HEADER HYDROLASE 08-MAR-16 5FYO TITLE CALCIUM-DEPENDENT PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM A TITLE 2 GRAM-NEGATIVE BACTERIUM, PSEUDOMONAS SP, APO FORM, CRYSTAL FORM 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS SP.; SOURCE 3 ORGANISM_TAXID: 306; SOURCE 4 EXPRESSION_SYSTEM: BACILLUS SUBTILIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 1423 KEYWDS HYDROLASE, PI-PLC, GRAM-NEGATIVE, CALCIUM-DEPENDENT, HYDROLASE APO KEYWDS 2 FORM EXPDTA X-RAY DIFFRACTION AUTHOR O.V.MOROZ,E.BLAGOVA,A.A.LEBEDEV,A.NORGAARD,D.R.SEGURA,T.H.BLICHER, AUTHOR 2 K.S.WILSON REVDAT 5 10-JAN-24 5FYO 1 REMARK LINK REVDAT 4 08-MAY-19 5FYO 1 REMARK ATOM REVDAT 3 23-AUG-17 5FYO 1 REMARK REVDAT 2 25-JAN-17 5FYO 1 JRNL REVDAT 1 18-JAN-17 5FYO 0 JRNL AUTH O.V.MOROZ,E.BLAGOVA,A.A.LEBEDEV,A.NRGAARD,D.R.SEGURA, JRNL AUTH 2 T.H.BLICHER,J.BRASK,K.S.WILSON JRNL TITL THE STRUCTURE OF A CALCIUM-DEPENDENT JRNL TITL 2 PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C FROM PSEUDOMONAS JRNL TITL 3 SP. 62186, THE FIRST FROM A GRAM-NEGATIVE BACTERIUM. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 73 32 2017 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 28045383 JRNL DOI 10.1107/S2059798316019616 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 80756 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 + TEST SET) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4381 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5878 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.1420 REMARK 3 BIN FREE R VALUE SET COUNT : 303 REMARK 3 BIN FREE R VALUE : 0.2260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4603 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 469 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : 0.44000 REMARK 3 B33 (A**2) : -0.88000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.064 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.592 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4798 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4340 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6516 ; 1.575 ; 1.915 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9990 ; 1.287 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 611 ; 6.329 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 233 ;35.202 ;25.021 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 756 ;11.233 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.374 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 667 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5707 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1202 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2417 ; 2.930 ; 2.157 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2416 ; 2.926 ; 2.156 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3039 ; 3.413 ; 3.247 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2378 ; 3.397 ; 2.394 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 9130 ; 2.605 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 161 ;37.158 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 9317 ;16.194 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. RESIDUES B87-B90 ARE DISORDERED REMARK 4 REMARK 4 5FYO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1290066392. