HEADER HYDROLASE 02-APR-04 1V0Y TITLE PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE TITLE 2 SUBSTRATE DIBUTYRYLPHOSPHATIDYLCHOLINE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE D; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.4.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP.; SOURCE 3 ORGANISM_TAXID: 172564; SOURCE 4 STRAIN: PMF KEYWDS PHOSPHOLIPASE D, HYDROLASE, SUBSTRATE SOAK, KEYWDS 2 DIBUTYRYLPHOSPHATIDYLCHOLINE, DIC4PC EXPDTA X-RAY DIFFRACTION AUTHOR I.LEIROS,S.MCSWEENEY,E.HOUGH REVDAT 3 13-DEC-23 1V0Y 1 LINK REVDAT 2 24-FEB-09 1V0Y 1 VERSN REVDAT 1 03-JUN-04 1V0Y 0 JRNL AUTH I.LEIROS,S.MCSWEENEY,E.HOUGH JRNL TITL THE REACTION MECHANISM OF PHOSPHOLIPASE D FROM STREPTOMYCES JRNL TITL 2 SP. STRAIN PMF. SNAPSHOTS ALONG THE REACTION PATHWAY REVEAL JRNL TITL 3 A PENTACOORDINATE REACTION INTERMEDIATE AND AN UNEXPECTED JRNL TITL 4 FINAL PRODUCT JRNL REF J.MOL.BIOL. V. 339 805 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15165852 JRNL DOI 10.1016/J.JMB.2004.04.003 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.LEIROS,F.SECUNDO,C.ZAMBONELLI,S.SERVI,E.HOUGH REMARK 1 TITL THE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D REMARK 1 REF STRUCTURE V. 8 655 2000 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 10873862 REMARK 1 DOI 10.1016/S0969-2126(00)00150-7 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 45138 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2377 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) : 1.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2984 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 149 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3709 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 413 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.79000 REMARK 3 B22 (A**2) : 1.57000 REMARK 3 B33 (A**2) : -0.83000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.44000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.104 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.298 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3745 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3316 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5112 ; 1.972 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7720 ; 0.979 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 487 ; 6.873 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 586 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4223 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 698 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 736 ; 0.253 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3838 ; 0.251 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2071 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 303 ; 0.156 ; 0.200 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): 9 ; 0.148 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 31 ; 0.284 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.133 ; 0.200 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): 2447 ; 1.029 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3911 ; 1.718 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1298 ; 2.680 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1201 ; 4.269 ; 4.500 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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. THIS ENTRY CONTAINS ATOMS THAT HAVE BEEN MODELED WITH REMARK 3 AN OCCUPANCY OF 0.00. REMARK 4 REMARK 4 1V0Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-APR-04. REMARK 100 THE DEPOSITION ID IS D_1290014931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.40 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 13.