HEADER HYDROLASE 23-SEP-19 6KZ9 TITLE CRYSTAL STRUCTURE OF PLANT PHOSPHOLIPASE D ALPHA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE D ALPHA 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOLIPASE D, PLD ALPHA 1,CHOLINE PHOSPHATASE 1,PLDALPHA, COMPND 5 PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D 1; COMPND 6 EC: 3.1.4.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: PLDALPHA1, PLD1, AT3G15730, MSJ11.13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOLIPASE D, CALCIUM ACTIVATION, C2 DOMAIN, PHOSPHATIDIC ACID, KEYWDS 2 INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.X.LI,F.YU,P.ZHANG REVDAT 4 27-MAR-24 6KZ9 1 REMARK REVDAT 3 22-JAN-20 6KZ9 1 JRNL REVDAT 2 06-NOV-19 6KZ9 1 TITLE REVDAT 1 30-OCT-19 6KZ9 0 JRNL AUTH J.LI,F.YU,H.GUO,R.XIONG,W.ZHANG,F.HE,M.ZHANG,P.ZHANG JRNL TITL CRYSTAL STRUCTURE OF PLANT PLD ALPHA 1 REVEALS CATALYTIC AND JRNL TITL 2 REGULATORY MECHANISMS OF EUKARYOTIC PHOSPHOLIPASE D. JRNL REF CELL RES. V. 30 61 2020 JRNL REFN ISSN 1001-0602 JRNL PMID 31619765 JRNL DOI 10.1038/S41422-019-0244-6 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 42.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 72802 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.660 REMARK 3 FREE R VALUE TEST SET COUNT : 1933 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 0.0000 - 4.3400 0.99 5258 144 0.1581 0.1625 REMARK 3 2 4.3400 - 3.4453 1.00 5267 144 0.1398 0.1554 REMARK 3 3 3.4453 - 3.0099 0.98 5187 142 0.1621 0.1810 REMARK 3 4 3.0099 - 2.7348 0.99 5233 144 0.1726 0.1860 REMARK 3 5 2.7348 - 2.5388 0.99 5242 144 0.1732 0.1994 REMARK 3 6 2.5388 - 2.3891 0.97 5101 139 0.1721 0.1930 REMARK 3 7 2.3891 - 2.2695 0.98 5137 142 0.1744 0.2235 REMARK 3 8 2.2695 - 2.1707 0.98 5132 142 0.1716 0.1940 REMARK 3 9 2.1707 - 2.0871 0.97 5116 137 0.1758 0.2086 REMARK 3 10 2.0871 - 2.0151 0.95 4977 136 0.1813 0.1983 REMARK 3 11 2.0151 - 1.9521 0.94 4959 135 0.1799 0.1901 REMARK 3 12 1.9521 - 1.8963 0.93 4816 136 0.1928 0.2267 REMARK 3 13 1.8963 - 1.8464 0.92 4817 127 0.2060 0.2325 REMARK 3 14 1.8464 - 1.8013 0.88 4627 121 0.2162 0.2735 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.60 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 : 0.010 6361 REMARK 3 ANGLE : 1.158 8620 REMARK 3 CHIRALITY : 0.084 910 REMARK 3 PLANARITY : 0.007 1128 REMARK 3 DIHEDRAL : 17.834 2361 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6KZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75085 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 42.395 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.6000 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) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.79800 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3000, 0.1M TRIS-HCL (PH REMARK 280 7.0), 0.2M CA(OAC)2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 