HEADER SUGAR BINDING PROTEIN 01-APR-21 7O3I TITLE CYSTAL STRUCTURE OF ZYMOGEN GRANULE PROTEIN 16 (ZG16) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZYMOGEN GRANULE MEMBRANE PROTEIN 16; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ZYMOGEN GRANULE PROTEIN 16,HZG16,SECRETORY LECTIN ZG16; COMPND 5 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: ZG16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BETA PRISM, GREEK KEY, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.JAVITT,D.FASS REVDAT 3 31-JAN-24 7O3I 1 REMARK REVDAT 2 24-NOV-21 7O3I 1 JRNL REVDAT 1 23-JUN-21 7O3I 0 JRNL AUTH G.JAVITT,A.KINZEL,N.REZNIK,D.FASS JRNL TITL CONFORMATIONAL SWITCHES AND REDOX PROPERTIES OF THE COLON JRNL TITL 2 CANCER-ASSOCIATED HUMAN LECTIN ZG16. JRNL REF FEBS J. V. 288 6465 2021 JRNL REFN ISSN 1742-464X JRNL PMID 34077620 JRNL DOI 10.1111/FEBS.16044 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 20346 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.780 REMARK 3 FREE R VALUE TEST SET COUNT : 1175 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 40.3200 - 3.0000 0.93 2430 146 0.1360 0.1545 REMARK 3 2 3.0000 - 2.3800 0.97 2428 150 0.1616 0.2102 REMARK 3 3 2.3800 - 2.0800 0.96 2350 142 0.1745 0.2094 REMARK 3 4 2.0800 - 1.8900 0.95 2344 141 0.1983 0.2475 REMARK 3 5 1.8900 - 1.7500 0.99 2401 152 0.1763 0.2264 REMARK 3 6 1.7500 - 1.6500 1.00 2440 151 0.2014 0.2437 REMARK 3 7 1.6500 - 1.5700 1.00 2422 151 0.2325 0.2753 REMARK 3 8 1.5700 - 1.5000 0.97 2356 142 0.2603 0.3114 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.176 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.371 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40 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 : 0.008 1196 REMARK 3 ANGLE : 0.972 1629 REMARK 3 CHIRALITY : 0.058 171 REMARK 3 PLANARITY : 0.007 208 REMARK 3 DIHEDRAL : 2.920 924 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 7O3I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-APR-21. REMARK 100 THE DEPOSITION ID IS D_1292115061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9724 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20346 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.323 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 3APA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M AMMONIUM SULFATE, 0.1 M BIS REMARK 280 -TRIS, PH 5.5, 1 % W/V PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.46350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.05750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.99800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.05750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.46350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.99800 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 TOTAL BURIED SURFACE AREA: 370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 SER A 163 REMARK 465 CYS A 164 REMARK 465 SER A 165 REMARK 465 ARG A 166 REMARK 465 CYS A 167 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 LYS A 122 CG CD CE NZ REMARK 470 SER A 162 OG 