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.47300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: BASED ON PDB ENTRY 1F0I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NH4AC, 0.1 M CITRATE PHOSPHATE REMARK 280 BUFFER AT PH5.4, 27.5% PEG 4000. CRYSTALS WERE THEREAFTER REMARK 280 BACKSOAKED TWICE IN A PHOSPHATE- FREE BUFFER TO REMOVE TRACE- REMARK 280 AMOUNTS OF PHOSPHATE., PH 5.40 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 28.23100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 THIS DATASET DESCRIBES A 30 MINUTE SUBSTRATE SOAK USING 2MM REMARK 400 DIBUTYRYLPHOSPHATIDYLCHOLINE. DIBUTYRYLPHOSPHATIDIC ACID IS REMARK 400 FOUND TO BE COVALENTLY LINKED TO AN ACTIVE SITE HISTIDINE, REMARK 400 IN A STATE THAT CLOSELY RESEMBLES THE 5-COORDINATED REMARK 400 TRANSITION STATE OF THE PHOSPHORUS. 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 ALA A 4 REMARK 465 ASP A 5 REMARK 465 VAL A 127 REMARK 465 TYR A 128 REMARK 465 HIS A 129 REMARK 465 MET A 130 REMARK 465 ASN A 131 REMARK 465 GLY A 383 REMARK 465 ALA A 384 REMARK 465 VAL A 385 REMARK 465 GLY A 386 REMARK 465 SER A 387 REMARK 465 GLY A 388 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 LYS A 60 CG CD CE NZ REMARK 480 LYS A 68 CG CD CE NZ REMARK 480 LYS A 115 CD CE NZ REMARK 480 LYS A 136 CG CD CE NZ REMARK 480 GLU A 140 CG CD OE1 OE2 REMARK 480 LYS A 147 CG CD CE NZ REMARK 480 GLU A 150 CG CD OE1 OE2 REMARK 480 ILE A 233 CB CG1 CG2 CD1 REMARK 480 TRP A 237 CZ2 CZ3 CH2 REMARK 480 ASN A 243 CB CG OD1 ND2 REMARK 480 LYS A 257 CD CE NZ REMARK 480 LYS A 334 CG CD CE NZ REMARK 480 ARG A 382 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 394 CD CE NZ REMARK 480 GLN A 415 CG CD OE1 NE2 REMARK 480 LYS A 438 CE NZ 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 OD1 ASP A 44 O HOH A 2081 2.18 REMARK 500 O HOH A 2288 O HOH A 2291 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 GLU A 150 CB GLU A 150 CG -0.429 REMARK 500 HIS A 170 CE1 HIS A 170 NE2 0.129 REMARK 500 HIS A 170 NE2 HIS A 170 CD2 -0.155 REMARK 500 LYS A 334 CB LYS A 334 CG -0.262 REMARK 500 ALA A 416 C ALA A 418 N 0.190 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 150 CA - CB - CG ANGL. DEV. = 24.9 DEGREES REMARK 500 HIS A 170 ND1 - CG - CD2 ANGL. DEV. = -9.1 DEGREES REMARK 500 HIS A 170 ND1 - CE1 - NE2 ANGL. DEV. = -6.9 DEGREES REMARK 500 HIS A 170 CG - CD2 - NE2 ANGL. DEV. = 22.6 DEGREES REMARK 500 ASP A 191 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 204 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 253 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 327 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 LYS A 334 CA - CB - CG ANGL. DEV. = 15.4 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 ARG A 83 -50.15 -136.25 REMARK 500 ILE A 133 90.19 81.40 REMARK 500 SER A 188 57.76 -91.57 REMARK 500 LEU A 194 -71.24 -115.46 REMARK 500 ALA A 312 34.54 -142.19 REMARK 500 TYR A 390 30.90 -96.17 REMARK 500 SER A 457 -57.98 -140.28 REMARK 500 LEU A 491 -60.57 -139.48 REMARK 500 CYS A 512 63.39 -151.20 REMARK 500 ASN A 513 68.21 -102.