOURCE 3 ORGANISM_COMMON: PACIFIC ELECTRIC RAY; SOURCE 4 ORGANISM_TAXID: 7787; SOURCE 5 VARIANT: G2 FORM; SOURCE 6 ORGAN: ELECTRIC ORGAN; SOURCE 7 TISSUE: ELECTROPLAQUE KEYWDS AGED ORGANOPHOSPHATE, DFP, SERINE HYDROLASE, NEUROTRANSMITTER KEYWDS 2 CLEAVAGE, CATALYTIC TRIAD, ALPHA/BETA HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.KRYGER,C.B.MILLARD,I.SILMAN,J.L.SUSSMAN REVDAT 8 23-AUG-23 2DFP 1 REMARK REVDAT 7 02-JUN-21 2DFP 1 REMARK HETSYN REVDAT 6 29-JUL-20 2DFP 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 13-JUL-11 2DFP 1 VERSN REVDAT 4 24-FEB-09 2DFP 1 VERSN REVDAT 3 01-APR-03 2DFP 1 JRNL REVDAT 2 27-MAR-00 2DFP 1 REMARK REVDAT 1 28-JUN-99 2DFP 0 JRNL AUTH C.B.MILLARD,G.KRYGER,A.ORDENTLICH,H.M.GREENBLATT,M.HAREL, JRNL AUTH 2 M.L.RAVES,Y.SEGALL,D.BARAK,A.SHAFFERMAN,I.SILMAN,J.L.SUSSMAN JRNL TITL CRYSTAL STRUCTURES OF AGED PHOSPHONYLATED JRNL TITL 2 ACETYLCHOLINESTERASE: NERVE AGENT REACTION PRODUCTS AT THE JRNL TITL 3 ATOMIC LEVEL. JRNL REF BIOCHEMISTRY V. 38 7032 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10353814 JRNL DOI 10.1021/BI982678L REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.L.SUSSMAN,M.HAREL,F.FROLOW,C.OEFNER,A.GOLDMAN,L.TOKER, REMARK 1 AUTH 2 I.SILMAN REMARK 1 TITL ATOMIC STRUCTURE OF ACETYLCHOLINESTERASE FROM TORPEDO REMARK 1 TITL 2 CALIFORNICA: A PROTOTYPIC ACETYLCHOLINE-BINDING PROTEIN REMARK 1 REF SCIENCE V. 253 872 1991 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.4 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 42208 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) : 0.186 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1874 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.38 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2760 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 129 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4270 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 376 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.06000 REMARK 3 B22 (A**2) : 8.06000 REMARK 3 B33 (A**2) : -16.10000 REMARK 3 B12 (A**2) : 8.63000 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.45 REMARK 3 LOW RESOLUTION CUTOFF (A) : 4.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.49 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.310 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 44.45 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 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : DFP.PAR, MES.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : DFP.TOP, MES.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2DFP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-98. REMARK 100 THE DEPOSITION ID IS D_1000000232. