HEADER IMMUNE SYSTEM 06-MAR-19 6JLI TITLE CRYSTAL STRUCTURE OF CTLD7 DOMAIN OF HUMAN PLA2R COMPND MOL_ID: 1; COMPND 2 MOLECULE: SECRETORY PHOSPHOLIPASE A2 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PLA2R; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CONTAINING A A CONSERVED N LINKED GLYCOSYLATION SITE COMPND 7 AT N1132. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PLA2R1; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS IMN, EPITOPE, PLA2R, CTLD7, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.YU,Z.HU,D.KONG,C.CHENG,Y.HE REVDAT 4 22-NOV-23 6JLI 1 HETSYN REVDAT 3 29-JUL-20 6JLI 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 04-SEP-19 6JLI 1 JRNL REVDAT 1 17-JUL-19 6JLI 0 JRNL AUTH B.YU,Z.HU,D.KONG,C.CHENG,Y.HE JRNL TITL CRYSTAL STRUCTURE OF THE CTLD7 DOMAIN OF HUMAN M-TYPE JRNL TITL 2 PHOSPHOLIPASE A2 RECEPTOR. JRNL REF J.STRUCT.BIOL. V. 207 295 2019 JRNL REFN ESSN 1095-8657 JRNL PMID 31271865 JRNL DOI 10.1016/J.JSB.2019.06.007 REMARK 2 REMARK 2 RESOLUTION. 1.78 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.570 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18279 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1828 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 35.3330 - 4.1792 1.00 1363 140 0.1856 0.2038 REMARK 3 2 4.1792 - 3.3179 1.00 1298 147 0.1555 0.1775 REMARK 3 3 3.3179 - 2.8987 1.00 1284 138 0.1601 0.1871 REMARK 3 4 2.8987 - 2.6338 1.00 1271 141 0.1550 0.2025 REMARK 3 5 2.6338 - 2.4451 1.00 1260 138 0.1568 0.1717 REMARK 3 6 2.4451 - 2.3010 1.00 1258 142 0.1520 0.1733 REMARK 3 7 2.3010 - 2.1857 1.00 1262 143 0.1480 0.1681 REMARK 3 8 2.1857 - 2.0906 1.00 1257 139 0.1532 0.1865 REMARK 3 9 2.0906 - 2.0101 1.00 1242 144 0.1573 0.1987 REMARK 3 10 2.0101 - 1.9408 1.00 1249 141 0.1523 0.1861 REMARK 3 11 1.9408 - 1.8801 1.00 1248 141 0.1553 0.1617 REMARK 3 12 1.8801 - 1.8263 1.00 1252 143 0.1550 0.2071 REMARK 3 13 1.8263 - 1.7783 0.98 1207 131 0.1578 0.2117 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.860 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 : 0.015 994 REMARK 3 ANGLE : 1.304 1355 REMARK 3 CHIRALITY : 0.076 149 REMARK 3 PLANARITY : 0.010 168 REMARK 3 DIHEDRAL : 3.234 755 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 6JLI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300011301. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : 18297 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.778 REMARK 200 RESOLUTION RANGE LOW (A) : 35.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 16.50 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28000 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: 5XTS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M AMMONIUM SULFATE REMARK 280 PH6.0, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.09400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.54700 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.54700 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.09400 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 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 ASN A 1108 REMARK 465 THR A 1109 REMARK 465 SER A 1110 REMARK 465 ASP A 1111 REMARK 465 MET A 1112 REMARK 465 TYR A 1113 REMARK 465 PRO A 1114 REMARK 465 MET A 1115 REMARK 465 PRO A 1116 REMARK 465 HIS A 1235 REMARK 465 HIS A 1236 REMARK 465 HIS A 1237 REMARK 465 HIS A 1238 REMARK 465 HIS A 1239 REMARK 465 HIS A 1240 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 HG SER A 1188 O HOH A 1402 1.57 REMARK 500 OE2 GLU A 1202 O HOH A 1401 2.16 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 CYS A1232 CB CYS A1232 SG -0.097 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 PHE A1197 45.84 -145.30 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 A1517 DISTANCE = 6.11 ANGSTROMS DBREF 6JLI A 1108 1234 UNP Q13018 PLA2R_HUMAN 1108 1234 SEQADV 6JLI HIS A 1235 UNP Q13018 EXPRESSION TAG SEQADV 6JLI HIS A 1236 UNP Q13018 EXPRESSION TAG SEQADV 6JLI HIS A 1237 UNP Q13018 EXPRESSION TAG SEQADV 6JLI HIS A 1238 UNP Q13018 EXPRESSION TAG SEQADV 6JLI HIS A 1239 UNP Q13018 EXPRESSION TAG SEQADV 6JLI HIS A 1240 UNP Q13018 EXPRESSION TAG SEQRES 1 A 133 ASN THR SER ASP MET TYR PRO MET PRO ASN THR LEU GLU SEQRES 2 A 133 TYR GLY ASN ARG THR TYR LYS ILE ILE ASN ALA ASN MET SEQRES 3 A 133 THR TRP TYR ALA ALA ILE LYS THR CYS LEU MET HIS LYS SEQRES 4 A 133 ALA GLN LEU VAL SER ILE THR ASP GLN TYR HIS GLN SER SEQRES 5 A 133 PHE LEU THR VAL VAL LEU ASN ARG LEU GLY TYR ALA HIS SEQRES 6 A 133 TRP ILE GLY LEU PHE THR THR ASP ASN GLY LEU ASN PHE SEQRES 7 A 133 ASP TRP SER ASP GLY THR LYS SER SER PHE THR PHE TRP SEQRES 8 A 133 LYS ASP GLU GLU SER SER LEU LEU GLY ASP CYS VAL PHE SEQRES 9 A 133 ALA ASP SER ASN GLY ARG TRP HIS SER THR ALA CYS GLU SEQRES 10 A 133 SER PHE LEU GLN GLY ALA ILE CYS HIS VAL HIS HIS HIS SEQRES 11 A 133 HIS HIS HIS HET NAG A1301 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 HOH *117(H2 O) HELIX 1 AA1 THR A 1134 HIS A 1145 1 12 HELIX 2 AA2 ASP A 1154 GLY A 1169 1 16 HELIX 3 AA3 GLU A 1201 LEU A 1205 5 5 SHEET 1 AA1 4 THR A1118 TYR A1121 0 SHEET 2 AA1 4 ARG A1124 MET A1133 -1 O TYR A1126 N LEU A1119 SHEET 3 AA1 4 LEU A1227 HIS A1233 -1 O CYS A1232 N LYS A1127 SHEET 4 AA1 4 GLN A1148 LEU A1149 -1 N GLN A1148 O HIS A1233 SHEET 1 AA2 4 ASP A1186 TRP A1187 0 SHEET 2 AA2 4 HIS A1172 PHE A1177 -1 N PHE A1177 O ASP A1186 SHEET 3 AA2 4 CYS A1209 ALA A1212 -1 O ALA A1212 N HIS A1172 SHEET 4 AA2 4 TRP A1218 THR A1221 -1 O HIS A1219 N PHE A1211 SSBOND 1 CYS A 1142 CYS A 1232 1555 1555 2.05 SSBOND 2 CYS A 1209 CYS A 1223 1555 1555 1.95 LINK ND2 ASN A1132 C1 NAG A1301 1555 1555 1.44 CRYST1 70.652 70.652 64.641 90.00 90.00 120.00 P 32 2 1 6 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 0.014154 0.008172 0.000000 0.00000 SCALE2 0.000000 0.016343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015470 0.00000