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 HG SER A 32 O HOH A 305 1.59 REMARK 500 O HOH A 440 O HOH A 444 1.86 REMARK 500 O HOH A 512 O HOH A 532 1.94 REMARK 500 O HOH A 422 O HOH A 480 1.97 REMARK 500 O HOH A 478 O HOH A 482 2.00 REMARK 500 O HOH A 351 O HOH A 481 2.01 REMARK 500 O HOH A 345 O HOH A 492 2.05 REMARK 500 O HOH A 303 O HOH A 471 2.07 REMARK 500 O HOH A 444 O HOH A 474 2.08 REMARK 500 O HOH A 413 O HOH A 431 2.09 REMARK 500 O HOH A 346 O HOH A 506 2.10 REMARK 500 O HOH A 445 O HOH A 506 2.11 REMARK 500 O HOH A 418 O HOH A 453 2.14 REMARK 500 OE2 GLU A 29 O HOH A 301 2.16 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 ASN A 57 -166.92 -111.57 REMARK 500 TRP A 103 -47.01 71.62 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 DBREF 7O3I A 21 167 UNP O60844 ZG16_HUMAN 21 167 SEQADV 7O3I GLY A 20 UNP O60844 EXPRESSION TAG SEQADV 7O3I SER A 32 UNP O60844 GLY 32 VARIANT SEQADV 7O3I VAL A 109 UNP O60844 LEU 109 VARIANT SEQRES 1 A 148 GLY ALA ARG SER SER SER TYR SER GLY GLU TYR GLY SER SEQRES 2 A 148 GLY GLY GLY LYS ARG PHE SER HIS SER GLY ASN GLN LEU SEQRES 3 A 148 ASP GLY PRO ILE THR ALA LEU ARG VAL ARG VAL ASN THR SEQRES 4 A 148 TYR TYR ILE VAL GLY LEU GLN VAL ARG TYR GLY LYS VAL SEQRES 5 A 148 TRP SER ASP TYR VAL GLY GLY ARG ASN GLY ASP LEU GLU SEQRES 6 A 148 GLU ILE PHE LEU HIS PRO GLY GLU SER VAL ILE GLN VAL SEQRES 7 A 148 SER GLY LYS TYR LYS TRP TYR LEU LYS LYS LEU VAL PHE SEQRES 8 A 148 VAL THR ASP LYS GLY ARG TYR LEU SER PHE GLY LYS ASP SEQRES 9 A 148 SER GLY THR SER PHE ASN ALA VAL PRO LEU HIS PRO ASN SEQRES 10 A 148 THR VAL LEU ARG PHE ILE SER GLY ARG SER GLY SER LEU SEQRES 11 A 148 ILE ASP ALA ILE GLY LEU HIS TRP ASP VAL TYR PRO SER SEQRES 12 A 148 SER CYS SER ARG CYS HET GOL A 201 8 HET CL A 202 1 HET CL A 203 1 HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *236(H2 O) HELIX 1 AA1 SER A 41 GLY A 47 5 7 SHEET 1 AA1 4 SER A 25 GLY A 31 0 SHEET 2 AA1 4 ILE A 150 ASP A 158 -1 O TRP A 157 N SER A 25 SHEET 3 AA1 4 VAL A 138 SER A 146 -1 N ARG A 140 O HIS A 156 SHEET 4 AA1 4 LYS A 36 SER A 39 -1 N LYS A 36 O SER A 146 SHEET 1 AA2 3 VAL A 71 TRP A 72 0 SHEET 2 AA2 3 ILE A 61 TYR A 68 -1 N TYR A 68 O VAL A 71 SHEET 3 AA2 3 VAL A 76 GLY A 77 -1 O VAL A 76 N LEU A 64 SHEET 1 AA3 4 VAL A 71 TRP A 72 0 SHEET 2 AA3 4 ILE A 61 TYR A 68 -1 N TYR A 68 O VAL A 71 SHEET 3 AA3 4 ILE A 49 VAL A 56 -1 N THR A 50 O ARG A 67 SHEET 4 AA3 4 ASP A 82 PHE A 87 -1 O ASP A 82 N VAL A 56 SHEET 1 AA4 4 TYR A 117 GLY A 121 0 SHEET 2 AA4 4 LEU A 105 THR A 112 -1 N PHE A 110 O LEU A 118 SHEET 3 AA4 4 VAL A 94 TYR A 101 -1 N ILE A 95 O VAL A 111 SHEET 4 AA4 4 THR A 126 ALA A 130 -1 O ALA A 130 N VAL A 97 CISPEP 1 TYR A 160 PRO A 161 0 -1.98 SITE 1 AC1 8 GLY A 35 TYR A 104 GLY A 147 SER A 148 SITE 2 AC1 8 LEU A 149 ASP A 151 HOH A 308 HOH A 326 SITE 1 AC2 5 SER A 25 TYR A 26 GLY A 78 ARG A 79 SITE 2 AC2 5 HOH A 500 SITE 1 AC3 2 TRP A 103 HOH A 355 CRYST1 38.927 55.996 58.115 90.00 90.00 90.00 P 21 21 21 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 0.025689 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017207 0.00000