59.44250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.72200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.44250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 63.72200 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 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 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 A1140 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1599 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 MET A 1 REMARK 465 GLY A 22 REMARK 465 GLY A 23 REMARK 465 GLY A 24 REMARK 465 VAL A 25 REMARK 465 ARG A 26 REMARK 465 GLN A 27 REMARK 465 GLY A 28 REMARK 465 PHE A 29 REMARK 465 LEU A 30 REMARK 465 GLY A 31 REMARK 465 LYS A 32 REMARK 465 ILE A 33 REMARK 465 LEU A 34 REMARK 465 ALA A 35 REMARK 465 ASN A 36 REMARK 465 VAL A 37 REMARK 465 GLU A 38 REMARK 465 GLU A 39 REMARK 465 THR A 40 REMARK 465 ILE A 41 REMARK 465 GLY A 42 REMARK 465 VAL A 43 REMARK 465 GLY A 44 REMARK 465 LYS A 45 REMARK 465 GLY A 46 REMARK 465 PRO A 313 REMARK 465 ASP A 314 REMARK 465 ASP A 315 REMARK 465 GLY A 316 REMARK 465 GLY A 317 REMARK 465 SER A 318 REMARK 465 ILE A 319 REMARK 465 VAL A 320 REMARK 465 GLN A 321 REMARK 465 SER A 322 REMARK 465 LEU A 323 REMARK 465 GLN A 324 REMARK 465 ILE A 325 REMARK 465 SER A 326 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 ASP A 442 OD2 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 OD2 ASP A 130 O HOH A 1001 1.81 REMARK 500 O HOH A 1608 O HOH A 1610 1.83 REMARK 500 O HOH A 1138 O HOH A 1243 1.86 REMARK 500 OE2 GLU A 47 O HOH A 1002 1.90 REMARK 500 O HOH A 1389 O HOH A 1391 1.90 REMARK 500 O HOH A 1492 O HOH A 1596 1.92 REMARK 500 NH1 ARG A 441 O HOH A 1003 1.93 REMARK 500 O HOH A 1525 O HOH A 1605 1.96 REMARK 500 O HOH A 1114 O HOH A 1169 1.99 REMARK 500 NH2 ARG A 345 O HOH A 1004 2.00 REMARK 500 NZ LYS A 398 O HOH A 1005 2.02 REMARK 500 NH1 ARG A 345 O HOH A 1006 2.03 REMARK 500 CG GLU A 47 O HOH A 1002 2.05 REMARK 500 O HOH A 1384 O HOH A 1608 2.10 REMARK 500 NZ LYS A 640 O HOH A 1007 2.10 REMARK 500 O HOH A 1025 O HOH A 1280 2.17 REMARK 500 OD2 ASP A 779 O HOH A 1008 2.17 REMARK 500 O ARG A 300 O HOH A 1009 2.17 REMARK 500 O HOH A 1509 O HOH A 1568 2.17 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 1428 O HOH A 1520 1554 1.94 REMARK 500 O HOH A 1169 O HOH A 1169 28510 2.13 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 152 CG GLU A 152 CD 0.092 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 GLN A 3 CB - CA - C ANGL. DEV. = 28.1 DEGREES REMARK 500 HIS A 4 C - N - CA ANGL. DEV. = 22.4 DEGREES REMARK 500 HIS A 4 N - CA - CB ANGL. DEV. = 25.7 DEGREES REMARK 500 GLU A 152 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 LYS A 162 CB - CA - C ANGL. DEV. = -17.5 DEGREES REMARK 500 ARG A 402 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 402 NE - CZ - NH2 ANGL. DEV. = -4.1 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 GLN A 3 -57.37 -140.82 REMARK 500 GLN A 57 -117.33 56.66 REMARK 500 ALA A 85 53.83 -154.53 REMARK 500 