HEADER PROTEIN TRANSPORT 11-JUL-17 5WF1 TITLE TEPSIN VHS/ENTHLIKE DOMAIN SEMET COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 278-409; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 3 ORGANISM_COMMON: HORSE; SOURCE 4 ORGANISM_TAXID: 9796; SOURCE 5 GENE: TEPSIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN TRAFFICKING, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.N.FRAZIER,A.E.MONKEN,L.P.JACKSON REVDAT 3 01-JAN-20 5WF1 1 REMARK REVDAT 2 30-AUG-17 5WF1 1 JRNL REVDAT 1 26-JUL-17 5WF1 0 JRNL AUTH T.L.ARCHULETA,M.N.FRAZIER,A.E.MONKEN,A.K.KENDALL,J.HARP, JRNL AUTH 2 A.J.MCCOY,N.CREANZA,L.P.JACKSON JRNL TITL STRUCTURE AND EVOLUTION OF ENTH AND VHS/ENTH-LIKE DOMAINS IN JRNL TITL 2 TEPSIN. JRNL REF TRAFFIC V. 18 590 2017 JRNL REFN ESSN 1600-0854 JRNL PMID 28691777 JRNL DOI 10.1111/TRA.12499 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 9830 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 991 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 29.3908 - 4.7026 0.99 1257 133 0.1775 0.1986 REMARK 3 2 4.7026 - 3.7350 1.00 1239 143 0.1572 0.1962 REMARK 3 3 3.7350 - 3.2636 1.00 1240 136 0.1772 0.1993 REMARK 3 4 3.2636 - 2.9655 1.00 1275 145 0.2044 0.2641 REMARK 3 5 2.9655 - 2.7531 1.00 1226 134 0.1893 0.2295 REMARK 3 6 2.7531 - 2.5909 1.00 1260 142 0.1918 0.2559 REMARK 3 7 2.5909 - 2.4612 1.00 1236 136 0.1833 0.2261 REMARK 3 8 2.4612 - 2.3541 0.99 1259 136 0.1773 0.2236 REMARK 3 9 2.3541 - 2.2635 1.00 1237 139 0.1824 0.2222 REMARK 3 10 2.2635 - 2.1854 1.00 1260 144 0.1890 0.2266 REMARK 3 11 2.1854 - 2.1171 1.00 1257 130 0.1932 0.2364 REMARK 3 12 2.1171 - 2.0566 1.00 1249 144 0.2000 0.2453 REMARK 3 13 2.0566 - 2.0025 0.99 1250 140 0.2224 0.2289 REMARK 3 14 2.0025 - 1.9537 0.97 1180 133 0.2811 0.3373 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.200 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 : 0.007 878 REMARK 3 ANGLE : 0.765 1186 REMARK 3 CHIRALITY : 0.043 145 REMARK 3 PLANARITY : 0.004 153 REMARK 3 DIHEDRAL : 2.260 543 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 5WF1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000228901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9904 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 48.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM TARTRATE DIBASIC REMARK 280 DIHYDRATE, 20% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 46.34800 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 23.17400 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 34.76100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 11.58700 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 57.93500 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 302 REMARK 465 PRO A 303 REMARK 465 LEU A 304 REMARK 465 GLY A 305 REMARK 465 SER A 306 REMARK 465 SER A 307 REMARK 465 TRP A 308 REMARK 465 ALA A 309 REMARK 465 PRO A 310 REMARK 465 SER A 311 REMARK 465 ASP A 312 REMARK 465 LEU A 313 REMARK 465 ALA A 314 REMARK 465 GLU A 315 REMARK 465 ARG A 316 REMARK 465 ALA A 317 REMARK 465 GLU A 318 REMARK 465 ALA A 319 REMARK 465 ARG A 435 REMARK 465 GLN A 436 REMARK 465 ARG A 437 REMARK 465 PRO A 438 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 CYS A 325 51.94 -112.88 REMARK 500 THR A 374 -171.29 -51.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 5WF1 A 307 438 UNP F6SIY5 F6SIY5_HORSE 278 409 SEQADV 5WF1 GLY A 302 UNP F6SIY5 EXPRESSION TAG SEQADV 5WF1 PRO A 303 UNP F6SIY5 EXPRESSION TAG SEQADV 5WF1 LEU A 304 UNP F6SIY5 EXPRESSION TAG SEQADV 5WF1 GLY A 305 UNP F6SIY5 EXPRESSION TAG SEQADV 5WF1 SER A 306 UNP F6SIY5 EXPRESSION TAG SEQRES 1 A 137 GLY PRO LEU GLY SER SER TRP ALA PRO SER ASP LEU ALA SEQRES 2 A 137 GLU ARG ALA GLU ALA MSE THR LEU SER ASP CYS GLN GLN SEQRES 3 A 137 GLU LEU SER LEU VAL GLN THR VAL THR ARG GLY SER ARG SEQRES 4 A 137 ALA PHE LEU SER ARG GLU GLU ALA GLN HIS PHE VAL LYS SEQRES 5 A 137 GLU CYS GLY LEU LEU ASN CYS GLU ALA VAL LEU GLU LEU SEQRES 6 A 137 LEU ILE CYS HIS LEU GLY GLY THR SER GLU CYS VAL GLN SEQRES 7 A 137 MSE ARG ALA LEU GLY ALA VAL ALA SER LEU GLY CYS THR SEQRES 8 A 137 ASP LEU LEU PRO GLN GLU HIS ILE LEU LEU LEU THR ARG SEQRES 9 A 137 PRO ARG LEU GLN GLU LEU SER ALA GLY SER PRO GLY PRO SEQRES 10 A 137 VAL THR ASN LYS ALA THR LYS ILE LEU ARG HIS PHE GLU SEQRES 11 A 137 ALA SER CYS ARG GLN ARG PRO MODRES 5WF1 MSE A 320 MET MODIFIED RESIDUE MODRES 5WF1 MSE A 380 MET MODIFIED RESIDUE HET MSE A 320 8 HET MSE A 380 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *66(H2 O) HELIX 1 AA1 CYS A 325 ARG A 337 1 13 HELIX 2 AA2 SER A 344 LEU A 358 1 15 HELIX 3 AA3 ASN A 359 HIS A 370 1 12 HELIX 4 AA4 SER A 375 CYS A 391 1 17 HELIX 5 AA5 PRO A 396 ALA A 413 1 18 HELIX 6 AA6 GLY A 417 CYS A 434 1 18 LINK C MSE A 320 N THR A 321 1555 1555 1.34 LINK C GLN A 379 N MSE A 380 1555 1555 1.33 LINK C MSE A 380 N ARG A 381 1555 1555 1.34 CRYST1 58.775 58.775 69.522 90.00 90.00 120.00 P 65 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 0.017014 0.009823 0.000000 0.00000 SCALE2 0.000000 0.019646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014384 0.00000 HETATM 1 N MSE A 320 -6.315 49.880 43.131 1.00 65.58 N HETATM 2 CA MSE A 320 -5.250 50.443 43.917 1.00 65.37 C HETATM 3 C MSE A 320 -4.358 51.332 43.084 1.00 64.33 C HETATM 4 O MSE A 320 -4.852 51.889 42.101 1.00 58.64 O HETATM 5 CB MSE A 320 -4.550 49.242 44.489 1.00 68.74 C HETATM 6 CG MSE A 320 -4.103 48.355 43.352 1.00 72.06 C HETATM 7 SE MSE A 320 -3.146 46.988 44.334 1.00118.34 SE HETATM 8 CE MSE A 320 -1.413 47.875 44.651 1.00 64.46 C