HEADER ERYTHROCYTE BINDING PROTEIN 25-FEB-15 4YFS TITLE STRUCTURE OF THE SYNTHETIC DUFFY BINDING PROTEIN (DBP) ANTIGEN DEKNULL TITLE 2 RELEVANT FOR MALARIA VACCINE DESIGN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUFFY RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 198-521; COMPND 5 SYNONYM: ERYTHROCYTE-BINDING PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM VIVAX; SOURCE 3 ORGANISM_TAXID: 126793; SOURCE 4 STRAIN: SALVADOR I; SOURCE 5 GENE: PVDR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DUFFY BINDING LIKE DOMAIN, INVASION, MALARIA, VACCINE, ERYTHROCYTE KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.CHEN,N.H.TOLIA REVDAT 6 27-SEP-23 4YFS 1 REMARK REVDAT 5 11-DEC-19 4YFS 1 REMARK REVDAT 4 17-JAN-18 4YFS 1 REMARK REVDAT 3 20-SEP-17 4YFS 1 SOURCE REMARK REVDAT 2 01-APR-15 4YFS 1 JRNL REVDAT 1 11-MAR-15 4YFS 0 JRNL AUTH E.CHEN,N.D.SALINAS,F.B.NTUMNGIA,J.H.ADAMS,N.H.TOLIA JRNL TITL STRUCTURAL ANALYSIS OF THE SYNTHETIC DUFFY BINDING PROTEIN JRNL TITL 2 (DBP) ANTIGEN DEKNULL RELEVANT FOR PLASMODIUM VIVAX MALARIA JRNL TITL 3 VACCINE DESIGN. JRNL REF PLOS NEGL TROP DIS V. 9 03644 2015 JRNL REFN ESSN 1935-2735 JRNL PMID 25793371 JRNL DOI 10.1371/JOURNAL.PNTD.0003644 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 17535 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1764 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 26.5381 - 4.9283 0.93 1226 141 0.2065 0.2242 REMARK 3 2 4.9283 - 3.9158 0.96 1207 138 0.1809 0.1799 REMARK 3 3 3.9158 - 3.4220 0.97 1233 130 0.1961 0.2736 REMARK 3 4 3.4220 - 3.1096 0.97 1221 134 0.2267 0.2542 REMARK 3 5 3.1096 - 2.8870 0.98 1221 135 0.2224 0.2814 REMARK 3 6 2.8870 - 2.7170 0.98 1226 143 0.2345 0.2886 REMARK 3 7 2.7170 - 2.5811 0.97 1197 132 0.2167 0.2552 REMARK 3 8 2.5811 - 2.4688 0.96 1190 135 0.2329 0.2681 REMARK 3 9 2.4688 - 2.3738 0.97 1206 134 0.2363 0.3115 REMARK 3 10 2.3738 - 2.2919 0.98 1224 136 0.2343 0.3119 REMARK 3 11 2.2919 - 2.2203 0.99 1196 129 0.2417 0.2713 REMARK 3 12 2.2203 - 2.1569 0.99 1218 143 0.2379 0.2834 REMARK 3 13 2.1569 - 2.1000 0.97 1206 134 0.2630 0.3264 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.004 2448 REMARK 3 ANGLE : 0.749 3289 REMARK 3 CHIRALITY : 0.029 348 REMARK 3 PLANARITY : 0.003 413 REMARK 3 DIHEDRAL : 13.989 933 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 4YFS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207380. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000087 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17538 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 26.537 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 2.930 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.74 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.110 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: 3RRC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M DI-SODIUM TARTRATE, 20% PEG REMARK 280 3350, AND MICROSEEDED INTO 0.2 M LITHIUM CHLORIDE, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 18.67500 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: 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 MET A -17 REMARK 465 GLY A -16 REMARK 465 THR A -15 REMARK 465 ILE A -14 REMARK 465 SER A -13 REMARK 465 SER A -12 REMARK 465 ALA A -11 REMARK 465 ILE A -10 REMARK 465 ILE A -9 REMARK 465 ASN A -8 REMARK 465 HIS A -7 REMARK 465 ALA A -6 REMARK 465 PHE A -5 REMARK 465 LEU A -4 REMARK 465 GLN A -3 REMARK 465 ASN A -2 REMARK 465 THR A -1 REMARK 465 VAL A 0 REMARK 465 MET A 1 REMARK 465 VAL A 41 REMARK 465 ASN A 42 REMARK 465 ASN A 43 REMARK 465 THR A 44 REMARK 465 ASP A 45 REMARK 465 THR A 46 REMARK 465 ASN A 47 REMARK 465 PHE A 48 REMARK 465 GLY A 257 REMARK 465 VAL A 296 REMARK 465 GLU A 297 REMARK 465 GLU A 298 REMARK 465 ALA A 299 REMARK 465 LYS A 300 REMARK 465 LYS A 301 REMARK 465 ASN A 302 REMARK 465 THR A 303 REMARK 465 GLN A 304 REMARK 465 GLU A 305 REMARK 465 VAL A 306 REMARK 465 VAL A 307 REMARK 465 THR A 308 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 ALA A 126 -178.56 -67.54 REMARK 500 LYS A 157 -144.35 56.21 REMARK 500 LYS A 215 1.04 -150.