PDB Short entry for 3O4P HEADER HYDROLASE 27-JUL-10 3O4P TITLE DFPASE AT 0.85 ANGSTROM RESOLUTION (H ATOMS INCLUDED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIISOPROPYL-FLUOROPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DFPASE; COMPND 5 EC: 3.1.8.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LOLIGO VULGARIS; SOURCE 3 ORGANISM_COMMON: COMMON EUROPEAN SQUID; SOURCE 4 ORGANISM_TAXID: 6622; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-PROPELLER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.LIEBSCHNER,M.ELIAS,J.KOEPKE,C.LECOMTE,B.GUILLOT,C.JELSCH, AUTHOR 2 E.CHABRIERE REVDAT 4 03-APR-24 3O4P 1 REMARK REVDAT 3 21-FEB-24 3O4P 1 REMARK LINK REVDAT 2 14-AUG-13 3O4P 1 JRNL REVDAT 1 17-AUG-11 3O4P 0 JRNL AUTH M.ELIAS,D.LIEBSCHNER,J.KOEPKE,C.LECOMTE,B.GUILLOT,C.JELSCH, JRNL AUTH 2 E.CHABRIERE JRNL TITL HYDROGEN ATOMS IN PROTEIN STRUCTURES: HIGH-RESOLUTION X-RAY JRNL TITL 2 DIFFRACTION STRUCTURE OF THE DFPASE. JRNL REF BMC RES NOTES V. 6 308 2013 JRNL REFN ESSN 1756-0500 JRNL PMID 23915572 JRNL DOI 10.1186/1756-0500-6-308 REMARK 2 REMARK 2 RESOLUTION. 0.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MOPRO REMARK 3 AUTHORS : GUILLOT,VIRY,GUILLOT,LECOMTE,JELSCH REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.80 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 241251 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : RFREE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.103 REMARK 3 FREE R VALUE : 0.121 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2463 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 : 2459 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 136 REMARK 3 SOLVENT ATOMS : 466 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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: REFINEMENT OF SOLVENT PARAMETERS REMARK 3 (EXPONENTIAL SCALING MODEL) AND POSITIONING OF WATER HYDROGEN REMARK 3 ATOMS. REMARK 4 REMARK 4 3O4P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-00 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.842 REMARK 200 MONOCHROMATOR : TRIANGULAR SI REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 264548 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: DFPASE MODEL FURNISHED BY J. KOEPKE. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 21.55700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.23350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.92450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.23350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.55700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.92450 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 MET A 1 CB CG SD CE REMARK 470 GLU A 2 CB CG CD OE1 OE2 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 HE22 GLN A 258 O1 EDO A 425 1.60 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 LYS A 27 CE LYS A 27 NZ -0.261 REMARK 500 ASN A 28 CG ASN A 28 OD1 0.200 REMARK 500 GLU A 39 CD GLU A 39 OE1 0.217 REMARK 500 GLU A 39 CD GLU A 39 OE2 -0.072 REMARK 500 ASN A 41 CA ASN A 41 CB 0.214 REMARK 500 ASN A 41 CB ASN A 41 CG 0.414 REMARK 500 ASN A 41 CG ASN A 41 OD1 0.387 REMARK 500 GLY A 42 C GLY A 42 O -0.113 REMARK 500 LYS A 43 CE LYS A 43 NZ 0.191 REMARK 