HEADER SUGAR BINDING PROTEIN 20-NOV-19 6V1C TITLE CRYSTAL STRUCTURE OF HUMAN TREFOIL FACTOR 3 IN COMPLEX WITH ITS TITLE 2 COGNATE LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: TREFOIL FACTOR 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: INTESTINAL TREFOIL FACTOR,HITF,POLYPEPTIDE P1.B,HP1.B; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TFF3, ITF, TFI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TREFOIL FACTOR, LECTIN, MUCIN BINDING PROTEIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.JARVA,J.P.LINGFORD,A.JOHN,N.E.SCOTT,E.D.GODDARD-BORGER REVDAT 4 11-OCT-23 6V1C 1 HETSYN REVDAT 3 29-JUL-20 6V1C 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL LINK SITE ATOM REVDAT 2 27-MAY-20 6V1C 1 JRNL REVDAT 1 11-DEC-19 6V1C 0 JRNL AUTH M.A.JARVA,J.P.LINGFORD,A.JOHN,N.M.SOLER,N.E.SCOTT, JRNL AUTH 2 E.D.GODDARD-BORGER JRNL TITL TREFOIL FACTORS SHARE A LECTIN ACTIVITY THAT DEFINES THEIR JRNL TITL 2 ROLE IN MUCUS. JRNL REF NAT COMMUN V. 11 2265 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32404934 JRNL DOI 10.1038/S41467-020-16223-7 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 9706 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 464 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 34.5350 - 2.2356 1.00 3221 156 0.1742 0.1926 REMARK 3 2 2.2356 - 1.7745 1.00 3015 165 0.1718 0.1556 REMARK 3 3 1.7745 - 1.5502 1.00 3006 143 0.1748 0.2617 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.54 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6V1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000245280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9536 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9760 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 43.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.50 REMARK 200 R MERGE FOR SHELL (I) : 2.02100 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: 2PSP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M NH4SO4, 0.2 M POTASSIUM SODIUM REMARK 280 TARTRATE, AND 0.1 M TRISODIUM CITRATE-CITRIC ACID, PH 5.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 43.74000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.79400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.79400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.87000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.79400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.79400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.61000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.79400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.79400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.87000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.79400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.79400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.61000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 43.74000 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, B 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 238 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 GLU A 2 REMARK 465 TYR A 3 REMARK 465 SER A 57 REMARK 465 THR A 58 REMARK 465 LEU A 59 REMARK 465 GLU A 60 REMARK 465 MLY A 61 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 56 CB CG CD OE1 OE2 DBREF 6V1C A 1 58 UNP Q07654 TFF3_HUMAN 36 93 SEQADV 6V1C SER A 57 UNP Q07654 CYS 92 ENGINEERED MUTATION SEQADV 6V1C LEU A 59 UNP Q07654 EXPRESSION TAG SEQADV 6V1C GLU A 60 UNP Q07654 EXPRESSION TAG SEQADV 6V1C MLY A 61 UNP Q07654 EXPRESSION TAG SEQRES 1 A 61 GLU GLU TYR VAL GLY LEU SER ALA ASN GLN CYS ALA VAL SEQRES 2 A 61 PRO ALA MLY ASP ARG VAL ASP CYS GLY TYR PRO HIS VAL SEQRES 3 A 61 THR PRO MLY GLU CYS ASN ASN ARG GLY CYS CYS PHE ASP SEQRES 4 A 61 SER ARG ILE PRO GLY VAL PRO TRP CYS PHE MLY PRO LEU SEQRES 5 A 61 GLN GLU ALA GLU SER THR LEU GLU MLY MODRES 6V1C MLY A 16 LYS MODIFIED RESIDUE MODRES 6V1C MLY A 29 LYS MODIFIED RESIDUE MODRES 6V1C MLY A 50 LYS MODIFIED RESIDUE HET MLY A 16 27 HET MLY A 29 27 HET MLY A 50 27 HET GAL B 1 23 HET NDG B 2 28 HETNAM MLY N-DIMETHYL-LYSINE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN NDG N-ACETYL-ALPHA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NDG ALPHA-D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2- HETSYN 3 NDG ACETAMIDO-2-DEOXY-GLUCOSE; 2-(ACETYLAMINO)-2-DEOXY-A- HETSYN 4 NDG D-GLUCOPYRANOSE FORMUL 1 MLY 3(C8 H18 N2 O2) FORMUL 2 GAL C6 H12 O6 FORMUL 2 NDG C8 H15 N O6 FORMUL 3 HOH *38(H2 O) HELIX 1 AA1 ALA A 8 ALA A 12 5 5 HELIX 2 AA2 PRO A 14 ARG A 18 5 5 HELIX 3 AA3 THR A 27 ARG A 34 1 8 SHEET 1 AA1 2 CYS A 37 PHE A 38 0 SHEET 2 AA1 2 CYS A 48 PHE A 49 -1 O PHE A 49 N CYS A 37 SSBOND 1 CYS A 11 CYS A 37 1555 1555 2.01 SSBOND 2 CYS A 21 CYS A 36 1555 1555 2.00 SSBOND 3 CYS A 31 CYS A 48 1555 1555 2.09 LINK C ALA A 15 N MLY A 16 1555 1555 1.33 LINK C MLY A 16 N ASP A 17 1555 1555 1.33 LINK C PRO A 28 N MLY A 29 1555 1555 1.33 LINK C MLY A 29 N GLU A 30 1555 1555 1.33 LINK C PHE A 49 N MLY A 50 1555 1555 1.33 LINK C MLY A 50 N PRO A 51 1555 1555 1.35 LINK O4 GAL B 1 C1 NDG B 2 1555 1555 1.42 CRYST1 37.588 37.588 87.480 90.00 90.00 90.00 P 41 21 2 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 0.026604 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011431 0.00000