LYS A 162 -7.79 64.16 REMARK 500 ASP A 187 176.22 59.49 REMARK 500 HIS A 224 -42.69 -133.45 REMARK 500 SER A 344 115.01 -173.44 REMARK 500 GLU A 349 -10.64 63.84 REMARK 500 THR A 380 -72.81 -122.78 REMARK 500 ASP A 385 59.34 -149.56 REMARK 500 GLN A 388 78.10 -157.12 REMARK 500 ILE A 446 -50.88 -122.94 REMARK 500 ASP A 515 -54.20 -122.24 REMARK 500 THR A 662 151.10 -46.90 REMARK 500 ASP A 669 15.81 59.32 REMARK 500 ARG A 688 -77.75 -101.77 REMARK 500 HIS A 704 -73.25 -74.08 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 GLN A 3 HIS A 4 -131.23 REMARK 500 THR A 327 MET A 328 104.99 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 GLN A 3 -15.79 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 901 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 187 OD1 REMARK 620 2 ASP A 187 OD2 54.5 REMARK 620 3 GLU A 722 OE1 124.6 86.0 REMARK 620 4 GLU A 722 OE2 167.0 112.5 47.5 REMARK 620 N 1 2 3 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 901 DBREF 6KZ9 A 1 810 UNP Q38882 PLDA1_ARATH 1 810 SEQRES 1 A 810 MET ALA GLN HIS LEU LEU HIS GLY THR LEU HIS ALA THR SEQRES 2 A 810 ILE TYR GLU VAL ASP ALA LEU HIS GLY GLY GLY VAL ARG SEQRES 3 A 810 GLN GLY PHE LEU GLY LYS ILE LEU ALA ASN VAL GLU GLU SEQRES 4 A 810 THR ILE GLY VAL GLY LYS GLY GLU THR GLN LEU TYR ALA SEQRES 5 A 810 THR ILE ASP LEU GLN LYS ALA ARG VAL GLY ARG THR ARG SEQRES 6 A 810 LYS ILE LYS ASN GLU PRO LYS ASN PRO LYS TRP TYR GLU SEQRES 7 A 810 SER PHE HIS ILE TYR CYS ALA HIS LEU ALA SER ASP ILE SEQRES 8 A 810 ILE PHE THR VAL LYS ASP ASP ASN PRO ILE GLY ALA THR SEQRES 9 A 810 LEU ILE GLY ARG ALA TYR ILE PRO VAL ASP GLN VAL ILE SEQRES 10 A 810 ASN GLY GLU GLU VAL ASP GLN TRP VAL GLU ILE LEU ASP SEQRES 11 A 810 ASN ASP ARG ASN PRO ILE GLN GLY GLY SER LYS ILE HIS SEQRES 12 A 810 VAL LYS LEU GLN TYR PHE HIS VAL GLU GLU ASP ARG ASN SEQRES 13 A 810 TRP ASN MET GLY ILE LYS SER ALA LYS PHE PRO GLY VAL SEQRES 14 A 810 PRO TYR THR PHE PHE SER GLN ARG GLN GLY CYS LYS VAL SEQRES 15 A 810 SER LEU TYR GLN ASP ALA HIS ILE PRO ASP ASN PHE VAL SEQRES 16 A 810 PRO ARG ILE PRO LEU ALA GLY GLY LYS ASN TYR GLU PRO SEQRES 17 A 810 GLN ARG CYS TRP GLU ASP ILE PHE ASP ALA ILE SER ASN SEQRES 18 A 810 ALA LYS HIS LEU ILE TYR ILE THR GLY TRP SER VAL TYR SEQRES 19 A 810 ALA GLU ILE ALA LEU VAL ARG ASP SER ARG ARG PRO LYS SEQRES 20 A 810 PRO GLY GLY ASP VAL THR ILE GLY GLU LEU LEU LYS LYS SEQRES 21 A 810 LYS ALA SER GLU GLY VAL ARG VAL LEU LEU LEU VAL TRP SEQRES 22 A 810 ASP ASP ARG THR SER VAL ASP VAL LEU LYS LYS ASP GLY SEQRES 23 A 810 LEU MET ALA THR HIS ASP GLU GLU THR GLU ASN PHE PHE SEQRES 24 A 810 ARG GLY SER ASP VAL HIS CYS ILE LEU CYS PRO ARG ASN SEQRES 25 A 810 PRO ASP ASP GLY GLY SER ILE VAL GLN SER LEU GLN ILE SEQRES 26 A 810 SER THR MET PHE THR HIS HIS GLN LYS ILE VAL VAL VAL SEQRES 27 A 810 ASP SER GLU MET PRO SER ARG GLY GLY SER GLU MET ARG SEQRES 28 A 810 ARG ILE VAL SER PHE VAL GLY GLY ILE ASP LEU CYS ASP SEQRES 29 A 