500 GLU A 65 CD GLU A 65 OE2 0.113 REMARK 500 ASN A 67 CG ASN A 67 OD1 0.230 REMARK 500 GLU A 104 CG GLU A 104 CD -0.106 REMARK 500 LYS A 109 CD LYS A 109 CE 0.297 REMARK 500 LYS A 109 CE LYS A 109 NZ 0.155 REMARK 500 GLU A 112 CB GLU A 112 CG 0.143 REMARK 500 GLU A 112 CD GLU A 112 OE2 -0.180 REMARK 500 GLU A 150 CG GLU A 150 CD -0.137 REMARK 500 GLU A 150 CD GLU A 150 OE2 0.172 REMARK 500 ASN A 183 CG ASN A 183 OD1 -0.144 REMARK 500 ASN A 183 CG ASN A 183 ND2 0.210 REMARK 500 GLU A 235 CG GLU A 235 CD 0.099 REMARK 500 ARG A 264 CD ARG A 264 NE 0.130 REMARK 500 ARG A 264 NE ARG A 264 CZ -0.289 REMARK 500 ARG A 264 CZ ARG A 264 NH2 0.171 REMARK 500 GLN A 278 CG GLN A 278 CD -0.160 REMARK 500 GLN A 278 CD GLN A 278 OE1 0.435 REMARK 500 GLN A 298 CD GLN A 298 OE1 -0.210 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 GLU A 2 C - N - CA ANGL. DEV. = 21.2 DEGREES REMARK 500 ASN A 41 OD1 - CG - ND2 ANGL. DEV. = 27.2 DEGREES REMARK 500 ASN A 41 CB - CG - ND2 ANGL. DEV. = -23.0 DEGREES REMARK 500 LYS A 43 CG - CD - CE ANGL. DEV. = 49.9 DEGREES REMARK 500 LYS A 43 CD - CE - NZ ANGL. DEV. = 26.2 DEGREES REMARK 500 ARG A 50 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 50 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 GLU A 112 OE1 - CD - OE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 GLU A 112 CG - CD - OE1 ANGL. DEV. = -21.4 DEGREES REMARK 500 GLU A 112 CG - CD - OE2 ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG A 114 CD - NE - CZ ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG A 114 NH1 - CZ - NH2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 114 NE - CZ - NH1 ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG A 114 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 115 CD - NE - CZ ANGL. DEV. = 22.0 DEGREES REMARK 500 ARG A 115 CD - NE - CZ ANGL. DEV. = 11.4 DEGREES REMARK 500 ARG A 115 NH1 - CZ - NH2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG A 115 NE - CZ - NH2 ANGL. DEV. = 7.7 DEGREES REMARK 500 TYR A 126 CB - CG - CD2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ASP A 143 CB - CG - OD1 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG A 146 CB - CA - C ANGL. DEV. = -15.2 DEGREES REMARK 500 GLU A 150 CG - CD - OE1 ANGL. DEV. = 13.1 DEGREES REMARK 500 THR A 169 CA - CB - CG2 ANGL. DEV. = -11.1 DEGREES REMARK 500 MET A 182 CG - SD - CE ANGL. DEV. = -12.4 DEGREES REMARK 500 ARG A 186 CD - NE - CZ ANGL. DEV. = 20.0 DEGREES REMARK 500 ARG A 186 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 186 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 186 NE - CZ - NH2 ANGL. DEV. = 9.1 DEGREES REMARK 500 GLU A 235 OE1 - CD - OE2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 236 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG A 264 NH1 - CZ - NH2 ANGL. DEV. = -11.7 DEGREES REMARK 500 ARG A 264 NE - CZ - NH1 ANGL. DEV. = 12.2 DEGREES REMARK 500 PHE A 311 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 ILE A 313 CA - CB - CG1 ANGL. DEV. = -12.4 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 GLU A 2 108.02 -12.46 REMARK 500 ILE A 3 129.92 80.89 REMARK 500 ALA A 20 125.39 -34.75 REMARK 500 ALA A 45 47.70 -152.40 REMARK 500 SER A 147 38.29 -89.31 REMARK 500 ALA A 170 