HEADER HYDROLASE 06-SEP-19 6U8Z TITLE CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN PHOSPHOLIPASE D1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE D1,PHOSPHOLIPASE D1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 330-500,643-1074; COMPND 5 SYNONYM: HPLD1, CHOLINE PHOSPHATASE 1, PHOSPHATIDYLCHOLINE- COMPND 6 HYDROLYZING PHOSPHOLIPASE D1; COMPND 7 EC: 3.1.4.4; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PLD1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFASTBAC HTB KEYWDS PHOSPHOLIPASE D1, PLD, PHOSPHOHISTIDINE, PIP2 BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.Z.BOWLING,M.V.AIROLA REVDAT 2 01-APR-20 6U8Z 1 JRNL REVDAT 1 18-MAR-20 6U8Z 0 JRNL AUTH F.Z.BOWLING,C.M.SALAZAR,J.A.BELL,T.S.HUQ,M.A.FROHMAN, JRNL AUTH 2 M.V.AIROLA JRNL TITL CRYSTAL STRUCTURE OF HUMAN PLD1 PROVIDES INSIGHT INTO JRNL TITL 2 ACTIVATION BY PI(4,5)P2AND RHOA. JRNL REF NAT.CHEM.BIOL. V. 16 400 2020 JRNL REFN ESSN 1552-4469 JRNL PMID 32198492 JRNL DOI 10.1038/S41589-020-0499-8 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 3 NUMBER OF REFLECTIONS : 58064 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1816 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 54.7590 - 4.2305 1.00 5216 166 0.1720 0.2005 REMARK 3 2 4.2305 - 3.3580 1.00 4938 160 0.1386 0.1862 REMARK 3 3 3.3580 - 2.9336 0.99 4836 155 0.1553 0.1970 REMARK 3 4 2.9336 - 2.6654 0.98 4740 153 0.1603 0.1953 REMARK 3 5 2.6654 - 2.4743 0.97 4695 149 0.1660 0.2008 REMARK 3 6 2.4743 - 2.3285 0.95 4590 149 0.1714 0.2258 REMARK 3 7 2.3285 - 2.2118 0.94 4473 136 0.1834 0.2465 REMARK 3 8 2.2118 - 2.1156 0.90 4325 141 0.1912 0.2178 REMARK 3 9 2.1156 - 2.0341 0.87 4124 135 0.2113 0.2817 REMARK 3 10 2.0341 - 1.9639 0.82 3935 126 0.2346 0.2480 REMARK 3 11 1.9639 - 1.9025 0.78 3694 121 0.2640 0.3204 REMARK 3 12 1.9025 - 1.8481 0.72 3424 115 0.3085 0.3679 REMARK 3 13 1.8481 - 1.7995 0.69 3258 110 0.3389 0.3591 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.95 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 336:1074 OR RESID 1075:1274 ) REMARK 3 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.897 70.850 103.093 REMARK 3 T TENSOR REMARK 3 T11: 0.3704 T22: 0.1997 REMARK 3 T33: 0.2670 T12: -0.0799 REMARK 3 T13: -0.0042 T23: -0.0248 REMARK 3 L TENSOR REMARK 3 L11: 1.2622 L22: 0.6667 REMARK 3 L33: 3.9283 L12: -0.3152 REMARK 3 L13: 0.9760 L23: 0.0688 REMARK 3 S TENSOR REMARK 3 S11: -0.1138 S12: -0.3384 S13: 0.0485 REMARK 3 S21: -0.1683 S22: 0.1334 S23: 0.0037 REMARK 3 S31: -0.6729 S32: -0.1823 S33: -0.0405 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6U8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000244136. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X17B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64302 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.799 REMARK 200 RESOLUTION RANGE LOW (A) : 79.