HEADER TRANSFERASE 14-JAN-14 4OFF TITLE CRYSTAL STRUCTURE OF APO CARBOXY CGMP BINDING DOMAIN OF PLASMODIUM TITLE 2 FALCIPARUM PKG COMPND MOL_ID: 1; COMPND 2 MOLECULE: CGMP-DEPENDENT PROTEIN KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL CGMP BINDING DOMAIN, UNP RESIDUES 401-542; COMPND 5 EC: 2.7.11.12; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 5833; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: DELTA CYA TP2000; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PQTEV KEYWDS PHOSPHATE BINDING CASSETTE/CYCLIC GMP BINDING DOMAIN/PKG, KEYWDS 2 SERINE/THREONINE KINASE, TF2I, IRAG, CGMP BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.J.KIM,E.SANABRIA FIGUEROA,C.KIM REVDAT 3 28-FEB-24 4OFF 1 REMARK SEQADV REVDAT 2 11-FEB-15 4OFF 1 JRNL REVDAT 1 21-JAN-15 4OFF 0 JRNL AUTH J.J.KIM,C.FLUECK,E.FRANZ,E.SANABRIA-FIGUEROA,E.THOMPSON, JRNL AUTH 2 R.LORENZ,D.BERTINETTI,D.A.BAKER,F.W.HERBERG,C.KIM JRNL TITL CRYSTAL STRUCTURES OF THE CARBOXYL CGMP BINDING DOMAIN OF JRNL TITL 2 THE PLASMODIUM FALCIPARUM CGMP-DEPENDENT PROTEIN KINASE JRNL TITL 3 REVEAL A NOVEL CAPPING TRIAD CRUCIAL FOR MEROZOITE EGRESS. JRNL REF PLOS PATHOG. V. 11 04639 2015 JRNL REFN ISSN 1553-7366 JRNL PMID 25646845 JRNL DOI 10.1371/JOURNAL.PPAT.1004639 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10438 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 520 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 27.2386 - 2.9964 0.99 2586 133 0.1628 0.2046 REMARK 3 2 2.9964 - 2.3787 1.00 2475 131 0.1939 0.2434 REMARK 3 3 2.3787 - 2.0782 1.00 2450 129 0.1841 0.2493 REMARK 3 4 2.0782 - 1.8882 1.00 2407 127 0.1972 0.2602 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 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 : 0.007 1078 REMARK 3 ANGLE : 1.015 1455 REMARK 3 CHIRALITY : 0.042 156 REMARK 3 PLANARITY : 0.005 182 REMARK 3 DIHEDRAL : 13.232 413 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 4OFF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084424. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : KOHZU HDL-4 DOUBLE CRYSTAL, REMARK 200 DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10442 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.888 REMARK 200 RESOLUTION RANGE LOW (A) : 33.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 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: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 25 % (W/V) PEG REMARK 280 3350 AND 0.1 M BIS-TRIS PH 5.5. , VAPOR DIFFUSION, TEMPERATURE REMARK 280 295.1K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 12.89050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.39000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.84150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.39000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.89050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.84150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 GLY A 399 REMARK 465 SER A 400 REMARK 465 ASP A 401 REMARK 465 ALA A 402 REMARK 465 GLU A 527 REMARK 465 ARG A 528 REMARK 465 ILE A 529 REMARK 465 LYS A 530 REMARK 465 MET A 531 REMARK 465 GLN A 532 REMARK 465 ASP A 533 REMARK 465 THR A 534 REMARK 465 LYS A 535 REMARK 465 VAL A 536 REMARK 465 GLU A 537 REMARK 465 MET A 538 REMARK 465 ASP A 539 REMARK 465 GLU A 540 REMARK 465 LEU A 541 REMARK 465 GLU A 542 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 526 CG CD OE1 OE2 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 478 -2.16 69.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OFG RELATED DB: PDB DBREF 4OFF A 401 542 UNP Q8MMZ4 Q8MMZ4_PLAFA 401 542 SEQADV 4OFF GLY A 399 UNP Q8MMZ4 EXPRESSION TAG SEQADV 4OFF SER A 400 UNP Q8MMZ4 EXPRESSION TAG SEQRES 1 A 144 GLY SER ASP ALA SER ILE ASP TYR ASN ASN LYS LYS SER SEQRES 2 A 144 ILE ILE LYS LYS MET TYR ILE PHE ARG TYR LEU THR ASP SEQRES 3 A 144 LYS GLN CYS ASN LEU LEU ILE GLU ALA PHE ARG THR THR SEQRES 4 A 144 ARG TYR GLU GLU GLY ASP TYR ILE ILE GLN GLU GLY GLU SEQRES 5 A 144 VAL GLY SER ARG PHE TYR ILE ILE LYS ASN GLY GLU VAL SEQRES 6 A 144 GLU ILE VAL LYS ASN LYS LYS ARG LEU ARG THR LEU GLY SEQRES 7 A 144 LYS ASN ASP TYR PHE GLY GLU ARG ALA LEU LEU TYR ASP SEQRES 8 A 144 GLU PRO ARG THR ALA SER VAL ILE SER LYS VAL ASN ASN SEQRES 9 A 144 VAL GLU CYS TRP PHE VAL ASP LYS SER VAL PHE LEU GLN SEQRES 10 A 144 ILE ILE GLN GLY PRO MET LEU ALA HIS LEU GLU GLU ARG SEQRES 11 A 144 ILE LYS MET GLN ASP THR LYS VAL GLU MET ASP GLU LEU SEQRES 12 A 144 GLU HET SO4 A 601 5 HET SO4 A 602 5 HET SO4 A 603 5 HET SO4 A 604 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 HOH *51(H2 O) HELIX 1 1 SER A 403 LYS A 415 1 13 HELIX 2 2 MET A 416 ARG A 420 5 5 HELIX 3 3 THR A 423 PHE A 434 1 12 HELIX 4 4 GLY A 482 LEU A 487 5 6 HELIX 5 5 LYS A 510 GLN A 518 1 9 HELIX 6 6 GLY A 519 LEU A 522 5 4 SHEET 1 A 4 ARG A 435 TYR A 439 0 SHEET 2 A 4 VAL A 503 ASP A 509 -1 O CYS A 505 N THR A 437 SHEET 3 A 4 ARG A 454 ASN A 460 -1 N ILE A 457 O TRP A 506 SHEET 4 A 4 TYR A 480 PHE A 481 -1 O PHE A 481 N TYR A 456 SHEET 1 B 4 TYR A 444 ILE A 446 0 SHEET 2 B 4 SER A 495 SER A 498 -1 O VAL A 496 N ILE A 445 SHEET 3 B 4 VAL A 463 LYS A 467 -1 N VAL A 466 O SER A 495 SHEET 4 B 4 LYS A 470 LEU A 475 -1 O LEU A 472 N ILE A 465 SITE 1 AC1 5 ARG A 435 THR A 436 HOH A 708 HOH A 741 SITE 2 AC1 5 HOH A 745 SITE 1 AC2 3 THR A 423 ASP A 424 LYS A 499 SITE 1 AC3 7 GLY A 452 SER A 453 ARG A 454 TYR A 456 SITE 2 AC3 7 ARG A 492 HOH A 705 HOH A 709 SITE 1 AC4 6 GLU A 490 ARG A 492 THR A 493 HIS A 524 SITE 2 AC4 6 LEU A 525 HOH A 748 CRYST1 25.781 57.683 82.780 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.038788 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012080 0.00000