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42208 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.2 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS 0.4 REMARK 200 STARTING MODEL: PDB ENTRY 2ACE REMARK 200 REMARK 200 REMARK: USED COMPOSITE OMIT MAP METHOD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.8, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 45.62700 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 91.25400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 91.25400 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 45.62700 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: TORPEDO CALIFONICA ACETYLCHOLINESTERASE IS A G2 DIMER IN REMARK 300 SOLUTION (SEE SUSSMAN 1988). THE ASYMMETRIC UNIT CONTAINS A REMARK 300 MONOMER, WITH THE CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATING REMARK 300 THE TWO MONOMERS IN A DIMER. BIOMOLECULE: THE ENZYME IS A REMARK 300 GPI-ANCHORED DIMER, THE TWO MONOMERS IN THE DIMER ARE REMARK 300 RELATED BY THE CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AND THUS REMARK 300 GENERATE A FOUR HELIX BUNDLE A365-A375 AND A518-A535. REMARK 300 DFP WAS REACTED WITH THE ENZYME IN SOLUTION. REMARK 300 THE SOLUTION OF THE INHIBITED ENZYME WAS DIALYZED TO REMOVE REMARK 300 EXCESS ORGANOPHOSPHATE, CHECKED FOR ACTIVITY AND FOUND TO REMARK 300 REMARK 300 REMARK 300 REACT LIKE "AGED" PHOSPHYLATED ACHE, AND THEN SUBJECTED TO REMARK 300 CRYSTALLIZATION. THIS STRUCTURE IS MORE COMPLETE THAN REMARK 300 THE STARTING MODEL OF THE NATIVE STRUCTURE (PDB ID 2ACE). REMARK 300 RESIDUES THAT ARE NOT SEEN IN THE CRYSTAL STRUCTURE DUE TO REMARK 300 DISORDER INCLUDE THE N-TERMINAL RESIDUE ASP 1 AND THE REMARK 300 C-TERMINAL RESIDUES AFTER THR 535. THR 535 IS THE LAST REMARK 300 RESIDUE OBSERVED AT THE C-TERMINUS. 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, C 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 136.88100 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2116 LIES ON A SPECIAL POSITION. 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 O HOH A 2057 O HOH A 2058 2.13 REMARK 500 O HOH A 2082 O HOH A 2083 2.18 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 SER A 228 CB SER A 228 OG -0.078 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 VAL A 129 CB - CA - C ANGL. DEV. = -11.8 DEGREES REMARK 500 ARG A 216 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 216 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 221 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 221 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 426 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 426 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 LEU A 494 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 LEU A 531 CA - CB - CG ANGL. DEV. = 18.3 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 HIS A 3 98.00 117.93 REMARK 500 LYS A 11 -9.74 -58.30 REMARK 500 LEU A 23 55.40 36.86 REMARK 500 SER A 25 -159.18 -130.18 REMARK 500 PHE A 45 -8.94 78.10 REMARK 500 ALA A 60 52.54 -109.53 REMARK 500 SER A 108 78.06 -158.67 REMARK 500 ASN A 167 17.03 55.93 REMARK 500 MIS A 200 -122.78 56.78 REMARK 500 GLU A 299 -76.74 -120.44 REMARK 500 THR A 317 -156.47 -163.54 REMARK 500 ASP A 326 60.67 -113.69 REMARK 500 ASP A 380 58.17 -153.23 REMARK 500 VAL A 400 -60.50 -133.22 REMARK 500 PRO A 485 -73.38 -27.44 REMARK 500 GLN A 526 -59.93 -120.