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CITRATE, 15% PEG3350, REMARK 280 PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 119.82500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.60450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.60450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.91250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.60450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.60450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 179.73750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.60450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.60450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.91250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.60450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.60450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 179.73750 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 0.00000 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 119.82500 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 TOTAL BURIED SURFACE AREA: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A 330 REMARK 465 GLY A 331 REMARK 465 THR A 332 REMARK 465 ASN A 333 REMARK 465 PHE A 334 REMARK 465 LEU A 335 REMARK 465 SER A 455 REMARK 465 SER A 456 REMARK 465 THR A 457 REMARK 465 VAL A 458 REMARK 465 TYR A 459 REMARK 465 GLN A 659 REMARK 465 LEU A 660 REMARK 465 ASP A 661 REMARK 465 LYS A 662 REMARK 465 PRO A 663 REMARK 465 PHE A 664 REMARK 465 ALA A 665 REMARK 465 ASP A 666 REMARK 465 PHE A 667 REMARK 465 ALA A 727 REMARK 465 HIS A 728 REMARK 465 GLY A 829 REMARK 465 ASP A 830 REMARK 465 ILE A 831 REMARK 465 SER A 832 REMARK 465 THR A 833 REMARK 465 SER A 1060 REMARK 465 VAL A 1061 REMARK 465 GLY A 1062 REMARK 465 THR A 1063 REMARK 465 LYS A 1064 REMARK 465 GLU A 1065 REMARK 465 ALA A 1066 REMARK 465 ILE A 1067 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 GLU A 424 CG CD OE1 OE2 REMARK 470 LEU A 425 CG CD1 CD2 REMARK 470 LEU A 427 CG CD1 CD2 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 HZ3 LYS A 710 O HOH A 1201 1.41 REMARK 500 HG SER A 1053 O HOH A 1208 1.57 REMARK 500 O HOH A 1217 O HOH A 1574 1.65 REMARK 500 O HOH A 1586 O HOH A 1613 1.79 REMARK 500 O HOH A 1403 O HOH A 1469 1.84 REMARK 500 O HOH A 1225 O HOH A 1605 1.87 REMARK 500 O HOH A 1498 O HOH A 1621 1.91 REMARK 500 O HOH A 1598 O HOH A 1654 1.92 REMARK 500 O HOH A 1313 O HOH A 1457 1.94 REMARK 500 O HOH A 1345 O HOH A 1512 1.94 REMARK 500 NZ LYS A 710 O HOH A 1201 1.96 REMARK 500 O HOH A 1497 O HOH A 1629 1.98 REMARK 500 O HOH A 1552 O HOH A 1649 1.98 REMARK 500 O HOH A 1315 O HOH A 1473 2.04 REMARK 500 O TYR A 757 O HOH A 1202 2.05 REMARK 500 O HOH A 1497 O HOH A 1537 2.06 REMARK 500 O HOH A 1536 O HOH A 1658 2.06 REMARK 