810 GLY ARG TYR ASP THR PRO PHE HIS SER LEU PHE ARG THR SEQRES 30 A 810 LEU ASP THR VAL HIS HIS ASP ASP PHE HIS GLN PRO ASN SEQRES 31 A 810 PHE THR GLY ALA ALA ILE THR LYS GLY GLY PRO ARG GLU SEQRES 32 A 810 PRO TRP HIS ASP ILE HIS SER ARG LEU GLU GLY PRO ILE SEQRES 33 A 810 ALA TRP ASP VAL MET TYR ASN PHE GLU GLN ARG TRP SER SEQRES 34 A 810 LYS GLN GLY GLY LYS ASP ILE LEU VAL LYS LEU ARG ASP SEQRES 35 A 810 LEU SER ASP ILE ILE ILE THR PRO SER PRO VAL MET PHE SEQRES 36 A 810 GLN GLU ASP HIS ASP VAL TRP ASN VAL GLN LEU PHE ARG SEQRES 37 A 810 SER ILE ASP GLY GLY ALA ALA ALA GLY PHE PRO GLU SER SEQRES 38 A 810 PRO GLU ALA ALA ALA GLU ALA GLY LEU VAL SER GLY LYS SEQRES 39 A 810 ASP ASN ILE ILE ASP ARG SER ILE GLN ASP ALA TYR ILE SEQRES 40 A 810 HIS ALA ILE ARG ARG ALA LYS ASP PHE ILE TYR VAL GLU SEQRES 41 A 810 ASN GLN TYR PHE LEU GLY SER SER PHE ALA TRP ALA ALA SEQRES 42 A 810 ASP GLY ILE THR PRO GLU ASP ILE ASN ALA LEU HIS LEU SEQRES 43 A 810 ILE PRO LYS GLU LEU SER LEU LYS ILE VAL SER LYS ILE SEQRES 44 A 810 GLU LYS GLY GLU LYS PHE ARG VAL TYR VAL VAL VAL PRO SEQRES 45 A 810 MET TRP PRO GLU GLY LEU PRO GLU SER GLY SER VAL GLN SEQRES 46 A 810 ALA ILE LEU ASP TRP GLN ARG ARG THR MET GLU MET MET SEQRES 47 A 810 TYR LYS ASP VAL ILE GLN ALA LEU ARG ALA GLN GLY LEU SEQRES 48 A 810 GLU GLU ASP PRO ARG ASN TYR LEU THR PHE PHE CYS LEU SEQRES 49 A 810 GLY ASN ARG GLU VAL LYS LYS ASP GLY GLU TYR GLU PRO SEQRES 50 A 810 ALA GLU LYS PRO ASP PRO ASP THR ASP TYR MET ARG ALA SEQRES 51 A 810 GLN GLU ALA ARG ARG PHE MET ILE TYR VAL HIS THR LYS SEQRES 52 A 810 MET MET ILE VAL ASP ASP GLU TYR ILE ILE ILE GLY SER SEQRES 53 A 810 ALA ASN ILE ASN GLN ARG SER MET ASP GLY ALA ARG ASP SEQRES 54 A 810 SER GLU ILE ALA MET GLY GLY TYR GLN PRO HIS HIS LEU SEQRES 55 A 810 SER HIS ARG GLN PRO ALA ARG GLY GLN ILE HIS GLY PHE SEQRES 56 A 810 ARG MET SER LEU TRP TYR GLU HIS LEU GLY MET LEU ASP SEQRES 57 A 810 GLU THR PHE LEU ASP PRO SER SER LEU GLU CYS ILE GLU SEQRES 58 A 810 LYS VAL ASN ARG ILE SER ASP LYS TYR TRP ASP PHE TYR SEQRES 59 A 810 SER SER GLU SER LEU GLU HIS ASP LEU PRO GLY HIS LEU SEQRES 60 A 810 LEU ARG TYR PRO ILE GLY VAL ALA SER GLU GLY ASP ILE SEQRES 61 A 810 THR GLU LEU PRO GLY PHE GLU PHE PHE PRO ASP THR LYS SEQRES 62 A 810 ALA ARG ILE LEU GLY THR LYS SER ASP TYR LEU PRO PRO SEQRES 63 A 810 ILE LEU THR THR HET CA A 901 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *628(H2 O) HELIX 1 AA1 ASP A 114 VAL A 116 5 3 HELIX 2 AA2 GLU A 152 ASP A 154 5 3 HELIX 3 AA3 ARG A 210 ALA A 222 1 13 HELIX 4 AA4 THR A 253 GLU A 264 1 12 HELIX 5 AA5 ASP A 275 SER A 278 5 4 HELIX 6 AA6 VAL A 279 GLY A 286 1 8 HELIX 7 AA7 HIS A 291 ARG A 300 1 10 HELIX 8 AA8 ALA A 395 GLY A 399 5 5 HELIX 9 AA9 GLY A 414 GLY A 432 1 19 HELIX 10 AB1 LYS A 439 SER A 444 5 6 HELIX 11 AB2 SER A 481 ALA A 488 1 8 HELIX 12 AB3 SER A 501 ALA A 513 1 13 HELIX 13 AB4 SER A 527 TRP A 531 5 5 HELIX 14 AB5 THR A 537 ILE A 541 5 5 HELIX 