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALA A 416 -13.79 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 A2031 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH A2035 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH A2060 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A2084 DISTANCE = 6.42 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HI5 A1515 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1V0S RELATED DB: PDB REMARK 900 UNINHIBITED PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF. REMARK 900 RELATED ID: 1V0T RELATED DB: PDB REMARK 900 PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE REMARK 900 PRODUCT GLYCEROPHOSPHATE. REMARK 900 RELATED ID: 1V0U RELATED DB: PDB REMARK 900 PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE REMARK 900 PRODUCT GLYCEROPHOSPHATE. REMARK 900 RELATED ID: 1V0R RELATED DB: PDB REMARK 900 TUNGSTATE INHIBITED PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN REMARK 900 RELATED ID: 1V0W RELATED DB: PDB REMARK 900 PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE REMARK 900 SUBSTRATE DIBUTYRYLPHOSPHATIDYLCHOLINE. REMARK 900 RELATED ID: 1V0V RELATED DB: PDB REMARK 900 PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE REMARK 900 SUBSTRATE DIBUTYRYLPHOSPHATIDYLCHOLINE. REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS SEQUENCE HAS NOT BEEN DEPOSITED TO UNIPROT AT THE REMARK 999 TIME OF STRUCTURE DEPOSITION. DBREF 1V0Y A 4 290 PDB 1V0Y 1V0Y 4 290 DBREF 1V0Y A 294 302 PDB 1V0Y 1V0Y 294 302 DBREF 1V0Y A 304 514 PDB 1V0Y 1V0Y 304 514 SEQRES 1 A 506 ALA ASP SER ALA THR PRO HIS LEU ASP ALA VAL GLU GLN SEQRES 2 A 506 THR LEU ARG GLN VAL SER PRO GLY LEU GLU GLY ASP VAL SEQRES 3 A 506 TRP GLU ARG THR SER GLY ASN LYS LEU ASP GLY SER ALA SEQRES 4 A 506 ALA ASP PRO SER ASP TRP LEU LEU GLN THR PRO GLY CYS SEQRES 5 A 506 TRP GLY ASP ASP LYS CYS ALA ASP ARG VAL GLY THR LYS SEQRES 6 A 506 ARG LEU LEU ALA LYS MET THR GLU ASN ILE GLY ASN ALA SEQRES 7 A 506 THR ARG THR VAL ASP ILE SER THR LEU ALA PRO PHE PRO SEQRES 8 A 506 ASN GLY ALA PHE GLN ASP ALA ILE VAL ALA GLY LEU LYS SEQRES 9 A 506 GLU SER ALA ALA LYS GLY ASN LYS LEU LYS VAL ARG ILE SEQRES 10 A 506 LEU VAL GLY ALA ALA PRO VAL TYR HIS MET ASN VAL ILE SEQRES 11 A 506 PRO SER LYS TYR ARG ASP GLU LEU THR ALA LYS LEU GLY SEQRES 12 A 506 LYS ALA ALA GLU ASN ILE THR LEU ASN VAL ALA SER MET SEQRES 13 A 506 THR THR SER LYS THR ALA PHE SER TRP ASN HIS SER LYS SEQRES 14 A 506 ILE LEU VAL VAL ASP GLY GLN SER ALA LEU THR GLY GLY SEQRES 15 A 506 ILE ASN SER TRP LYS ASP ASP TYR LEU ASP THR THR HIS SEQRES 16 A 506 PRO VAL SER ASP VAL ASP LEU ALA LEU THR GLY PRO ALA SEQRES 17 A 506 ALA GLY SER ALA GLY ARG TYR LEU ASP THR LEU TRP THR SEQRES 18 A 506 TRP THR CYS GLN ASN LYS SER ASN ILE ALA SER VAL TRP SEQRES 19 A 506 PHE ALA ALA SER GLY ASN ALA GLY CYS MET PRO THR MET SEQRES 20 A 506 HIS LYS ASP THR ASN PRO LYS ALA SER PRO ALA THR GLY SEQRES 21 A 506 ASN VAL PRO VAL ILE ALA VAL GLY GLY LEU GLY VAL GLY SEQRES 22 A 506 ILE LYS ASP VAL ASP PRO LYS SER THR PHE ARG PRO ASP SEQRES 23 A 506 LEU PRO THR ALA SER ASP THR LYS CYS VAL VAL GLY LEU SEQRES 24 A 506 HIS ASP ASN THR ASN ALA ASP ARG ASP TYR ASP THR VAL SEQRES 25 A 506 ASN PRO GLU GLU SER ALA LEU ARG ALA LEU VAL ALA SER SEQRES 26 A 506 ALA LYS GLY HIS ILE GLU ILE SER GLN GLN ASP LEU ASN SEQRES 27 A 506 ALA THR CYS PRO PRO LEU PRO ARG TYR ASP ILE ARG LEU SEQRES 28 A 506 TYR ASP ALA LEU ALA ALA LYS MET ALA ALA GLY VAL LYS SEQRES 29 A 506 