500 OD1 ASN A 855 O HOH A 1203 2.08 REMARK 500 OE2 GLU A 1028 O HOH A 1204 2.10 REMARK 500 O HOH A 1416 O HOH A 1629 2.10 REMARK 500 OH TYR A 872 O HOH A 1205 2.16 REMARK 500 OE2 GLU A 363 O HOH A 1206 2.16 REMARK 500 O HOH A 1509 O HOH A 1661 2.17 REMARK 500 O HOH A 1291 O HOH A 1474 2.17 REMARK 500 O HOH A 1220 O HOH A 1403 2.17 REMARK 500 OD1 ASP A 973 O HOH A 1207 2.18 REMARK 500 O HOH A 1220 O HOH A 1549 2.18 REMARK 500 O HOH A 1223 O HOH A 1471 2.18 REMARK 500 O HOH A 1414 O HOH A 1475 2.18 REMARK 500 O HOH A 1465 O HOH A 1578 2.19 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 NZ LYS A 1022 O HOH A 1674 4464 2.06 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 TYR A 946 CE2 TYR A 946 CD2 0.105 REMARK 500 CYS A 959 CB CYS A 959 SG 0.184 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 ASP A 402 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 GLY A 428 N - CA - C ANGL. DEV. = 15.0 DEGREES REMARK 500 ARG A 670 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 700 NE - CZ - NH2 ANGL. DEV. = -5.5 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 ASN A 357 169.91 68.88 REMARK 500 GLU A 374 -50.70 -130.75 REMARK 500 SER A 473 -31.32 -134.97 REMARK 500 ASP A 496 57.68 -160.05 REMARK 500 ASP A 656 45.80 -144.90 REMARK 500 HIS A 775 -49.92 -136.47 REMARK 500 PHE A 784 61.77 -150.97 REMARK 500 SER A 786 -155.62 -162.04 REMARK 500 CYS A 787 90.86 71.69 REMARK 500 LYS A 791 -54.00 -139.22 REMARK 500 CYS A 851 2.08 -151.66 REMARK 500 SER A 897 153.66 -39.81 REMARK 500 ASN A 905 -5.31 -140.92 REMARK 500 ARG A 923 -112.91 -101.31 REMARK 500 VAL A 986 -63.39 -108.48 REMARK 500 LEU A1057 7.40 -66.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 427 GLY A 428 139.79 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 A1669 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A1670 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A1671 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A1672 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A1673 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH A1674 DISTANCE = 7.43 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO3 A 1101 DBREF 6U8Z A 330 500 UNP Q13393 PLD1_HUMAN 330 500 DBREF 6U8Z A 643 1074 UNP Q13393 PLD1_HUMAN 643 1074 SEQRES 1 A 603 HIS GLY THR ASN PHE LEU LYS ASP HIS ARG PHE GLY SER SEQRES 2 A 603 TYR ALA ALA ILE GLN GLU ASN ALA LEU ALA LYS TRP TYR SEQRES 3 A 603 VAL ASN ALA LYS GLY TYR PHE GLU ASP VAL ALA ASN ALA SEQRES 4 A 603 MET GLU GLU ALA ASN GLU GLU ILE PHE ILE THR ASP TRP SEQRES 5 A 603 TRP LEU SER PRO GLU ILE PHE LEU LYS ARG PRO VAL VAL SEQRES 6 A 603 GLU GLY ASN ARG TRP ARG LEU ASP CYS ILE LEU LYS ARG SEQRES 7 A 603 LYS ALA GLN GLN GLY VAL ARG ILE PHE ILE MET LEU TYR SEQRES 8 A 603 LYS GLU VAL GLU LEU ALA LEU GLY ILE ASN SER GLU TYR SEQRES 9 A 603 THR