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85192 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 48.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.5000 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 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: PHASER REMARK 200 STARTING MODEL: 3H4W REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350 24-27%, CAPS/BICINE MIX PH 9.0 REMARK 280 -10 GRID, BEST CRYSTALS CLOSER TO PH 10, SEEDING FROM PACT H4 REMARK 280 (0.2M KSCN, 20% PEG3350, BIS TRIS PROPANE PH 8.5), ORYX ROBOT, REMARK 280 24 WELL PLATE, HANGING DROPS, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.67000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.00500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.33500 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 56.67000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.33500 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 85.00500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 A2072 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2163 LIES ON A SPECIAL POSITION. 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 ASP B 87 REMARK 465 GLY B 88 REMARK 465 THR B 89 REMARK 465 GLY B 90 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 55 CZ NH1 NH2 REMARK 480 LYS A 91 CD CE NZ REMARK 480 LYS A 250 CE NZ REMARK 480 ARG A 284 CD NE CZ NH1 REMARK 480 ARG B 55 NE CZ NH1 NH2 REMARK 480 LYS B 91 CG CD CE NZ REMARK 480 LYS B 250 CE NZ REMARK 480 GLN B 271 CD OE1 NE2 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 NZ LYS A 250 O HOH A 2247 1.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2267 O HOH A 2267 65-15 0.52 REMARK 500 NE ARG B 284 O HOH A 2269 24-15 1.97 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 ARG A 55 NE ARG A 55 CZ -0.251 REMARK 500 LYS A 91 CG LYS A 91 CD -0.213 REMARK 500 ARG A 284 CG ARG A 284 CD -0.183 REMARK 500 ARG A 284 CZ ARG A 284 NH2 -0.363 REMARK 500 ARG B 55 CD ARG B 55 NE -0.514 REMARK 500 LYS B 250 CD LYS B 250 CE -0.558 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 LEU A 196 CB - CG - CD2 ANGL. DEV. = 19.3 DEGREES REMARK 500 GLU A 201 OE1 - CD - OE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 284 CG - CD - NE ANGL. DEV. = -13.5 DEGREES REMARK 500 ARG A 284 NH1 - CZ - NH2 ANGL. DEV. = -24.6 DEGREES REMARK 500 ARG A 284 NE - CZ - NH2 ANGL. DEV. = 17.2 DEGREES REMARK 500 ARG B 55 CG - CD - NE ANGL. DEV. = 17.9 DEGREES REMARK 500 LEU B 196 CB - CG - CD2 ANGL. DEV. = 15.9 