HEADER SIGNALING PROTEIN 14-AUG-19 6U0A TITLE HUMAN ANGIOPOIETIN-LIKE 4 C-TERMINAL DOMAIN (CANGPTL4) WITH GLYCEROL COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANGIOPOIETIN-RELATED PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 185-400; COMPND 5 SYNONYM: ANGIOPOIETIN-LIKE PROTEIN 4,HEPATIC FIBRINOGEN/ANGIOPOIETIN- COMPND 6 RELATED PROTEIN,HFARP; COMPND 7 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: ANGPTL4, ARP4, HFARP, PGAR, PP1158, PSEC0166, UNQ171/PRO197; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: T7 SHUFFLE; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: RESISTANCE TO PHAGE T1 (FHUA2); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS FIBRINOGEN-LIKE DOMAIN, ANGIOGENESIS, CANCER CELLS, METASTASIS, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.L.TARVER,Q.YUAN,A.J.SINGHAL,R.RAMAKER,S.COOPER,M.L.PUSEY REVDAT 3 11-OCT-23 6U0A 1 REMARK REVDAT 2 18-DEC-19 6U0A 1 REMARK REVDAT 1 09-OCT-19 6U0A 0 JRNL AUTH C.L.TARVER,Q.YUAN,A.J.SINGHAL,R.RAMAKER,S.COOPER,M.L.PUSEY JRNL TITL CRYSTAL STRUCTURES OF ANGIOPOIETIN-LIKE 4 C-TERMINAL DOMAIN JRNL TITL 2 (CANGPTL4) REVEAL A BINDING POCKET WITH MULTIPLE LIGANDS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 20254 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1924 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 47.1600 - 5.0800 0.99 1471 154 0.2443 0.2593 REMARK 3 2 5.0800 - 4.0300 0.99 1400 148 0.1941 0.2140 REMARK 3 3 4.0300 - 3.5200 0.99 1370 144 0.1968 0.2041 REMARK 3 4 3.5200 - 3.2000 0.99 1384 139 0.2051 0.2290 REMARK 3 5 3.2000 - 2.9700 0.99 1346 144 0.2037 0.2220 REMARK 3 6 2.9700 - 2.7900 0.98 1334 136 0.2008 0.2293 REMARK 3 7 2.7900 - 2.6500 0.97 1321 140 0.2128 0.2341 REMARK 3 8 2.6500 - 2.5400 0.96 1304 135 0.2148 0.2562 REMARK 3 9 2.5400 - 2.4400 0.95 1275 132 0.2196 0.2348 REMARK 3 10 2.4400 - 2.3600 0.94 1266 140 0.2277 0.2901 REMARK 3 11 2.3600 - 2.2800 0.93 1235 131 0.2195 0.2689 REMARK 3 12 2.2800 - 2.2200 0.92 1244 125 0.2482 0.2976 REMARK 3 13 2.2200 - 2.1600 0.89 1213 131 0.2424 0.2970 REMARK 3 14 2.1600 - 2.1100 0.89 1167 125 0.2593 0.2988 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) : 0.207 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.925 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.12 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 : 0.006 1783 REMARK 3 ANGLE : 1.031 2416 REMARK 3 CHIRALITY : 0.057 241 REMARK 3 PLANARITY : 0.005 317 REMARK 3 DIHEDRAL : 21.005 653 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 6U0A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243633. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20254 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 47.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.63900 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: PHASER REMARK 200 STARTING MODEL: 1Z3S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES 7.5, 0.1 M SODIUM REMARK 280 CHLORIDE, AND 1.6 M AMMONIUM SULFATE THIS SOLUTION WITH 20% REMARK 280 GLYCEROL WAS USED AS A CRYOPROTECTANT, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 19.78050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 19.78050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 66.74450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.43400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 66.74450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.43400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.78050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 