HEADER UNKNOWN FUNCTION 08-NOV-16 5TVD TITLE CRYSTAL STRUCTURE OF TM16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TM16; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-211; COMPND 5 SYNONYM: UNCHARACTERIZED PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHURIS MURIS; SOURCE 3 ORGANISM_COMMON: MOUSE WHIPWORM; SOURCE 4 ORGANISM_TAXID: 70415; SOURCE 5 EXPRESSION_SYSTEM: PICHIA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4919 KEYWDS PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR O.A.ASOJO REVDAT 4 04-OCT-23 5TVD 1 REMARK REVDAT 3 27-SEP-17 5TVD 1 REMARK REVDAT 2 20-SEP-17 5TVD 1 JRNL REVDAT 1 30-AUG-17 5TVD 0 JRNL AUTH Z.LIU,A.KELLEHER,S.TABB,J.WEI,J.POLLET,P.J.HOTEZ, JRNL AUTH 2 M.E.BOTTAZZI,B.ZHAN,O.A.ASOJO JRNL TITL IDENTIFICATION, CHARACTERIZATION, AND STRUCTURE OF TM16 FROM JRNL TITL 2 TRICHURIS MURIS. JRNL REF J PARASITOL RES V.2017 42789 2017 JRNL REFN ISSN 2090-0023 JRNL PMID 28884022 JRNL DOI 10.1155/2017/4342789 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11RC2_2531: ???) 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 17884 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.390 REMARK 3 FREE R VALUE TEST SET COUNT : 964 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 19.9290 - 3.3128 0.99 2521 136 0.1500 0.1625 REMARK 3 2 3.3128 - 2.6314 1.00 2427 144 0.1641 0.1948 REMARK 3 3 2.6314 - 2.2993 1.00 2418 127 0.1780 0.2136 REMARK 3 4 2.2993 - 2.0893 0.99 2412 127 0.1694 0.1995 REMARK 3 5 2.0893 - 1.9397 0.99 2400 139 0.1761 0.2333 REMARK 3 6 1.9397 - 1.8254 1.00 2382 151 0.1878 0.2368 REMARK 3 7 1.8254 - 1.7341 0.99 2360 140 0.2190 0.2589 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.31 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 : 0.006 1459 REMARK 3 ANGLE : 0.822 1985 REMARK 3 CHIRALITY : 0.055 209 REMARK 3 PLANARITY : 0.006 260 REMARK 3 DIHEDRAL : 3.106 854 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 5TVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1000224877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17974 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.734 REMARK 200 RESOLUTION RANGE LOW (A) : 19.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.04017 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.17770 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.580 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: 1BD9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22 MG/ML TM16 IN 5MM BIS(2 REMARK 280 -HYDROXYETHYL)AMINOTRIS(HYDROXYMETHYL)METHANE PH 6.5 BUFFER 0.1 REMARK 280 M HEPES PH 7.5, 10% (V/V) ISOPROPANOL, 20% (W/V) PEG 4000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 42.98500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.98500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.85000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 364 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 369 LIES ON A SPECIAL POSITION. 