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 SER A 4 53.04 -142.60 REMARK 500 ASP A 56 -152.87 -120.24 REMARK 500 GLN A 145 -127.84 50.95 REMARK 500 GLN A 145 -126.31 48.95 REMARK 500 THR A 204 -129.32 43.57 REMARK 500 THR A 204 -128.85 43.57 REMARK 500 ASN A 216 21.37 -145.36 REMARK 500 SER B 4 50.67 -141.97 REMARK 500 ASP B 56 -151.22 -119.97 REMARK 500 GLN B 145 -125.33 51.26 REMARK 500 THR B 204 -130.13 42.99 REMARK 500 ASN B 216 21.11 -148.35 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 ARG A 284 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2001 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH A2003 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A2005 DISTANCE = 7.00 ANGSTROMS REMARK 525 HOH A2010 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A2102 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A2103 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A2107 DISTANCE = 6.28 ANGSTROMS 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 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 27 OD1 REMARK 620 2 GLU A 48 OE2 87.6 REMARK 620 3 ASP A 50 OD1 90.9 103.8 REMARK 620 4 ASP A 119 OD2 177.2 93.3 86.3 REMARK 620 5 HOH A2035 O 99.6 85.9 166.0 83.0 REMARK 620 6 HOH A2036 O 87.6 162.2 93.4 92.2 78.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 27 OD1 REMARK 620 2 GLU B 48 OE2 86.5 REMARK 620 3 ASP B 50 OD1 90.6 102.7 REMARK 620 4 ASP B 119 OD2 175.6 93.0 85.2 REMARK 620 5 HOH B2031 O 99.9 89.3 164.5 84.5 REMARK 620 6 HOH B2032 O 87.6 163.6 92.6 94.1 76.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FYP RELATED DB: PDB REMARK 900 CALCIUM-DEPENDENT PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM A REMARK 900 GRAM-NEGATIVE BACTERIUM, PSEUDOMONAS SP, APO FORM, CRYSTAL FORM 2 REMARK 900 RELATED ID: 5FYR RELATED DB: PDB REMARK 900 CALCIUM-DEPENDENT PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM A REMARK 900 GRAM-NEGATIVE BACTERIUM, PSEUDOMONAS SP, MYOINOSITOL COMPLEX DBREF 5FYO A 1 298 PDB 5FYO 5FYO 1 298 DBREF 5FYO B 1 298 PDB 5FYO 5FYO 1 298 SEQRES 1 A 298 ALA GLN GLU SER PRO ALA PHE ILE ASP PRO ALA SER TRP SEQRES 2 A 298 ASN THR PRO PHE ASN GLY ILE ALA GLN VAL ALA CYS HIS SEQRES 3 A 298 ASN CYS TYR GLU LYS GLN TYR ALA ASN THR PHE SER SER SEQRES 4 A 298 VAL LEU ASP SER VAL ARG THR LEU GLU LEU ASP PHE TRP SEQRES 5 A 298 ASP GLN ARG ASP ALA VAL SER GLY GLY SER PRO HIS HIS SEQRES 6 A 298 TRP PHE VAL ARG HIS ASN PRO GLY THR LEU PHE GLN SER SEQRES 7 A 298 GLY ASN ASP ASN ASN CYS THR GLY ASP GLY THR GLY LYS SEQRES 8 A 298 ASN ASP LEU GLU ALA CYS LEU ASN ASP VAL LYS ASN TRP SEQRES 9 A 298 SER ASP LYS HIS PRO GLY HIS PHE PRO ILE THR LEU ILE SEQRES 10 A 298 LEU ASP LYS LYS GLN GLY TRP SER LYS GLU SER SER GLY SEQRES 11 A 298 ARG THR PRO LYS ASP PHE ASP GLU LEU VAL ALA ARG VAL SEQRES 12 A 298 PHE GLN GLY LYS LEU PHE THR PRO GLN ASP LEU ALA THR SEQRES 13 A 298 HIS ILE GLY SER GLY ALA