PDB Short entry for 6V1D HEADER SUGAR BINDING PROTEIN 20-NOV-19 6V1D TITLE CRYSTAL STRUCTURE OF HUMAN TREFOIL FACTOR 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TREFOIL FACTOR 1; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: BREAST CANCER ESTROGEN-INDUCIBLE PROTEIN,PNR-2,POLYPEPTIDE COMPND 5 P1.A,HP1.A,PROTEIN PS2; COMPND 6 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: TFF1, BCEI, PS2; 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 3 11-OCT-23 6V1D 1 REMARK REVDAT 2 27-MAY-20 6V1D 1 JRNL REVDAT 1 11-DEC-19 6V1D 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 6044 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.590 REMARK 3 FREE R VALUE TEST SET COUNT : 338 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 41.3440 - 3.0236 0.98 2881 177 0.1804 0.2089 REMARK 3 2 3.0236 - 2.4000 0.98 2825 161 0.2186 0.2576 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.85 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 6V1D 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_1000245281. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6054 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 41.344 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.26600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.98300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 46.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M AMMONIUM SULFATE, 0.1 M TRIS-HCL, REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 20.95250 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 350 REMARK 350 BIOMOLECULE: 3 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: C 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 GLU A 50 REMARK 465 LYS A 51 REMARK 465 GLU B 50 REMARK 465 LYS B 51 REMARK 465 LEU C 49 REMARK 465 GLU C 50 REMARK 465 LYS C 51 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 ASP A 33 113.21 -162.03 REMARK 500 ASP B 33 108.67 -167.49 REMARK 500 ASP C 33 102.42 -166.34 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 A 134 DISTANCE = 6.28 ANGSTROMS DBREF 6V1D A 1 48 UNP P04155 TFF1_HUMAN 27 74 DBREF 6V1D B 1 48 UNP P04155 TFF1_HUMAN 27 74 DBREF 6V1D C 1 48 UNP P04155 TFF1_HUMAN 27 74 SEQADV 6V1D LEU A 49 UNP P04155 EXPRESSION TAG SEQADV 6V1D GLU A 50 UNP P04155 EXPRESSION TAG SEQADV 6V1D LYS A 51 UNP P04155 EXPRESSION TAG SEQADV 6V1D LEU B 49 UNP P04155 EXPRESSION TAG SEQADV 6V1D GLU B 50 UNP P04155 EXPRESSION TAG SEQADV 6V1D LYS B 51 UNP P04155 EXPRESSION TAG SEQADV 6V1D LEU C 49 UNP P04155 EXPRESSION TAG SEQADV 6V1D GLU C 50 UNP P04155 EXPRESSION TAG SEQADV 6V1D LYS C 51 UNP P04155 EXPRESSION TAG SEQRES 1 A 51 PCA THR GLU THR CYS THR VAL ALA PRO ARG GLU ARG GLN SEQRES 2 A 51 ASN CYS GLY PHE PRO GLY VAL THR PRO SER GLN CYS ALA SEQRES 3 A 51 ASN