66.74450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 67.43400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 19.78050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 66.74450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 67.43400 REMARK 290 SMTRY3 8 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 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 OE1 GLN A 372 NZ LYS A 375 2.08 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 HIS A 231 -32.44 -150.20 REMARK 500 LEU A 345 -116.76 -97.40 REMARK 500 ASN A 358 97.40 -163.59 REMARK 500 SER A 366 -156.52 -143.55 REMARK 500 TRP A 383 -74.20 -96.78 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 GOL A 501 DBREF 6U0A A 185 400 UNP Q9BY76 ANGL4_HUMAN 185 400 SEQRES 1 A 216 PRO ARG ASP CYS GLN GLU LEU PHE GLN VAL GLY GLU ARG SEQRES 2 A 216 GLN SER GLY LEU PHE GLU ILE GLN PRO GLN GLY SER PRO SEQRES 3 A 216 PRO PHE LEU VAL ASN CYS LYS MET THR SER ASP GLY GLY SEQRES 4 A 216 TRP THR VAL ILE GLN ARG ARG HIS ASP GLY SER VAL ASP SEQRES 5 A 216 PHE ASN ARG PRO TRP GLU ALA TYR LYS ALA GLY PHE GLY SEQRES 6 A 216 ASP PRO HIS GLY GLU PHE TRP LEU GLY LEU GLU LYS VAL SEQRES 7 A 216 HIS SER ILE THR GLY ASP ARG ASN SER ARG LEU ALA VAL SEQRES 8 A 216 GLN LEU ARG ASP TRP ASP GLY ASN ALA GLU LEU LEU GLN SEQRES 9 A 216 PHE SER VAL HIS LEU GLY GLY GLU ASP THR ALA TYR SER SEQRES 10 A 216 LEU GLN LEU THR ALA PRO VAL ALA GLY GLN LEU GLY ALA SEQRES 11 A 216 THR THR VAL PRO PRO SER GLY LEU SER VAL PRO PHE SER SEQRES 12 A 216 THR TRP ASP GLN ASP HIS ASP LEU ARG ARG ASP LYS ASN SEQRES 13 A 216 CYS ALA LYS SER LEU SER GLY GLY TRP TRP PHE GLY THR SEQRES 14 A 216 CYS SER HIS SER ASN LEU ASN GLY GLN TYR PHE ARG SER SEQRES 15 A 216 ILE PRO GLN GLN ARG GLN LYS LEU LYS LYS GLY ILE PHE SEQRES 16 A 216 TRP LYS THR TRP ARG GLY ARG TYR TYR PRO LEU GLN ALA SEQRES 17 A 216 THR THR MET LEU ILE GLN PRO MET HET GOL A 501 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *49(H2 O) HELIX 1 AA1 ASP A 187 VAL A 194 1 8 HELIX 2 AA2 PRO A 240 GLY A 247 1 8 HELIX 3 AA3 GLY A 258 GLY A 267 1 10 HELIX 4 AA4 GLY A 295 ALA A 299 5 5 HELIX 5 AA5 THR A 305 LEU A 312 1 8 HELIX 6 AA6 ASN A 340 LEU A 345 1 6 HELIX 7 AA7 GLN A 370 LYS A 375 1 6 HELIX 8 AA8 LYS A 381 GLY A 385 1 5 SHEET 1 AA1 5 GLY A 200 ILE A 204 0 SHEET 2 AA1 5 PHE A 212 THR A 219 -1 O CYS A 216 N GLY A 200 SHEET 3 AA1 5 GLY A 222 ARG A 230 -1 O GLY A 222 N THR A 219 SHEET 4 AA1 5 PHE A 255 TRP A 256 -1 O PHE A 255 N ARG A 229 SHEET 5 AA1 5 PHE A 248 GLY A 249 -1 N PHE A 248 O TRP A 256 SHEET 1 AA2 8 GLY A 200 ILE A 204 0 SHEET 2 AA2 8 PHE A 212 THR A 219 -1 O CYS A 216 N GLY A 200 SHEET 3 AA2 8 GLY A 222 ARG A 230 -1 O GLY A 222 N THR A 219 SHEET 4 AA2 8 ALA A 392 PRO A 399 -1 O ILE A 397 N THR A 225 SHEET 5 AA2 8 SER A 271 ARG A 278 -1 N GLN A 276 O THR A 394 SHEET 6 AA2 8 ALA A 284 LEU A 293 -1 O PHE A 289 N LEU A 273 SHEET 7 AA2 8 LEU A 302 LEU A 304 -1 O GLN A 303 N HIS A 292 SHEET 8 AA2 8 LEU A 322 VAL A 324 -1 O LEU A 322 N LEU A 304 SHEET 1 AA3 2 SER A 357 ASN A 358 0 SHEET 2 AA3 2 PHE A 379 TRP A 380 -1 O PHE A 379 N ASN A 358 SSBOND 1 CYS A 188 CYS A 216 1555 1555 2.05 SSBOND 2 CYS A 341 CYS A 354 1555 1555 2.04 SITE 1 AC1 4 LEU A 302 TRP A 349 TRP A 350 SER A 357 CRYST1 133.489 134.868 39.561 90.00 90.00 90.00 C 2 2 21 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 0.007491 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007415 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025277 0.00000