GLY ALA LEU GLN GLY ASN LEU SEQRES 14 A 298 LYS GLY LYS SER TRP PRO THR ALA ASN ASP LEU GLN GLY SEQRES 15 A 298 LYS VAL LEU LEU VAL LEU ASN HIS SER GLU ASN GLN LYS SEQRES 16 A 298 LEU SER GLN TYR ALA GLU ALA ARG THR SER LYS ALA LYS SEQRES 17 A 298 VAL PHE ILE SER PRO VAL THR ASN GLY GLN ASN ASP ILE SEQRES 18 A 298 SER GLY LYS VAL SER GLY MET SER SER GLN SER SER GLY SEQRES 19 A 298 TYR VAL ALA MET ASN ASN MET GLY LYS GLY ASP LYS SER SEQRES 20 A 298 TRP ALA LYS GLN ALA PHE ALA TYR SER HIS ILE GLY ARG SEQRES 21 A 298 VAL TRP GLY ASP ASP GLU VAL SER PHE ALA GLN HIS ILE SEQRES 22 A 298 ASN GLN LYS ILE ASN LEU SER ALA TYR TYR ARG PHE ALA SEQRES 23 A 298 ALA GLN SER ALA GLY GLY TYR ARG ILE ARG PRO PHE SEQRES 1 B 298 ALA GLN GLU SER PRO ALA PHE ILE ASP PRO ALA SER TRP SEQRES 2 B 298 ASN THR PRO PHE ASN GLY ILE ALA GLN VAL ALA CYS HIS SEQRES 3 B 298 ASN CYS TYR GLU LYS GLN TYR ALA ASN THR PHE SER SER SEQRES 4 B 298 VAL LEU ASP SER VAL ARG THR LEU GLU LEU ASP PHE TRP SEQRES 5 B 298 ASP GLN ARG ASP ALA VAL SER GLY GLY SER PRO HIS HIS SEQRES 6 B 298 TRP PHE VAL ARG HIS ASN PRO GLY THR LEU PHE GLN SER SEQRES 7 B 298 GLY ASN ASP ASN ASN CYS THR GLY ASP GLY THR GLY LYS SEQRES 8 B 298 ASN ASP LEU GLU ALA CYS LEU ASN ASP VAL LYS ASN TRP SEQRES 9 B 298 SER ASP LYS HIS PRO GLY HIS PHE PRO ILE THR LEU ILE SEQRES 10 B 298 LEU ASP LYS LYS GLN GLY TRP SER LYS GLU SER SER GLY SEQRES 11 B 298 ARG THR PRO LYS ASP PHE ASP GLU LEU VAL ALA ARG VAL SEQRES 12 B 298 PHE GLN GLY LYS LEU PHE THR PRO GLN ASP LEU ALA THR SEQRES 13 B 298 HIS ILE GLY SER GLY ALA GLY ALA LEU GLN GLY ASN LEU SEQRES 14 B 298 LYS GLY LYS SER TRP PRO THR ALA ASN ASP LEU GLN GLY SEQRES 15 B 298 LYS VAL LEU LEU VAL LEU ASN HIS SER GLU ASN GLN LYS SEQRES 16 B 298 LEU SER GLN TYR ALA GLU ALA ARG THR SER LYS ALA LYS SEQRES 17 B 298 VAL PHE ILE SER PRO VAL THR ASN GLY GLN ASN ASP ILE SEQRES 18 B 298 SER GLY LYS VAL SER GLY MET SER SER GLN SER SER GLY SEQRES 19 B 298 TYR VAL ALA MET ASN ASN MET GLY LYS GLY ASP LYS SER SEQRES 20 B 298 TRP ALA LYS GLN ALA PHE ALA TYR SER HIS ILE GLY ARG SEQRES 21 B 298 VAL TRP GLY ASP ASP GLU VAL SER PHE ALA GLN HIS ILE SEQRES 22 B 298 ASN GLN LYS ILE ASN LEU SER ALA TYR TYR ARG PHE ALA SEQRES 23 B 298 ALA GLN SER ALA GLY GLY TYR ARG ILE ARG PRO PHE HET CA A 301 1 HET EDO A 401 4 HET CA B 301 1 HET EDO B 402 4 HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 CA 2(CA 2+) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 7 HOH *469(H2 O) HELIX 1 1 ASP A 9 TRP A 13 5 5 HELIX 2 2 PHE A 37 SER A 43 5 7 HELIX 3 3 ASP A 93 HIS A 108 1 16 HELIX 4 4 LYS A 126 GLY A 130 5 5 HELIX 5 5 THR A 132 GLN A 145 1 14 HELIX 6 6 THR A 150 GLY A 159 1 10 HELIX 7 7 GLY A 161 GLY A 163 5 3 HELIX 8 8 ALA A 164 LEU A 169 1 6 HELIX 9 9 GLU A 192 THR A 204 1 13 HELIX 10 10 SER A 205 ALA A 207 5 3 HELIX 11 11 GLN A 218 GLY A 223 1 6 HELIX 12 12 SER A 229 GLY A 234 1 6 HELIX 13 13 GLY A 244 SER A 