LYS GLY CYS CYS PHE ASP ASP THR VAL ARG GLY VAL SEQRES 4 A 51 PRO TRP CYS PHE TYR PRO ASN THR ILE LEU GLU LYS SEQRES 1 B 51 PCA THR GLU THR CYS THR VAL ALA PRO ARG GLU ARG GLN SEQRES 2 B 51 ASN CYS GLY PHE PRO GLY VAL THR PRO SER GLN CYS ALA SEQRES 3 B 51 ASN LYS GLY CYS CYS PHE ASP ASP THR VAL ARG GLY VAL SEQRES 4 B 51 PRO TRP CYS PHE TYR PRO ASN THR ILE LEU GLU LYS SEQRES 1 C 51 PCA THR GLU THR CYS THR VAL ALA PRO ARG GLU ARG GLN SEQRES 2 C 51 ASN CYS GLY PHE PRO GLY VAL THR PRO SER GLN CYS ALA SEQRES 3 C 51 ASN LYS GLY CYS CYS PHE ASP ASP THR VAL ARG GLY VAL SEQRES 4 C 51 PRO TRP CYS PHE TYR PRO ASN THR ILE LEU GLU LYS MODRES 6V1D PCA A 1 GLN MODIFIED RESIDUE MODRES 6V1D PCA B 1 GLN MODIFIED RESIDUE MODRES 6V1D PCA C 1 GLN MODIFIED RESIDUE HET PCA A 1 8 HET PCA B 1 8 HET PCA C 1 8 HETNAM PCA PYROGLUTAMIC ACID FORMUL 1 PCA 3(C5 H7 N O3) FORMUL 4 HOH *96(H2 O) HELIX 1 AA1 ALA A 8 ARG A 12 5 5 HELIX 2 AA2 THR A 21 LYS A 28 1 8 HELIX 3 AA3 ALA B 8 ARG B 12 5 5 HELIX 4 AA4 THR B 21 LYS B 28 1 8 HELIX 5 AA5 ALA C 8 ARG C 12 5 5 HELIX 6 AA6 THR C 21 LYS C 28 1 8 SHEET 1 AA1 2 GLU A 3 THR A 4 0 SHEET 2 AA1 2 ASN A 46 THR A 47 -1 O ASN A 46 N THR A 4 SHEET 1 AA2 2 CYS A 31 PHE A 32 0 SHEET 2 AA2 2 CYS A 42 PHE A 43 -1 O PHE A 43 N CYS A 31 SHEET 1 AA3 2 GLU B 3 THR B 4 0 SHEET 2 AA3 2 ASN B 46 THR B 47 -1 O ASN B 46 N THR B 4 SHEET 1 AA4 2 CYS B 31 PHE B 32 0 SHEET 2 AA4 2 CYS B 42 PHE B 43 -1 O PHE B 43 N CYS B 31 SHEET 1 AA5 2 GLU C 3 THR C 4 0 SHEET 2 AA5 2 ASN C 46 THR C 47 -1 O ASN C 46 N THR C 4 SHEET 1 AA6 2 CYS C 31 PHE C 32 0 SHEET 2 AA6 2 CYS C 42 PHE C 43 -1 O PHE C 43 N CYS C 31 SSBOND 1 CYS A 5 CYS A 31 1555 1555 2.03 SSBOND 2 CYS A 15 CYS A 30 1555 1555 2.03 SSBOND 3 CYS A 25 CYS A 42 1555 1555 2.03 SSBOND 4 CYS B 5 CYS B 31 1555 1555 2.03 SSBOND 5 CYS B 15 CYS B 30 1555 1555 2.03 SSBOND 6 CYS B 25 CYS B 42 1555 1555 2.03 SSBOND 7 CYS C 5 CYS C 31 1555 1555 2.03 SSBOND 8 CYS C 15 CYS C 30 1555 1555 2.03 SSBOND 9 CYS C 25 CYS C 42 1555 1555 2.03 LINK C PCA A 1 N THR A 2 1555 1555 1.33 LINK C PCA B 1 N THR B 2 1555 1555 1.33 LINK C PCA C 1 N THR C 2 1555 1555 1.33 CRYST1 44.928 41.905 45.831 90.00 115.57 90.00 P 1 21 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 0.022258 0.000000 0.010647 0.00000 SCALE2 0.000000 0.023864 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024187 0.00000 HETATM 1 N PCA A 1 -9.214 -2.673 1.624 1.00 23.18 N HETATM 2 CA PCA A 1 -8.339 -2.591 2.790 1.00 22.87 C HETATM 3 CB PCA A 1 -9.146 -2.716 4.081 1.00 18.53 C HETATM 4 CG PCA A 1 -10.569 -3.063 3.692 1.00 24.00 C HETATM 5 CD PCA A 1 -10.532 -2.959 2.192 1.00 23.20 C HETATM 6 OE PCA A 1 -11.550 -3.096 1.517 1.00 36.34 O HETATM 7 C PCA A 1 -7.249 -3.652 2.786 1.00 18.81 C HETATM 8 O PCA A 1 -7.444 -4.766 2.303 1.00 17.92 O