LYS ARG THR LEU MET ARG LEU HIS PRO ASN ILE LYS SEQRES 10 A 603 VAL MET ARG HIS PRO ASP HIS VAL SER SER THR VAL TYR SEQRES 11 A 603 LEU TRP ALA HIS HIS GLU LYS LEU VAL ILE ILE ASP GLN SEQRES 12 A 603 SER VAL ALA PHE VAL GLY GLY ILE ASP LEU ALA TYR GLY SEQRES 13 A 603 ARG TRP ASP ASP ASN GLU HIS ARG LEU THR ASP VAL GLY SEQRES 14 A 603 SER VAL PHE TRP HIS GLY LYS ASP TYR CYS ASN PHE VAL SEQRES 15 A 603 PHE LYS ASP TRP VAL GLN LEU ASP LYS PRO PHE ALA ASP SEQRES 16 A 603 PHE ILE ASP ARG TYR SER THR PRO ARG MET PRO TRP HIS SEQRES 17 A 603 ASP ILE ALA SER ALA VAL HIS GLY LYS ALA ALA ARG ASP SEQRES 18 A 603 VAL ALA ARG HIS PHE ILE GLN ARG TRP ASN PHE THR LYS SEQRES 19 A 603 ILE MET LYS SER LYS TYR ARG SER LEU SER TYR PRO PHE SEQRES 20 A 603 LEU LEU PRO LYS SER GLN THR THR ALA HIS GLU LEU ARG SEQRES 21 A 603 TYR GLN VAL PRO GLY SER VAL HIS ALA ASN VAL GLN LEU SEQRES 22 A 603 LEU ARG SER ALA ALA ASP TRP SER ALA GLY ILE LYS TYR SEQRES 23 A 603 HIS GLU GLU SER ILE HIS ALA ALA TYR VAL HIS VAL ILE SEQRES 24 A 603 GLU ASN SER ARG HIS TYR ILE TYR ILE GLU ASN GLN PHE SEQRES 25 A 603 PHE ILE SER CYS ALA ASP ASP LYS VAL VAL PHE ASN LYS SEQRES 26 A 603 ILE GLY ASP ALA ILE ALA GLN ARG ILE LEU LYS ALA HIS SEQRES 27 A 603 ARG GLU ASN GLN LYS TYR ARG VAL TYR VAL VAL ILE PRO SEQRES 28 A 603 LEU LEU PRO GLY PHE GLU GLY ASP ILE SER THR GLY GLY SEQRES 29 A 603 GLY ASN ALA LEU GLN ALA ILE MET HIS PHE ASN TYR ARG SEQRES 30 A 603 THR MET CYS ARG GLY GLU ASN SER ILE LEU GLY GLN LEU SEQRES 31 A 603 LYS ALA GLU LEU GLY ASN GLN TRP ILE ASN TYR ILE SER SEQRES 32 A 603 PHE CYS GLY LEU ARG THR HIS ALA GLU LEU GLU GLY ASN SEQRES 33 A 603 LEU VAL THR GLU LEU ILE TYR VAL HIS SER LYS LEU LEU SEQRES 34 A 603 ILE ALA ASP ASP ASN THR VAL ILE ILE GLY SER ALA ASN SEQRES 35 A 603 ILE ASN ASP ARG SER MET LEU GLY LYS ARG ASP SER GLU SEQRES 36 A 603 MET ALA VAL ILE VAL GLN ASP THR GLU THR VAL PRO SER SEQRES 37 A 603 VAL MET ASP GLY LYS GLU TYR GLN ALA GLY ARG PHE ALA SEQRES 38 A 603 ARG GLY LEU ARG LEU GLN CYS PHE ARG VAL VAL LEU GLY SEQRES 39 A 603 TYR LEU ASP ASP PRO SER GLU ASP ILE GLN ASP PRO VAL SEQRES 40 A 603 SER ASP LYS PHE PHE LYS GLU VAL TRP VAL SER THR ALA SEQRES 41 A 603 ALA ARG ASN ALA THR ILE TYR ASP LYS VAL PHE ARG CYS SEQRES 42 A 603 LEU PRO ASN ASP GLU VAL HIS ASN LEU ILE GLN LEU ARG SEQRES 43 A 603 ASP PHE ILE ASN LYS PRO VAL LEU ALA LYS GLU ASP PRO SEQRES 44 A 603 ILE ARG ALA GLU GLU GLU LEU LYS LYS ILE ARG GLY PHE SEQRES 45 A 603 LEU VAL GLN PHE PRO PHE TYR PHE LEU SER GLU GLU SER SEQRES 46 A 603 LEU LEU PRO SER VAL GLY THR LYS GLU ALA ILE VAL PRO SEQRES 47 A 603 MET GLU VAL TRP THR HET PO3 A1101 4 HETNAM PO3 PHOSPHITE ION FORMUL 2 PO3 O3 P 3- FORMUL 3 HOH *474(H2 O) HELIX 1 AA1 HIS A 338 SER A 342 5 5 HELIX 2 AA2 ASN A 357 GLU A 371 1 15 HELIX 3 AA3 ARG A 400 GLN A 411 1 12 HELIX 4 AA4 ASN A 