15 AB6 LEU A 546 GLY A 562 1 17 HELIX 16 AB7 SER A 581 GLN A 609 1 29 HELIX 17 AB8 ASP A 614 ASN A 617 5 4 HELIX 18 AB9 THR A 645 ARG A 654 1 10 HELIX 19 AC1 ASN A 680 ASP A 685 1 6 HELIX 20 AC2 GLY A 710 GLY A 725 1 16 HELIX 21 AC3 ASP A 728 ASP A 733 5 6 HELIX 22 AC4 SER A 736 SER A 756 1 21 HELIX 23 AC5 PRO A 805 THR A 810 1 6 SHEET 1 AA1 4 LYS A 75 ALA A 88 0 SHEET 2 AA1 4 HIS A 4 VAL A 17 -1 N LEU A 10 O ILE A 82 SHEET 3 AA1 4 LYS A 141 HIS A 150 -1 O PHE A 149 N THR A 9 SHEET 4 AA1 4 VAL A 122 GLU A 127 -1 N VAL A 122 O LEU A 146 SHEET 1 AA2 4 ALA A 59 ARG A 63 0 SHEET 2 AA2 4 LEU A 50 LEU A 56 -1 N ILE A 54 O VAL A 61 SHEET 3 AA2 4 ASP A 90 ASP A 97 -1 O LYS A 96 N TYR A 51 SHEET 4 AA2 4 THR A 104 PRO A 112 -1 O ILE A 111 N ILE A 91 SHEET 1 AA315 HIS A 305 CYS A 309 0 SHEET 2 AA315 ARG A 267 TRP A 273 1 N VAL A 272 O CYS A 309 SHEET 3 AA315 LEU A 225 GLY A 230 1 N ILE A 226 O ARG A 267 SHEET 4 AA315 ILE A 335 GLU A 341 -1 O VAL A 337 N TYR A 227 SHEET 5 AA315 ARG A 351 GLY A 358 -1 O PHE A 356 N VAL A 336 SHEET 6 AA315 ILE A 408 GLU A 413 -1 O LEU A 412 N SER A 355 SHEET 7 AA315 ARG A 177 GLN A 186 -1 N TYR A 185 O HIS A 409 SHEET 8 AA315 TRP A 462 ASP A 471 -1 O VAL A 464 N ARG A 177 SHEET 9 AA315 GLU A 691 TYR A 697 -1 O ALA A 693 N PHE A 467 SHEET 10 AA315 TYR A 671 GLY A 675 -1 N ILE A 674 O MET A 694 SHEET 11 AA315 LYS A 663 VAL A 667 -1 N VAL A 667 O TYR A 671 SHEET 12 AA315 PHE A 516 ASN A 521 -1 N TYR A 518 O ILE A 666 SHEET 13 AA315 ARG A 566 VAL A 570 1 O TYR A 568 N VAL A 519 SHEET 14 AA315 LEU A 619 ARG A 627 1 O PHE A 622 N VAL A 569 SHEET 15 AA315 ARG A 655 MET A 657 -1 O PHE A 656 N ASN A 626 SHEET 1 AA410 VAL A 491 SER A 492 0 SHEET 2 AA410 ILE A 497 ARG A 500 -1 O ILE A 498 N VAL A 491 SHEET 3 AA410 TRP A 462 ASP A 471 -1 N ILE A 470 O ASP A 499 SHEET 4 AA410 GLU A 691 TYR A 697 -1 O ALA A 693 N PHE A 467 SHEET 5 AA410 TYR A 671 GLY A 675 -1 N ILE A 674 O MET A 694 SHEET 6 AA410 LYS A 663 VAL A 667 -1 N VAL A 667 O TYR A 671 SHEET 7 AA410 PHE A 516 ASN A 521 -1 N TYR A 518 O ILE A 666 SHEET 8 AA410 ARG A 566 VAL A 570 1 O TYR A 568 N VAL A 519 SHEET 9 AA410 LEU A 619 ARG A 627 1 O PHE A 622 N VAL A 569 SHEET 10 AA410 LEU A 767 ARG A 769 -1 O LEU A 768 N CYS A 623 SHEET 1 AA5 2 TRP A 405 HIS A 406 0 SHEET 2 AA5 2 TYR A 659 VAL A 660 1 O TYR A 659 N HIS A 406 SHEET 1 AA6 2 ILE A 772 VAL A 774 0 SHEET 2 AA6 2 ILE A 780 GLU A 782 -1 O THR A 781 N GLY A 773 LINK OD1 ASP A 187 CA CA A 901 1555 1555 2.49 LINK OD2 ASP A 187 CA CA A 901 1555 1555 2.18 LINK OE1 GLU A 722 CA CA A 901 1555 1555 2.99 LINK OE2 GLU A 722 CA CA A 901 1555 1555 2.10 CISPEP 1 GLY A 400 PRO A 401 0 2.90 SITE 1 AC1 4 ASP A 187 HIS A 372 HIS A 406 GLU A 722 CRYST1 118.885 127.444 55.363 90.00 95.47 90.00 C 1 2 1 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 0.008411 0.000000 0.000806 0.00000 SCALE2 0.000000 0.007847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018145 0.00000