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 4YFS A -15 308 UNP P22290 PVDR_PLAVS 198 521 SEQADV 4YFS MET A -17 UNP P22290 INITIATING METHIONINE SEQADV 4YFS GLY A -16 UNP P22290 EXPRESSION TAG SEQADV 4YFS ALA A 126 UNP P22290 ASP 339 CONFLICT SEQADV 4YFS SER A 127 UNP P22290 GLU 340 CONFLICT SEQADV 4YFS THR A 128 UNP P22290 LYS 341 CONFLICT SEQADV 4YFS ALA A 130 UNP P22290 GLN 343 CONFLICT SEQADV 4YFS THR A 131 UNP P22290 GLN 344 CONFLICT SEQADV 4YFS SER A 132 UNP P22290 ARG 345 CONFLICT SEQADV 4YFS THR A 134 UNP P22290 LYS 347 CONFLICT SEQADV 4YFS SER A 135 UNP P22290 GLN 348 CONFLICT SEQRES 1 A 326 MET GLY THR ILE SER SER ALA ILE ILE ASN HIS ALA PHE SEQRES 2 A 326 LEU GLN ASN THR VAL MET LYS ASN CYS ASN TYR LYS ARG SEQRES 3 A 326 LYS ARG ARG GLU ARG ASP TRP ASP CYS ASN THR LYS LYS SEQRES 4 A 326 ASP VAL CYS ILE PRO ASP ARG ARG TYR GLN LEU CYS MET SEQRES 5 A 326 LYS GLU LEU THR ASN LEU VAL ASN ASN THR ASP THR ASN SEQRES 6 A 326 PHE HIS ARG ASP ILE THR PHE ARG LYS LEU TYR LEU LYS SEQRES 7 A 326 ARG LYS LEU ILE TYR ASP ALA ALA VAL GLU GLY ASP LEU SEQRES 8 A 326 LEU LEU LYS LEU ASN ASN TYR ARG TYR ASN LYS ASP PHE SEQRES 9 A 326 CYS LYS ASP ILE ARG TRP SER LEU GLY ASP PHE GLY ASP SEQRES 10 A 326 ILE ILE MET GLY THR ASP MET GLU GLY ILE GLY TYR SER SEQRES 11 A 326 LYS VAL VAL GLU ASN ASN LEU ARG SER ILE PHE GLY THR SEQRES 12 A 326 ALA SER THR ALA ALA THR SER ARG THR SER TRP TRP ASN SEQRES 13 A 326 GLU SER LYS ALA GLN ILE TRP THR ALA MET MET TYR SER SEQRES 14 A 326 VAL LYS LYS ARG LEU LYS GLY ASN PHE ILE TRP ILE CYS SEQRES 15 A 326 LYS LEU ASN VAL ALA VAL ASN ILE GLU PRO GLN ILE TYR SEQRES 16 A 326 ARG TRP ILE ARG GLU TRP GLY ARG ASP TYR VAL SER GLU SEQRES 17 A 326 LEU PRO THR GLU VAL GLN LYS LEU LYS GLU LYS CYS ASP SEQRES 18 A 326 GLY LYS ILE ASN TYR THR ASP LYS LYS VAL CYS LYS VAL SEQRES 19 A 326 PRO PRO CYS GLN ASN ALA CYS LYS SER TYR ASP GLN TRP SEQRES 20 A 326 ILE THR ARG LYS LYS ASN GLN TRP ASP VAL LEU SER ASN SEQRES 21 A 326 LYS PHE ILE SER VAL LYS ASN ALA GLU LYS VAL GLN THR SEQRES 22 A 326 ALA GLY ILE VAL THR PRO TYR ASP ILE LEU LYS GLN GLU SEQRES 23 A 326 LEU ASP GLU PHE ASN GLU VAL ALA PHE GLU ASN GLU ILE SEQRES 24 A 326 ASN LYS ARG ASP GLY ALA TYR ILE GLU LEU CYS VAL CYS SEQRES 25 A 326 SER VAL GLU GLU ALA LYS LYS ASN THR GLN GLU VAL VAL SEQRES 26 A 326 THR FORMUL 2 HOH *128(H2 O) HELIX 1 AA1 PRO A 26 GLN A 31 1 6 HELIX 2 AA2 MET A 34 ASN A 39 1 6 HELIX 3 AA3 ASP A 51 ASN A 78 1 28 HELIX 4 AA4 ASN A 83 GLY A 103 1 21 HELIX 5 AA5 GLY A 110 GLY A 124 1 15 HELIX 6 AA6 THR A 128 MET A 149 1 22 HELIX 7 AA7 MET A 149 LYS A 157 1 9 HELIX 8 AA8 GLY A 158 ILE A 163 5 6 HELIX 9 AA9 LYS A 165 ASN A 171 1 7 HELIX 10 AB1 PRO A 174 ASP A 203 1 30 HELIX 11 AB2 LYS A 211 LYS A 215 5 5 HELIX 12 AB3 VAL A 216 GLU A 251 1 36 HELIX 13 AB4 THR A 260 LEU A 269 1 10 HELIX 14 AB5 ASN A 273 ASN A 282 1 10 HELIX 15 AB6 ASP A 285 VAL A 293 1 9 SSBOND 1 CYS A 4 CYS A 33 1555 1555 2.03 SSBOND 2 CYS A 17 CYS A 24 1555 1555 2.04 SSBOND 3 CYS A 87 CYS A 164 1555 1555 2.04 SSBOND 4 CYS A 202 CYS A 219 1555 1555 2.04 SSBOND 5 CYS A 214 CYS A 294 1555 1555 2.03 SSBOND 6 CYS A 223 CYS A 292 1555 1555 2.04 CRYST1 55.630 37.350 78.200 90.00 108.77 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 0.017976 0.000000 0.006109 0.00000 SCALE2 0.000000 0.026774 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013506 0.00000