430 HIS A 442 1 13 HELIX 5 AA5 HIS A 645 TYR A 649 5 5 HELIX 6 AA6 GLY A 687 LYS A 708 1 22 HELIX 7 AA7 SER A 709 ARG A 712 5 4 HELIX 8 AA8 ALA A 749 GLY A 754 1 6 HELIX 9 AA9 SER A 761 SER A 773 1 13 HELIX 10 AB1 LYS A 796 GLU A 811 1 16 HELIX 11 AB2 GLY A 835 CYS A 851 1 17 HELIX 12 AB3 SER A 856 GLY A 866 1 11 HELIX 13 AB4 ASN A 867 ASN A 871 5 5 HELIX 14 AB5 ASN A 915 LEU A 920 1 6 HELIX 15 AB6 ARG A 950 GLY A 965 1 16 HELIX 16 AB7 SER A 971 GLN A 975 5 5 HELIX 17 AB8 SER A 979 VAL A 986 1 8 HELIX 18 AB9 VAL A 986 ARG A 1003 1 18 HELIX 19 AC1 ASN A 1012 LYS A 1022 1 11 HELIX 20 AC2 VAL A 1024 ASP A 1029 1 6 HELIX 21 AC3 ASP A 1029 LYS A 1038 1 10 HELIX 22 AC4 PRO A 1069 TRP A 1073 5 5 SHEET 1 AA115 ILE A 445 HIS A 450 0 SHEET 2 AA115 ARG A 414 TYR A 420 1 N ILE A 417 O LYS A 446 SHEET 3 AA115 GLU A 375 ASP A 380 1 N ILE A 376 O PHE A 416 SHEET 4 AA115 LYS A 466 ILE A 470 -1 O ILE A 469 N PHE A 377 SHEET 5 AA115 VAL A 474 GLY A 478 -1 O PHE A 476 N VAL A 468 SHEET 6 AA115 ILE A 681 HIS A 686 -1 O VAL A 685 N ALA A 475 SHEET 7 AA115 GLN A 347 VAL A 356 -1 N LYS A 353 O ALA A 684 SHEET 8 AA115 VAL A 738 ALA A 748 -1 O VAL A 742 N GLN A 347 SHEET 9 AA115 GLU A 926 GLN A 932 -1 O GLN A 932 N ASN A 741 SHEET 10 AA115 THR A 906 GLY A 910 -1 N ILE A 909 O VAL A 929 SHEET 11 AA115 LYS A 898 ALA A 902 -1 N ALA A 902 O THR A 906 SHEET 12 AA115 TYR A 776 ASN A 781 -1 N GLU A 780 O LEU A 899 SHEET 13 AA115 ARG A 816 VAL A 820 1 O TYR A 818 N ILE A 779 SHEET 14 AA115 ILE A 873 LEU A 884 1 O CYS A 876 N VAL A 819 SHEET 15 AA115 ASN A 887 LEU A 892 -1 O VAL A 889 N ALA A 882 SHEET 1 AA2 9 GLU A 759 GLU A 760 0 SHEET 2 AA2 9 VAL A 738 ALA A 748 -1 N ALA A 748 O GLU A 759 SHEET 3 AA2 9 GLU A 926 GLN A 932 -1 O GLN A 932 N ASN A 741 SHEET 4 AA2 9 THR A 906 GLY A 910 -1 N ILE A 909 O VAL A 929 SHEET 5 AA2 9 LYS A 898 ALA A 902 -1 N ALA A 902 O THR A 906 SHEET 6 AA2 9 TYR A 776 ASN A 781 -1 N GLU A 780 O LEU A 899 SHEET 7 AA2 9 ARG A 816 VAL A 820 1 O TYR A 818 N ILE A 779 SHEET 8 AA2 9 ILE A 873 LEU A 884 1 O CYS A 876 N VAL A 819 SHEET 9 AA2 9 LEU A1044 GLN A1046 -1 O VAL A1045 N GLY A 877 SHEET 1 AA3 2 TRP A 678 HIS A 679 0 SHEET 2 AA3 2 TYR A 894 VAL A 895 1 O TYR A 894 N HIS A 679 SHEET 1 AA4 2 THR A 936 MET A 941 0 SHEET 2 AA4 2 LYS A 944 GLY A 949 -1 O TYR A 946 N SER A 939 LINK NE2 HIS A 464 P PO3 A1101 1555 1555 1.68 CISPEP 1 ARG A 391 PRO A 392 0 0.37 CISPEP 2 HIS A 450 PRO A 451 0 -1.87 CISPEP 3 LEU A 1005 PRO A 1006 0 8.32 SITE 1 AC1 8 HIS A 464 LYS A 466 GLN A 782 HIS A 896 SITE 2 AC1 8 LYS A 898 ASN A 913 HOH A1260 HOH A1454 CRYST1 75.209 75.209 239.650 90.00 90.00 90.00 P 41 21 2 8 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 0.013296 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013296 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004173 0.00000