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 442 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 DFP, AGED ORGANOPHOSPHATE REMARK 600 REMARK 600 MES, USED AS THE CRYSTALLIZATION BUFFER REMARK 600 REMARK 600 THERE ARE 5 NAG GROUPS NUMBERED 3001-3005 IN THIS STRUCTURE REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: TRIAD REMARK 800 REMARK 800 SITE_IDENTIFIER: OPB REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: ORGANOPHOSPHATE SITE DBREF 2DFP A 2 535 UNP P04058 ACES_TORCA 23 556 SEQRES 1 A 534 ASP HIS SER GLU LEU LEU VAL ASN THR LYS SER GLY LYS SEQRES 2 A 534 VAL MET GLY THR ARG VAL PRO VAL LEU SER SER HIS ILE SEQRES 3 A 534 SER ALA PHE LEU GLY ILE PRO PHE ALA GLU PRO PRO VAL SEQRES 4 A 534 GLY ASN MET ARG PHE ARG ARG PRO GLU PRO LYS LYS PRO SEQRES 5 A 534 TRP SER GLY VAL TRP ASN ALA SER THR TYR PRO ASN ASN SEQRES 6 A 534 CYS GLN GLN TYR VAL ASP GLU GLN PHE PRO GLY PHE SER SEQRES 7 A 534 GLY SER GLU MET TRP ASN PRO ASN ARG GLU MET SER GLU SEQRES 8 A 534 ASP CYS LEU TYR LEU ASN ILE TRP VAL PRO SER PRO ARG SEQRES 9 A 534 PRO LYS SER THR THR VAL MET VAL TRP ILE TYR GLY GLY SEQRES 10 A 534 GLY PHE TYR SER GLY SER SER THR LEU ASP VAL TYR ASN SEQRES 11 A 534 GLY LYS TYR LEU ALA TYR THR GLU GLU VAL VAL LEU VAL SEQRES 12 A 534 SER LEU SER TYR ARG VAL GLY ALA PHE GLY PHE LEU ALA SEQRES 13 A 534 LEU HIS GLY SER GLN GLU ALA PRO GLY ASN VAL GLY LEU SEQRES 14 A 534 LEU ASP GLN ARG MET ALA LEU GLN TRP VAL HIS ASP ASN SEQRES 15 A 534 ILE GLN PHE PHE GLY GLY ASP PRO LYS THR VAL THR ILE SEQRES 16 A 534 PHE GLY GLU MIS ALA GLY GLY ALA SER VAL GLY MET HIS SEQRES 17 A 534 ILE LEU SER PRO GLY SER ARG ASP LEU PHE ARG ARG ALA SEQRES 18 A 534 ILE LEU GLN SER GLY SER PRO ASN CYS PRO TRP ALA SER SEQRES 19 A 534 VAL SER VAL ALA GLU GLY ARG ARG ARG ALA VAL GLU LEU SEQRES 20 A 534 GLY ARG ASN LEU ASN CYS ASN LEU ASN SER ASP GLU GLU SEQRES 21 A 534 LEU ILE HIS CYS LEU ARG GLU LYS LYS PRO GLN GLU LEU SEQRES 22 A 534 ILE ASP VAL GLU TRP ASN VAL LEU PRO PHE ASP SER ILE SEQRES 23 A 534 PHE ARG PHE SER PHE VAL PRO VAL ILE ASP GLY GLU PHE SEQRES 24 A 534 PHE PRO THR SER LEU GLU SER MET LEU ASN SER GLY ASN SEQRES 25 A 534 PHE LYS LYS THR GLN ILE LEU LEU GLY VAL ASN LYS ASP SEQRES 26 A 534 GLU GLY SER PHE PHE LEU LEU TYR GLY ALA PRO GLY PHE SEQRES 27 A 534 SER LYS ASP SER GLU SER LYS ILE SER ARG GLU ASP PHE SEQRES 28 A 534 MET SER GLY VAL LYS LEU SER VAL PRO HIS ALA ASN ASP SEQRES 29 A 534 LEU GLY LEU ASP ALA VAL THR LEU GLN TYR THR ASP TRP SEQRES 30 A 534 MET ASP ASP ASN ASN GLY ILE LYS ASN ARG ASP GLY LEU SEQRES 31 A 534 ASP ASP ILE VAL GLY ASP HIS ASN VAL ILE CYS PRO LEU SEQRES 32 A 534 MET HIS PHE VAL ASN LYS TYR THR LYS PHE GLY ASN GLY SEQRES 33 A 534 THR TYR LEU TYR PHE PHE ASN HIS ARG ALA SER ASN LEU SEQRES 34 A 534 VAL TRP PRO GLU TRP MET GLY VAL ILE HIS GLY TYR GLU SEQRES 35 A 534 ILE GLU PHE VAL PHE GLY LEU PRO LEU VAL LYS GLU LEU SEQRES 36 A 534 ASN TYR THR ALA GLU GLU GLU ALA LEU SER ARG ARG ILE SEQRES 37 A 534 MET HIS TYR TRP ALA THR PHE ALA LYS THR GLY ASN PRO SEQRES 38 A 534 ASN GLU PRO HIS SER GLN GLU SER LYS TRP PRO LEU PHE SEQRES 39 A 534 THR THR LYS GLU GLN LYS PHE ILE ASP LEU ASN THR GLU SEQRES 40 A 534 PRO MET LYS VAL HIS GLN