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 GLU A 1 REMARK 465 PHE A 2 REMARK 465 MET A 3 REMARK 465 SER A 4 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 REMARK 465 HIS A 194 REMARK 465 HIS A 195 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 O HOH A 247 O HOH A 289 2.08 REMARK 500 O HOH A 350 O HOH A 440 2.14 REMARK 500 O HOH A 390 O HOH A 392 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 376 O HOH A 395 1545 2.01 REMARK 500 O HOH A 370 O HOH A 414 1565 2.16 REMARK 500 REMARK 500 REMARK: NULL DBREF1 5TVD A 3 189 UNP A0A0N5DEJ7_TRIMR DBREF2 5TVD A A0A0N5DEJ7 25 211 SEQADV 5TVD GLU A 1 UNP A0A0N5DEJ EXPRESSION TAG SEQADV 5TVD PHE A 2 UNP A0A0N5DEJ EXPRESSION TAG SEQADV 5TVD LYS A 159 UNP A0A0N5DEJ ARG 181 CONFLICT SEQADV 5TVD HIS A 190 UNP A0A0N5DEJ EXPRESSION TAG SEQADV 5TVD HIS A 191 UNP A0A0N5DEJ EXPRESSION TAG SEQADV 5TVD HIS A 192 UNP A0A0N5DEJ EXPRESSION TAG SEQADV 5TVD HIS A 193 UNP A0A0N5DEJ EXPRESSION TAG SEQADV 5TVD HIS A 194 UNP A0A0N5DEJ EXPRESSION TAG SEQADV 5TVD HIS A 195 UNP A0A0N5DEJ EXPRESSION TAG SEQRES 1 A 195 GLU PHE MET SER SER ASN VAL ALA GLY LYS PHE ALA GLU SEQRES 2 A 195 HIS GLY VAL VAL PRO ASP VAL VAL ALA LYS ALA PRO GLN SEQRES 3 A 195 LEU LEU CYS SER ALA THR TYR ALA SER GLY VAL SER ALA SEQRES 4 A 195 GLU LEU GLY ASN VAL LEU THR PRO THR GLN VAL LYS GLU SEQRES 5 A 195 PRO PRO LYS LEU HIS TRP GLU ALA ASP SER SER SER LEU SEQRES 6 A 195 TYR THR LEU VAL LEU THR ASP PRO ASP ALA PRO SER ARG SEQRES 7 A 195 SER SER PRO LYS PHE ARG GLU TRP HIS HIS TRP LEU ILE SEQRES 8 A 195 VAL ASN ILE PRO GLY ASP LYS VAL ALA GLN GLY GLU THR SEQRES 9 A 195 LEU SER GLU TYR ILE GLY SER GLY PRO PRO LYS GLY THR SEQRES 10 A 195 GLY LEU HIS ARG TYR VAL PHE LEU VAL TYR LYS GLN SER SEQRES 11 A 195 GLY LYS ILE ARG ASP ALA ASP HIS GLY HIS LEU THR ASN SEQRES 12 A 195 ARG SER GLY ASP GLY ARG GLY GLY PHE SER ALA ALA LYS SEQRES 13 A 195 PHE ALA LYS LYS HIS ASN LEU GLY ASP PRO ILE ALA GLY SEQRES 14 A 195 ASN LEU TYR GLN ALA GLN TRP ASP ASP TYR VAL PRO LYS SEQRES 15 A 195 LEU TYR GLU GLN LEU GLY GLY HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *244(H2 O) HELIX 1 AA1 ASN A 6 HIS A 14 1 9 HELIX 2 AA2 GLY A 15 VAL A 20 1 6 HELIX 3 AA3 LYS A 98 GLY A 102 5 5 HELIX 4 AA4 SER A 153 HIS A 161 1 9 HELIX 5 AA5 TYR A 179 LEU A 187 1 9 SHEET 1 AA1 6 LEU A 27 LEU A 28 0 SHEET 2 AA1 6 ALA A 168 ALA A 174 1 O GLY A 169 N LEU A 27 SHEET 3 AA1 6 HIS A 120 LYS A 128 -1 N TYR A 122 O TYR A 172 SHEET 4 AA1 6 LEU A 65 ASP A 72 -1 N THR A 71 O VAL A 123 SHEET 5 AA1 6 TRP A 86 PRO A 95 -1 O TRP A 86 N ASP A 72 SHEET 6 AA1 6 GLU A 103 SER A 106 -1 O GLU A 103 N VAL A 92 SHEET 1 AA2 2 SER A 30 THR A 32 0 SHEET 2 AA2 2 LYS A 55 HIS A 57 -1 O LYS A 55 N THR A 32 CISPEP 1 VAL A 17 PRO A 18 0 5.81 CISPEP 2 ALA A 75 PRO A 76 0 -2.11 CISPEP 3 ARG A 84 GLU A 85 0 -14.19 CRYST1 85.970 31.700 63.750 90.00 97.30 90.00 C 1 2 1 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 0.011632 0.000000 0.001490 0.00000 SCALE2 0.000000 0.031546 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015814 0.00000