38.13 70.38 REMARK 500 PHE A 173 64.40 68.68 REMARK 500 ASN A 175 -101.69 -136.76 REMARK 500 TYR A 188 -11.42 -144.15 REMARK 500 ASN A 213 42.50 71.49 REMARK 500 ASP A 229 -102.18 -113.03 REMARK 500 PRO A 266 41.34 -87.03 REMARK 500 PHE A 311 -123.24 -95.91 REMARK 500 ILE A 313 -66.08 -107.66 REMARK 500 ILE A 313 -55.51 -152.74 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 GLN A 278 0.10 SIDE CHAIN 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 CA A 491 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 21 OE2 REMARK 620 2 ASN A 120 OD1 101.9 REMARK 620 3 ASN A 175 OD1 155.7 75.3 REMARK 620 4 ASP A 229 OD1 96.5 149.7 78.0 REMARK 620 5 HOH A 502 O 75.7 73.1 124.7 135.5 REMARK 620 6 HOH A 524 O 74.5 90.8 81.4 71.1 142.1 REMARK 620 7 HOH A 604 O 127.5 109.5 74.7 76.5 74.7 143.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 492 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 232 OD2 REMARK 620 2 LEU A 273 O 86.1 REMARK 620 3 HOH A 509 O 84.1 167.6 REMARK 620 4 HOH A 615 O 174.1 88.4 101.7 REMARK 620 5 HOH A 623 O 95.0 89.7 83.7 86.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 423 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 424 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 425 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 426 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 427 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 428 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 433 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 434 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DXE A 442 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DXE A 443 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MXE A 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MXE A 452 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 461 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 462 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ME2 A 471 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 491 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 492 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PJX RELATED DB: PDB REMARK 900 DFPASE AT 0.85 A RESOLUTION (NO H ATOMS) DBREF 3O4P A 1 314 UNP Q7SIG4 DFPA_LOLVU 1 314 SEQRES 1 A 314 MET GLU ILE PRO VAL ILE GLU PRO LEU PHE THR LYS VAL SEQRES 2 A 314 THR GLU ASP ILE PRO GLY ALA GLU GLY PRO VAL PHE ASP SEQRES 3 A 314 LYS ASN GLY ASP PHE TYR ILE VAL ALA PRO GLU VAL GLU SEQRES 4 A 314 VAL ASN GLY LYS PRO ALA GLY GLU ILE LEU ARG ILE ASP SEQRES 5 A 314 LEU LYS THR GLY LYS LYS THR VAL ILE CYS LYS PRO GLU SEQRES 6 A 314 VAL ASN GLY TYR GLY GLY ILE PRO ALA GLY CYS GLN CYS SEQRES 7 A 314 ASP ARG ASP ALA ASN GLN LEU PHE VAL ALA ASP MET ARG SEQRES 8 A 314 LEU GLY LEU LEU VAL VAL GLN THR ASP GLY THR PHE GLU SEQRES 9 A 314 GLU ILE ALA LYS LYS ASP SER GLU GLY ARG ARG MET GLN SEQRES 10 A 314 GLY CYS ASN ASP CYS ALA PHE ASP TYR GLU GLY ASN LEU SEQRES 11 A 314 TRP ILE THR ALA PRO ALA GLY GLU VAL ALA PRO ALA ASP SEQRES 12 A 314 TYR THR ARG SER MET GLN GLU LYS PHE GLY SER ILE TYR SEQRES 13 A 314 CYS PHE THR THR ASP GLY GLN MET ILE GLN VAL ASP THR SEQRES 14 A 314 ALA PHE GLN PHE PRO ASN GLY ILE ALA VAL ARG HIS MET SEQRES 15 A 314 ASN ASP GLY