ARG LEU ARG VAL GLN MET CYS SEQRES 41 A 534 VAL PHE TRP ASN GLN PHE LEU PRO LYS LEU LEU ASN ALA SEQRES 42 A 534 THR MODRES 2DFP ASN A 59 ASN GLYCOSYLATION SITE MODRES 2DFP ASN A 416 ASN GLYCOSYLATION SITE MODRES 2DFP ASN A 457 ASN GLYCOSYLATION SITE MODRES 2DFP MIS A 200 SER MONOISOPROPYLPHOSPHORYLSERINE HET MIS A 200 13 HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET NAG A3001 14 HET MES A4001 12 HETNAM MIS MONOISOPROPYLPHOSPHORYLSERINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 1 MIS C6 H14 N O6 P FORMUL 2 NAG 5(C8 H15 N O6) FORMUL 5 MES C6 H13 N O4 S FORMUL 6 HOH *376(H2 O) HELIX 1 1 GLY A 41 MET A 43 5 3 HELIX 2 2 SER A 79 GLU A 82 1 4 HELIX 3 3 ASP A 128 TYR A 130 5 3 HELIX 4 4 LYS A 133 GLU A 139 1 7 HELIX 5 5 GLY A 151 PHE A 155 1 5 HELIX 6 6 VAL A 168 ASN A 183 1 16 HELIX 7 7 ILE A 184 PHE A 187 5 4 HELIX 8 8 GLY A 202 LEU A 211 1 10 HELIX 9 9 PRO A 213 ARG A 216 1 4 HELIX 10 10 VAL A 238 ASN A 251 1 14 HELIX 11 11 ASP A 259 GLU A 268 1 10 HELIX 12 12 PRO A 271 VAL A 277 1 7 HELIX 13 13 GLU A 278 ASN A 280 5 3 HELIX 14 14 LEU A 305 SER A 311 1 7 HELIX 15 15 SER A 329 GLY A 335 1 7 HELIX 16 16 ARG A 349 SER A 359 1 11 HELIX 17 17 ASP A 365 TYR A 375 1 11 HELIX 18 18 GLY A 384 ASN A 399 1 16 HELIX 19 19 ILE A 401 PHE A 414 1 14 HELIX 20 20 GLU A 434 MET A 436 5 3 HELIX 21 21 ILE A 444 VAL A 447 1 4 HELIX 22 22 LEU A 450 LEU A 452 5 3 HELIX 23 23 LYS A 454 LEU A 456 5 3 HELIX 24 24 ALA A 460 THR A 479 1 20 HELIX 25 25 VAL A 518 ASN A 525 1 8 HELIX 26 26 PHE A 527 ALA A 534 1 8 SHEET 1 A 3 LEU A 7 THR A 10 0 SHEET 2 A 3 GLY A 13 MET A 16 -1 N VAL A 15 O VAL A 8 SHEET 3 A 3 VAL A 57 ALA A 60 1 N TRP A 58 O LYS A 14 SHEET 1 B11 MET A 16 PRO A 21 0 SHEET 2 B11 HIS A 26 PRO A 34 -1 O ALA A 29 N THR A 18 SHEET 3 B11 TYR A 96 PRO A 102 -1 N ILE A 99 O PHE A 30 SHEET 4 B11 VAL A 142 SER A 147 -1 N LEU A 143 O TRP A 100 SHEET 5 B11 THR A 110 TYR A 116 1 N MET A 112 O VAL A 142 SHEET 6 B11 THR A 193 GLU A 199 1 O THR A 195 N VAL A 113 SHEET 7 B11 ARG A 221 SER A 226 1 N ILE A 223 O ILE A 196 SHEET 8 B11 GLN A 318 ASN A 324 1 N GLY A 322 O LEU A 224 SHEET 9 B11 GLY A 417 PHE A 423 1 N TYR A 421 O LEU A 321 SHEET 10 B11 PHE A 502 LEU A 505 1 N ILE A 503 O LEU A 420 SHEET 11 B11 MET A 510 GLN A 514 -1 N HIS A 513 O PHE A 502 SSBOND 1 CYS A 67 CYS A 94 1555 1555 2.05 SSBOND 2 CYS A 254 CYS A 265 1555 1555 2.05 SSBOND 3 CYS A 402 CYS A 521 1555 1555 2.02 LINK ND2 ASN A 59 C1 NAG A3001 1555 1555 1.48 LINK C GLU A 199 N MIS A 200 1555 1555 1.34 LINK C MIS A 200 N ALA A 201 1555 1555 1.33 LINK ND2 ASN A 416 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 457 C1 NAG C 1 1555 1555 1.48 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.41 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.40 CISPEP 1 SER A 103 PRO A 104 0 -0.08 SITE 1 CAT 3 MIS A 200 GLU A 327 HIS A 440 SITE 1 OPB 1 MIS A 200 CRYST1 112.636 112.636 136.881 90.00 90.00 120.00 P 31 2 1 6 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 0.008878 0.005126 0.000000 0.00000 SCALE2 0.000000 0.010252 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007306 0.00000