247 5 4 HELIX 14 14 TRP A 248 TYR A 255 1 8 HELIX 15 15 SER A 268 GLN A 275 1 8 HELIX 16 16 ASP B 9 TRP B 13 5 5 HELIX 17 17 PHE B 37 SER B 43 5 7 HELIX 18 18 ASP B 93 HIS B 108 1 16 HELIX 19 19 LYS B 126 GLY B 130 5 5 HELIX 20 20 THR B 132 GLN B 145 1 14 HELIX 21 21 THR B 150 GLY B 159 1 10 HELIX 22 22 GLY B 161 GLY B 163 5 3 HELIX 23 23 ALA B 164 LEU B 169 1 6 HELIX 24 24 GLU B 192 THR B 204 1 13 HELIX 25 25 SER B 205 ALA B 207 5 3 HELIX 26 26 GLN B 218 GLY B 223 1 6 HELIX 27 27 SER B 229 GLY B 234 1 6 HELIX 28 28 GLY B 244 SER B 247 5 4 HELIX 29 29 TRP B 248 TYR B 255 1 8 HELIX 30 30 SER B 268 GLN B 275 1 8 SHEET 1 AA 5 MET A 238 GLY A 242 0 SHEET 2 AA 5 ILE A 258 TRP A 262 1 O ILE A 258 N ASN A 239 SHEET 3 AA 5 LEU A 279 TYR A 282 1 O LEU A 279 N VAL A 261 SHEET 4 AA 5 ILE A 20 CYS A 25 1 O GLN A 22 N SER A 280 SHEET 5 AA 5 ILE A 295 PRO A 297 -1 O ARG A 296 N ALA A 21 SHEET 1 AB 5 PHE A 67 VAL A 68 0 SHEET 2 AB 5 THR A 46 TRP A 52 -1 O TRP A 52 N PHE A 67 SHEET 3 AB 5 ILE A 114 LYS A 120 1 O THR A 115 N LEU A 47 SHEET 4 AB 5 VAL A 184 ASN A 189 1 O LEU A 185 N LEU A 116 SHEET 5 AB 5 PHE A 210 ILE A 211 1 O PHE A 210 N LEU A 188 SHEET 1 BA 5 MET B 238 GLY B 242 0 SHEET 2 BA 5 ILE B 258 TRP B 262 1 O ILE B 258 N ASN B 239 SHEET 3 BA 5 LEU B 279 TYR B 282 1 O LEU B 279 N VAL B 261 SHEET 4 BA 5 ILE B 20 CYS B 25 1 O GLN B 22 N SER B 280 SHEET 5 BA 5 ILE B 295 PRO B 297 -1 O ARG B 296 N ALA B 21 SHEET 1 BB 5 PHE B 67 VAL B 68 0 SHEET 2 BB 5 THR B 46 TRP B 52 -1 O TRP B 52 N PHE B 67 SHEET 3 BB 5 ILE B 114 LYS B 120 1 O THR B 115 N LEU B 47 SHEET 4 BB 5 VAL B 184 ASN B 189 1 O LEU B 185 N LEU B 116 SHEET 5 BB 5 PHE B 210 ILE B 211 1 O PHE B 210 N LEU B 188 SSBOND 1 CYS A 25 CYS A 28 1555 1555 2.29 SSBOND 2 CYS A 84 CYS A 97 1555 1555 2.04 SSBOND 3 CYS B 25 CYS B 28 1555 1555 2.28 SSBOND 4 CYS B 84 CYS B 97 1555 1555 2.03 LINK OD1 ASN A 27 CA CA A 301 1555 1555 2.42 LINK OE2 GLU A 48 CA CA A 301 1555 1555 2.31 LINK OD1 ASP A 50 CA CA A 301 1555 1555 2.30 LINK OD2 ASP A 119 CA CA A 301 1555 1555 2.43 LINK CA CA A 301 O HOH A2035 1555 1555 2.55 LINK CA CA A 301 O HOH A2036 1555 1555 2.37 LINK OD1 ASN B 27 CA CA B 301 1555 1555 2.42 LINK OE2 GLU B 48 CA CA B 301 1555 1555 2.35 LINK OD1 ASP B 50 CA CA B 301 1555 1555 2.35 LINK OD2 ASP B 119 CA CA B 301 1555 1555 2.41 LINK CA CA B 301 O HOH B2031 1555 1555 2.56 LINK CA CA B 301 O HOH B2032 1555 1555 2.38 SITE 1 AC1 6 ASN A 27 GLU A 48 ASP A 50 ASP A 119 SITE 2 AC1 6 HOH A2035 HOH A2036 SITE 1 AC2 5 ASP A 53 GLN A 122 GLY A 123 SER A 125 SITE 2 AC2 5 ARG A 131 SITE 1 AC3 6 ASN B 27 GLU B 48 ASP B 50 ASP B 119 SITE 2 AC3 6 HOH B2031 HOH B2032 SITE 1 AC4 5 ASP B 53 GLN B 122 GLY B 123 SER B 125 SITE 2 AC4 5 ARG B 131 CRYST1 96.080 96.080 113.340 90.00 90.00 90.00 P 43 2 2 16 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 0.010408 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008823 0.00000