ARG PRO TYR GLN LEU ILE VAL ALA GLU THR SEQRES 16 A 314 PRO THR LYS LYS LEU TRP SER TYR ASP ILE LYS GLY PRO SEQRES 17 A 314 ALA LYS ILE GLU ASN LYS LYS VAL TRP GLY HIS ILE PRO SEQRES 18 A 314 GLY THR HIS GLU GLY GLY ALA ASP GLY MET ASP PHE ASP SEQRES 19 A 314 GLU ASP ASN ASN LEU LEU VAL ALA ASN TRP GLY SER SER SEQRES 20 A 314 HIS ILE GLU VAL PHE GLY PRO ASP GLY GLY GLN PRO LYS SEQRES 21 A 314 MET ARG ILE ARG CYS PRO PHE GLU LYS PRO SER ASN LEU SEQRES 22 A 314 HIS PHE LYS PRO GLN THR LYS THR ILE PHE VAL THR GLU SEQRES 23 A 314 HIS GLU ASN ASN ALA VAL TRP LYS PHE GLU TRP GLN ARG SEQRES 24 A 314 ASN GLY LYS LYS GLN TYR CYS GLU THR LEU LYS PHE GLY SEQRES 25 A 314 ILE PHE HET GOL A 401 6 HET GOL A 403 6 HET MES A 411 12 HET MES A 412 12 HET EDO A 421 4 HET EDO A 422 4 HET EDO A 423 4 HET EDO A 424 4 HET EDO A 425 4 HET EDO A 426 4 HET EDO A 427 4 HET EDO A 428 4 HET PGE A 433 10 HET PGE A 434 10 HET DXE A 442 6 HET DXE A 443 6 HET MXE A 451 5 HET MXE A 452 5 HET PEG A 461 7 HET PEG A 462 7 HET ME2 A 471 10 HET CA A 491 1 HET CA A 492 1 HETNAM GOL GLYCEROL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM PGE TRIETHYLENE GLYCOL HETNAM DXE 1,2-DIMETHOXYETHANE HETNAM MXE 2-METHOXYETHANOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ME2 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE HETNAM CA CALCIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 MES 2(C6 H13 N O4 S) FORMUL 6 EDO 8(C2 H6 O2) FORMUL 14 PGE 2(C6 H14 O4) FORMUL 16 DXE 2(C4 H10 O2) FORMUL 18 MXE 2(C3 H8 O2) FORMUL 20 PEG 2(C4 H10 O3) FORMUL 22 ME2 C7 H16 O3 FORMUL 23 CA 2(CA 2+) FORMUL 25 HOH *466(H2 O) HELIX 1 1 GLN A 304 THR A 308 5 5 SHEET 1 A 5 VAL A 5 ILE A 6 0 SHEET 2 A 5 MET A 261 ARG A 264 1 O ARG A 264 N ILE A 6 SHEET 3 A 5 HIS A 248 PHE A 252 -1 N ILE A 249 O ILE A 263 SHEET 4 A 5 LEU A 239 TRP A 244 -1 N VAL A 241 O GLU A 250 SHEET 5 A 5 GLY A 227 PHE A 233 -1 N ASP A 232 O LEU A 240 SHEET 1 B 4 THR A 11 THR A 14 0 SHEET 2 B 4 ALA A 291 GLU A 296 -1 O VAL A 292 N VAL A 13 SHEET 3 B 4 THR A 281 GLU A 286 -1 N ILE A 282 O PHE A 295 SHEET 4 B 4 PRO A 270 PHE A 275 -1 N HIS A 274 O PHE A 283 SHEET 1 C 4 GLU A 21 PHE A 25 0 SHEET 2 C 4 PHE A 31 ALA A 35 -1 O TYR A 32 N VAL A 24 SHEET 3 C 4 GLU A 47 ILE A 51 -1 O LEU A 49 N ILE A 33 SHEET 4 C 4 LYS A 58 CYS A 62 -1 O CYS A 62 N ILE A 48 SHEET 1 D 2 GLU A 39 VAL A 40 0 SHEET 2 D 2 LYS A 43 PRO A 44 -1 O LYS A 43 N VAL A 40 SHEET 1 E 2 GLU A 65 VAL A 66 0 SHEET 2 E 2 TYR A 69 GLY A 70 -1 O TYR A 69 N VAL A 66 SHEET 1 F 4 PRO A 73 CYS A 78 0 SHEET 2 F 4 GLN A 84 ASP A 89 -1 O PHE A 86 N GLN A 77 SHEET 3 F 4 GLY A 93 GLN A 98 -1 O GLY A 93 N ASP A 89 SHEET 4 F 4 PHE A 103 GLU A 105 -1 O GLU A 104 N VAL A 96 SHEET 1 G 4 ASP A 121 PHE A 124 0 SHEET 2 G 4 LEU A 130 ALA A 134 -1 O TRP A 131 N ALA A 123 SHEET 3 G 4 GLY A 153 PHE A 158 -1 O SER A 154 N ALA A 134 SHEET 4 G 4 MET A 164 PHE A 171 -1 O PHE A 171 N GLY A 153 SHEET 1 H 4 PRO A 174 HIS A 181 0 SHEET 2 H 4 PRO A 187 GLU A 194 -1 O GLN A 189 N ARG A 180 SHEET 3 H 4 LYS A 199 GLY A 207 -1 O TRP A 201 N VAL A 192 SHEET 4 H 4 LYS A 210 HIS A 219 -1 O LYS A 215 N SER A 202 LINK OE2 GLU A 21 CA CA A 491 1555 1555 2.35 LINK OD1 ASN A 120 CA CA A 491 1555 1555 2.33 LINK OD1 ASN A 175 CA CA A 491 