VAL ARG ILE VAL VAL SER ASP PRO ALA ASN ARG GLY ALA SEQRES 30 A 506 VAL GLY SER GLY GLY TYR SER GLN ILE LYS SER LEU SER SEQRES 31 A 506 GLU ILE SER ASP THR LEU ARG ASN ARG LEU ALA ASN ILE SEQRES 32 A 506 THR GLY GLY GLN GLN ALA ALA LYS THR ALA MET CYS SER SEQRES 33 A 506 ASN LEU GLN LEU ALA THR PHE ARG SER SER PRO ASN GLY SEQRES 34 A 506 LYS TRP ALA ASP GLY HIS PRO TYR ALA GLN HIS HIS LYS SEQRES 35 A 506 LEU VAL SER VAL ASP SER SER THR PHE TYR ILE GLY SER SEQRES 36 A 506 LYS ASN LEU TYR PRO SER TRP LEU GLN ASP PHE GLY TYR SEQRES 37 A 506 ILE VAL GLU SER PRO GLU ALA ALA LYS GLN LEU ASP ALA SEQRES 38 A 506 LYS LEU LEU ASP PRO GLN TRP LYS TYR SER GLN GLU THR SEQRES 39 A 506 ALA THR VAL ASP TYR ALA ARG GLY ILE CYS ASN ALA HET HI5 A1515 20 HETNAM HI5 2-(BUTYRYLOXY)-1-{[(TETRAHYDROXYPHOSPHORANYL) HETNAM 2 HI5 OXY]METHYL}ETHYL BUTYRATE FORMUL 2 HI5 C11 H23 O9 P FORMUL 3 HOH *413(H2 O) HELIX 1 1 THR A 8 SER A 22 1 15 HELIX 2 2 PRO A 23 LEU A 25 5 3 HELIX 3 3 ARG A 64 ASN A 80 1 17 HELIX 4 4 ASN A 95 LYS A 112 1 18 HELIX 5 5 ILE A 133 GLY A 146 1 14 HELIX 6 6 LYS A 147 GLU A 150 5 4 HELIX 7 7 TRP A 189 LEU A 194 1 6 HELIX 8 8 GLY A 209 ASN A 229 1 21 HELIX 9 9 THR A 249 ASN A 255 1 7 HELIX 10 10 ASP A 313 VAL A 319 1 7 HELIX 11 11 ASN A 320 SER A 332 1 13 HELIX 12 12 ASP A 355 ALA A 368 1 14 HELIX 13 13 ASP A 378 ARG A 382 5 5 HELIX 14 14 LEU A 396 GLY A 412 1 17 HELIX 15 15 GLY A 413 ASN A 425 1 12 HELIX 16 16 SER A 480 LEU A 491 1 12 HELIX 17 17 LEU A 491 GLN A 500 1 10 HELIX 18 18 GLU A 501 ALA A 503 5 3 HELIX 19 19 ALA A 508 GLY A 510 5 3 SHEET 1 AA12 LEU A 49 THR A 52 0 SHEET 2 AA12 ASP A 202 THR A 208 -1 O ASP A 202 N THR A 52 SHEET 3 AA12 TRP A 30 LEU A 38 -1 O LYS A 37 N THR A 208 SHEET 4 AA12 VAL A 265 LEU A 273 -1 O VAL A 265 N ASN A 36 SHEET 5 AA12 GLN A 472 GLU A 479 -1 O ASP A 473 N GLY A 272 SHEET 6 AA12 THR A 458 GLY A 462 -1 O PHE A 459 N VAL A 478 SHEET 7 AA12 LYS A 450 VAL A 454 -1 O LYS A 450 N GLY A 462 SHEET 8 AA12 HIS A 336 GLN A 341 -1 O GLU A 338 N SER A 453 SHEET 9 AA12 LYS A 371 VAL A 376 1 O LYS A 371 N ILE A 337 SHEET 10 AA12 LEU A 426 THR A 430 1 O GLN A 427 N ILE A 374 SHEET 11 AA12 VAL A 505 ASP A 506 -1 O VAL A 505 N LEU A 428 SHEET 12 AA12 ILE A 511 CYS A 512 -1 O ILE A 511 N ASP A 506 SHEET 1 AB 8 LEU A 49 THR A 52 0 SHEET 2 AB 8 ASP A 202 THR A 208 -1 O ASP A 202 N THR A 52 SHEET 3 AB 8 SER A 180 GLY A 184 -1 O ALA A 181 N LEU A 207 SHEET 4 AB 8 ILE A 173 VAL A 176 -1 O LEU A 174 N LEU A 182 SHEET 5 AB 8 THR A 84 LEU A 90 -1 O ASP A 86 N VAL A 175 SHEET 6 AB 8 LEU A 116 GLY A 123 1 O LYS A 117 N VAL A 85 SHEET 7 AB 8 ILE A 152 MET A 159 1 O THR A 153 N VAL A 118 SHEET 8 AB 8 VAL A 236 ALA A 240 -1 O TRP A 237 N SER A 158 SSBOND 1 CYS A 55 CYS A 61 1555 1555 2.03 SSBOND 2 CYS A 227 CYS A 246 1555 1555 2.04 SSBOND 3 CYS A 301 CYS A 348 1555 1555 2.10 SSBOND 4 CYS A 423 CYS A 512 1555 1555 1.99 LINK NE2 HIS A 170 P HI5 A1515 1555 1555 1.85 CISPEP 1 THR A 52 PRO A 53 0 -0.85 CISPEP 2 ALA A 91 PRO A 92 0 2.31 CISPEP 3 CYS A 348 PRO A 349 0 -12.91 CISPEP 4 PRO A 349 PRO A 350 0 2.45 SITE 1 AC1 10 LEU A 90 TRP A 168 HIS A 170 LYS A 172 SITE 2 AC1 10 ASN A 187 HIS A 448 LYS A 450 ASN A 465 SITE 3 AC1 10 TYR A 467 HOH A2413 CRYST1 57.369 56.462 68.762 90.00 93.74 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 0.017431 0.000000 0.001139 0.00000 SCALE2 0.000000 0.017711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014574 0.00000