1555 1555 2.40 LINK OD1 ASP A 229 CA CA A 491 1555 1555 2.36 LINK OD2 ASP A 232 CA CA A 492 1555 1555 2.21 LINK O LEU A 273 CA CA A 492 1555 1555 2.26 LINK CA CA A 491 O HOH A 502 1555 1555 2.48 LINK CA CA A 491 O HOH A 524 1555 1555 2.52 LINK CA CA A 491 O HOH A 604 1555 1555 2.35 LINK CA CA A 492 O HOH A 509 1555 1555 2.30 LINK CA CA A 492 O HOH A 615 1555 1555 2.25 LINK CA CA A 492 O HOH A 623 1555 1555 2.25 CISPEP 1 MET A 1 GLU A 2 0 1.73 CISPEP 2 MET A 1 GLU A 2 0 3.34 CISPEP 3 GLU A 2 ILE A 3 0 -4.91 CISPEP 4 GLU A 2 ILE A 3 0 2.92 CISPEP 5 ALA A 140 PRO A 141 0 14.89 SITE 1 AC1 6 GLU A 37 GLY A 312 ILE A 313 PHE A 314 SITE 2 AC1 6 DXE A 442 HOH A 619 SITE 1 AC2 8 PRO A 8 LEU A 9 PHE A 10 ASP A 143 SITE 2 AC2 8 LYS A 310 HOH A 559 HOH A 716 HOH A 728 SITE 1 AC3 13 GLU A 7 LYS A 43 PRO A 44 ASN A 67 SITE 2 AC3 13 GLY A 68 TYR A 69 ARG A 91 ARG A 264 SITE 3 AC3 13 PHE A 311 ME2 A 471 HOH A 508 HOH A 628 SITE 4 AC3 13 HOH A 728 SITE 1 AC4 8 GLU A 65 THR A 102 PHE A 103 GLN A 258 SITE 2 AC4 8 HOH A 598 HOH A 687 HOH A 830 HOH A1129 SITE 1 AC5 6 LYS A 57 VAL A 167 ASP A 168 ILE A 211 SITE 2 AC5 6 MXE A 451 HOH A 859 SITE 1 AC6 11 PHE A 86 PHE A 124 PHE A 158 THR A 159 SITE 2 AC6 11 THR A 160 PEG A 461 HOH A 517 HOH A 692 SITE 3 AC6 11 HOH A 702 HOH A 858 HOH A 979 SITE 1 AC7 7 ARG A 115 GLU A 138 ASN A 289 TRP A 293 SITE 2 AC7 7 HOH A 516 HOH A 617 HOH A 959 SITE 1 AC8 7 PRO A 196 LYS A 198 THR A 223 HIS A 224 SITE 2 AC8 7 PGE A 433 HOH A 647 HOH A 970 SITE 1 AC9 5 HIS A 219 ILE A 220 PRO A 221 GLN A 258 SITE 2 AC9 5 HOH A 876 SITE 1 BC1 8 MET A 148 ASP A 184 GLU A 225 PHE A 314 SITE 2 BC1 8 PGE A 433 HOH A 581 HOH A 906 HOH A1001 SITE 1 BC2 6 GLY A 256 GLY A 257 GLN A 258 LYS A 260 SITE 2 BC2 6 PEG A 462 HOH A 877 SITE 1 BC3 3 GLU A 37 HOH A1082 HOH A1125 SITE 1 BC4 12 MET A 148 GLN A 172 ASP A 184 PRO A 196 SITE 2 BC4 12 THR A 197 EDO A 424 EDO A 426 HOH A 644 SITE 3 BC4 12 HOH A 826 HOH A 970 HOH A1102 HOH A1103 SITE 1 BC5 12 ILE A 106 PHE A 158 GLY A 162 GLN A 163 SITE 2 BC5 12 THR A 279 LYS A 280 THR A 281 GLU A 296 SITE 3 BC5 12 HOH A 521 HOH A 544 HOH A 685 HOH A 735 SITE 1 BC6 5 TRP A 244 LYS A 269 HIS A 287 GOL A 401 SITE 2 BC6 5 HOH A 734 SITE 1 BC7 8 PRO A 8 LYS A 280 GLU A 296 TRP A 297 SITE 2 BC7 8 PEG A 461 HOH A 532 HOH A 770 HOH A 893 SITE 1 BC8 9 LYS A 58 THR A 59 ASN A 213 LYS A 214 SITE 2 BC8 9 EDO A 421 HOH A 569 HOH A 768 HOH A 859 SITE 3 BC8 9 HOH A 923 SITE 1 BC9 7 LYS A 151 THR A 169 ALA A 170 PHE A 171 SITE 2 BC9 7 GLU A 194 LYS A 214 HOH A 531 SITE 1 CC1 9 GLN A 84 ILE A 106 LYS A 280 EDO A 422 SITE 2 CC1 9 DXE A 443 HOH A 639 HOH A 702 HOH A 832 SITE 3 CC1 9 HOH A 858 SITE 1 CC2 9 LYS A 63 GLU A 65 ASP A 255 GLY A 256 SITE 2 CC2 9 GLY A 257 EDO A 427 HOH A 573 HOH A 629 SITE 3 CC2 9 HOH A 844 SITE 1 CC3 6 VAL A 5 GLU A 7 HIS A 248 ARG A 264 SITE 2 CC3 6 MES A 411 HOH A 976 SITE 1 CC4 7 GLU A 21 ASN A 120 ASN A 175 ASP A 229 SITE 2 CC4 7 HOH A 502 HOH A 524 HOH A 604 SITE 1 CC5 6 ASP A 232 LEU A 273 HIS A 274 HOH A 509 SITE 2 CC5 6 HOH A 615 HOH A 623 CRYST1 43.114 81.849 86.467 90.00 90.00 90.00 P 21 21 21 4 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 0.023194 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011565 0.00000